From 1de8b6a46da602dc22897086f32ae906769ae41a Mon Sep 17 00:00:00 2001 From: Alexis Renchon Date: Fri, 24 May 2024 11:16:49 -0700 Subject: [PATCH] Bucket diagnostics --- .buildkite/Manifest.toml | 91 +-- .buildkite/Project.toml | 2 + .github/workflows/ClimaLandSimulations.yml | 6 +- Artifacts.toml | 9 +- Project.toml | 2 + README.md | 1 + docs/Manifest.toml | 10 +- docs/Project.toml | 1 + docs/list_diagnostics.jl | 5 + docs/make.jl | 6 +- docs/src/diagnostics/available_diagnostics.md | 6 + .../src/diagnostics/developers_diagnostics.md | 121 ++++ docs/src/diagnostics/make_diagnostic_table.jl | 28 + docs/src/diagnostics/users_diagnostics.md | 133 ++++ experiments/Manifest.toml | 26 +- experiments/Project.toml | 2 + .../Bucket/global_bucket_function.jl | 36 + lib/ClimaLandSimulations/Project.toml | 8 +- lib/ClimaLandSimulations/README.md | 6 +- .../src/ClimaLandSimulations.jl | 1 + src/ClimaLand.jl | 5 + src/Diagnostics/Diagnostics.jl | 18 + src/Diagnostics/bucket_compute_methods.jl | 189 ++++++ src/Diagnostics/default_diagnostics.jl | 117 ++++ src/Diagnostics/define_diagnostics.jl | 622 ++++++++++++++++++ src/Diagnostics/diagnostic.jl | 99 +++ src/Diagnostics/soilcanopy_compute_methods.jl | 579 ++++++++++++++++ .../standard_diagnostic_frequencies.jl | 262 ++++++++ test/Project.toml | 4 + test/diagnostics/diagnostics_tests.jl | 9 + 30 files changed, 2330 insertions(+), 74 deletions(-) create mode 100644 docs/list_diagnostics.jl create mode 100644 docs/src/diagnostics/available_diagnostics.md create mode 100644 docs/src/diagnostics/developers_diagnostics.md create mode 100644 docs/src/diagnostics/make_diagnostic_table.jl create mode 100644 docs/src/diagnostics/users_diagnostics.md create mode 100644 src/Diagnostics/Diagnostics.jl create mode 100644 src/Diagnostics/bucket_compute_methods.jl create mode 100644 src/Diagnostics/default_diagnostics.jl create mode 100644 src/Diagnostics/define_diagnostics.jl create mode 100644 src/Diagnostics/diagnostic.jl create mode 100644 src/Diagnostics/soilcanopy_compute_methods.jl create mode 100644 src/Diagnostics/standard_diagnostic_frequencies.jl create mode 100644 test/diagnostics/diagnostics_tests.jl diff --git a/.buildkite/Manifest.toml b/.buildkite/Manifest.toml index da552fa2f8..ff971690de 100644 --- a/.buildkite/Manifest.toml +++ b/.buildkite/Manifest.toml @@ -2,7 +2,7 @@ julia_version = "1.10.4" manifest_format = "2.0" -project_hash = "dae5b8a0ef6cad3a789e38991e9bafc7e71f7ab5" +project_hash = "8f674e311ce137cbeb26c8e00409aca502afec54" [[deps.ADTypes]] git-tree-sha1 = "fa0822e5baee6e23081c2685ae27265dabee23d8" @@ -231,12 +231,6 @@ git-tree-sha1 = "9a9610fbe5779636f75229e423e367124034af41" uuid = "8e7c35d0-a365-5155-bbbb-fb81a777f24e" version = "0.16.43" -[[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" @@ -357,6 +351,20 @@ weakdeps = ["SparseArrays"] [deps.ChainRulesCore.extensions] ChainRulesCoreSparseArraysExt = "SparseArrays" +[[deps.ClimaAnalysis]] +deps = ["NCDatasets", "OrderedCollections", "Statistics"] +git-tree-sha1 = "af5e012e13bc9609f712dea0434cb4ce2b3e709e" +uuid = "29b5916a-a76c-4e73-9657-3c8fd22e65e6" +version = "0.5.2" + + [deps.ClimaAnalysis.extensions] + CairoMakieExt = "CairoMakie" + GeoMakieExt = "GeoMakie" + + [deps.ClimaAnalysis.weakdeps] + CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0" + GeoMakie = "db073c08-6b98-4ee5-b6a4-5efafb3259c6" + [[deps.ClimaComms]] git-tree-sha1 = "d76590e99fa942e07f1e992a4d4a5e25121a26d6" uuid = "3a4d1b5c-c61d-41fd-a00a-5873ba7a1b0d" @@ -378,8 +386,14 @@ weakdeps = ["CUDA", "Krylov"] ClimaCoreCUDAExt = "CUDA" KrylovExt = "Krylov" +[[deps.ClimaDiagnostics]] +deps = ["Accessors", "ClimaComms", "ClimaCore", "Dates", "NCDatasets", "SciMLBase"] +git-tree-sha1 = "aff194804df0fcfcf69a80c58978b84777272619" +uuid = "1ecacbb8-0713-4841-9a07-eb5aa8a2d53f" +version = "0.2.2" + [[deps.ClimaLand]] -deps = ["Adapt", "ArtifactWrappers", "ClimaComms", "ClimaCore", "ClimaUtilities", "DataFrames", "Dates", "DocStringExtensions", "Insolation", "Interpolations", "IntervalSets", "LazyArtifacts", "LinearAlgebra", "NCDatasets", "SciMLBase", "StaticArrays", "SurfaceFluxes", "Thermodynamics", "UnrolledUtilities"] +deps = ["Adapt", "ArtifactWrappers", "ClimaComms", "ClimaCore", "ClimaDiagnostics", "ClimaUtilities", "DataFrames", "Dates", "DocStringExtensions", "Insolation", "Interpolations", "IntervalSets", "LazyArtifacts", "LinearAlgebra", "NCDatasets", "SciMLBase", "StaticArrays", "SurfaceFluxes", "Thermodynamics", "UnrolledUtilities"] path = ".." uuid = "08f4d4ce-cf43-44bb-ad95-9d2d5f413532" version = "0.12.4" @@ -830,10 +844,10 @@ uuid = "c87230d0-a227-11e9-1b43-d7ebe4e7570a" version = "0.4.1" [[deps.FFMPEG_jll]] -deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "JLLWrappers", "LAME_jll", "Libdl", "Ogg_jll", "OpenSSL_jll", "Opus_jll", "PCRE2_jll", "Zlib_jll", "libaom_jll", "libass_jll", "libfdk_aac_jll", "libvorbis_jll", "x264_jll", "x265_jll"] -git-tree-sha1 = "466d45dc38e15794ec7d5d63ec03d776a9aff36e" +deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "JLLWrappers", "LAME_jll", "Libdl", "Ogg_jll", "OpenSSL_jll", "Opus_jll", "PCRE2_jll", "Pkg", "Zlib_jll", "libaom_jll", "libass_jll", "libfdk_aac_jll", "libvorbis_jll", "x264_jll", "x265_jll"] +git-tree-sha1 = "74faea50c1d007c85837327f6775bea60b5492dd" uuid = "b22a6f82-2f65-5046-a5b2-351ab43fb4e5" -version = "4.4.4+1" +version = "4.4.2+2" [[deps.FFTW]] deps = ["AbstractFFTs", "FFTW_jll", "LinearAlgebra", "MKL_jll", "Preferences", "Reexport"] @@ -1033,11 +1047,6 @@ 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 = "c154546e322a9c73364e8a60430b0f79b812d320" @@ -1103,12 +1112,6 @@ git-tree-sha1 = "7c82e6a6cd34e9d935e9aa4051b66c6ff3af59ba" uuid = "7746bdde-850d-59dc-9ae8-88ece973131d" version = "2.80.2+0" -[[deps.GnuTLS_jll]] -deps = ["Artifacts", "GMP_jll", "JLLWrappers", "Libdl", "Nettle_jll", "P11Kit_jll", "Zlib_jll"] -git-tree-sha1 = "383db7d3f900f4c1f47a8a04115b053c095e48d3" -uuid = "0951126a-58fd-58f1-b5b3-b08c7c4a876d" -version = "3.8.4+0" - [[deps.Graphics]] deps = ["Colors", "LinearAlgebra", "NaNMath"] git-tree-sha1 = "d61890399bc535850c4bf08e4e0d3a7ad0f21cbd" @@ -1129,9 +1132,9 @@ version = "1.11.1" [[deps.GridLayoutBase]] deps = ["GeometryBasics", "InteractiveUtils", "Observables"] -git-tree-sha1 = "fc713f007cff99ff9e50accba6373624ddd33588" +git-tree-sha1 = "6f93a83ca11346771a93bbde2bdad2f65b61498f" uuid = "3955a311-db13-416c-9275-1d80ed98e5e9" -version = "0.11.0" +version = "0.10.2" [[deps.Grisu]] git-tree-sha1 = "53bb909d1151e57e2484c3d1b53e19552b887fb2" @@ -1149,10 +1152,10 @@ weakdeps = ["MPI"] MPIExt = "MPI" [[deps.HDF5_jll]] -deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LazyArtifacts", "LibCURL_jll", "Libdl", "MPICH_jll", "MPIPreferences", "MPItrampoline_jll", "MicrosoftMPI_jll", "OpenMPI_jll", "OpenSSL_jll", "TOML", "Zlib_jll", "libaec_jll"] -git-tree-sha1 = "82a471768b513dc39e471540fdadc84ff80ff997" +deps = ["Artifacts", "JLLWrappers", "LibCURL_jll", "Libdl", "OpenSSL_jll", "Pkg", "Zlib_jll"] +git-tree-sha1 = "4cc2bb72df6ff40b055295fdef6d92955f9dede8" uuid = "0234f1f7-429e-5d53-9886-15a909be8d59" -version = "1.14.3+3" +version = "1.12.2+2" [[deps.HTTP]] deps = ["Base64", "CodecZlib", "ConcurrentUtilities", "Dates", "ExceptionUnwrapping", "Logging", "LoggingExtras", "MbedTLS", "NetworkOptions", "OpenSSL", "Random", "SimpleBufferStream", "Sockets", "URIs", "UUIDs"] @@ -1778,9 +1781,9 @@ uuid = "d6f4376e-aef5-505a-96c1-9c027394607a" [[deps.MathTeXEngine]] deps = ["AbstractTrees", "Automa", "DataStructures", "FreeTypeAbstraction", "GeometryBasics", "LaTeXStrings", "REPL", "RelocatableFolders", "UnicodeFun"] -git-tree-sha1 = "1865d0b8a2d91477c8b16b49152a32764c7b1f5f" +git-tree-sha1 = "96ca8a313eb6437db5ffe946c457a401bbb8ce1d" uuid = "0a4f8689-d25c-4efe-a92b-7142dfc1aa53" -version = "0.6.0" +version = "0.5.7" [[deps.MatrixFactorizations]] deps = ["ArrayLayouts", "LinearAlgebra", "Printf", "Random"] @@ -1916,10 +1919,10 @@ uuid = "71a1bf82-56d0-4bbc-8a3c-48b961074391" version = "0.1.5" [[deps.NetCDF_jll]] -deps = ["Artifacts", "Blosc_jll", "Bzip2_jll", "HDF5_jll", "JLLWrappers", "LazyArtifacts", "LibCURL_jll", "Libdl", "MPICH_jll", "MPIPreferences", "MPItrampoline_jll", "MicrosoftMPI_jll", "OpenMPI_jll", "TOML", "XML2_jll", "Zlib_jll", "Zstd_jll", "libzip_jll"] -git-tree-sha1 = "4686378c4ae1d1948cfbe46c002a11a4265dcb07" +deps = ["Artifacts", "HDF5_jll", "JLLWrappers", "LibCURL_jll", "Libdl", "Pkg", "XML2_jll", "Zlib_jll"] +git-tree-sha1 = "072f8371f74c3b9e1b26679de7fbf059d45ea221" uuid = "7243133f-43d8-5620-bbf4-c2c921802cf3" -version = "400.902.211+1" +version = "400.902.5+1" [[deps.Netpbm]] deps = ["FileIO", "ImageCore", "ImageMetadata"] @@ -1927,12 +1930,6 @@ git-tree-sha1 = "d92b107dbb887293622df7697a2223f9f8176fcd" uuid = "f09324ee-3d7c-5217-9330-fc30815ba969" version = "1.1.1" -[[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" version = "1.2.0" @@ -2058,12 +2055,6 @@ 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" @@ -3215,12 +3206,6 @@ git-tree-sha1 = "51b5eeb3f98367157a7a12a1fb0aa5328946c03c" uuid = "9a68df92-36a6-505f-a73e-abb412b6bfb4" version = "0.2.3+0" -[[deps.libaec_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "46bf7be2917b59b761247be3f317ddf75e50e997" -uuid = "477f73a3-ac25-53e9-8cc3-50b2fa2566f0" -version = "1.1.2+0" - [[deps.libaom_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] git-tree-sha1 = "1827acba325fdcdf1d2647fc8d5301dd9ba43a9d" @@ -3274,12 +3259,6 @@ 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 = "3282b7d16ae7ac3e57ec2f3fa8fafb564d8f9f7f" -uuid = "337d8026-41b4-5cde-a456-74a10e5b31d1" -version = "1.10.1+0" - [[deps.mtdev_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] git-tree-sha1 = "814e154bdb7be91d78b6802843f76b6ece642f11" diff --git a/.buildkite/Project.toml b/.buildkite/Project.toml index 04bc1a43be..3cee10ee64 100644 --- a/.buildkite/Project.toml +++ b/.buildkite/Project.toml @@ -5,8 +5,10 @@ BSON = "fbb218c0-5317-5bc6-957e-2ee96dd4b1f0" CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b" CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0" +ClimaAnalysis = "29b5916a-a76c-4e73-9657-3c8fd22e65e6" ClimaComms = "3a4d1b5c-c61d-41fd-a00a-5873ba7a1b0d" ClimaCore = "d414da3d-4745-48bb-8d80-42e94e092884" +ClimaDiagnostics = "1ecacbb8-0713-4841-9a07-eb5aa8a2d53f" ClimaLand = "08f4d4ce-cf43-44bb-ad95-9d2d5f413532" ClimaParams = "5c42b081-d73a-476f-9059-fd94b934656c" ClimaTimeSteppers = "595c0a79-7f3d-439a-bc5a-b232dc3bde79" diff --git a/.github/workflows/ClimaLandSimulations.yml b/.github/workflows/ClimaLandSimulations.yml index 76cdb84487..8f052c4820 100644 --- a/.github/workflows/ClimaLandSimulations.yml +++ b/.github/workflows/ClimaLandSimulations.yml @@ -19,13 +19,13 @@ jobs: - uses: julia-actions/setup-julia@latest with: version: '1.10' - - uses: julia-actions/cache@v2 + # - uses: julia-actions/cache@v2 - name: Install Julia dependencies run: > - julia --project= -e 'using Pkg; Pkg.develop(path="$(pwd())"); Pkg.develop(path="$(pwd())/lib/ClimaLandSimulations")' + julia --project=lib/ClimaLandSimulations -e 'using Pkg; Pkg.develop(path=".")' - name: Run the tests continue-on-error: true env: CI_OUTPUT_DIR: output run: > - julia --project= -e 'using Pkg; Pkg.test("ClimaLandSimulations")' + julia --project=lib/ClimaLandSimulations -e 'using Pkg; Pkg.test("ClimaLandSimulations")' diff --git a/Artifacts.toml b/Artifacts.toml index fdabc938f9..72a2073359 100644 --- a/Artifacts.toml +++ b/Artifacts.toml @@ -1,9 +1,12 @@ +[era5_land_forcing_data2021] +git-tree-sha1 = "ec424296df6b60cfe273ac8f981701fbbed0bd8a" + +[land_albedo] +git-tree-sha1 = "5f7141a13994d5b334f1240e1bd5474ad44d96c4" + [soil_params_Gupta2020_2022] git-tree-sha1 = "8e28b4274b10020b6cdd54b8e7585221379d9d33" [[soil_params_Gupta2020_2022.download]] sha256 = "97dcf1158cba03b1fd397262bdfaf85a523f57038c337bcce163e32664d3616b" url = "https://caltech.box.com/shared/static/f2y23qx0lggjskftzgh7ht7fsbh36gmm.gz" - -[era5_land_forcing_data2021] -git-tree-sha1 = "ec424296df6b60cfe273ac8f981701fbbed0bd8a" diff --git a/Project.toml b/Project.toml index e990493153..eba8a74e3f 100644 --- a/Project.toml +++ b/Project.toml @@ -8,6 +8,7 @@ Adapt = "79e6a3ab-5dfb-504d-930d-738a2a938a0e" ArtifactWrappers = "a14bc488-3040-4b00-9dc1-f6467924858a" ClimaComms = "3a4d1b5c-c61d-41fd-a00a-5873ba7a1b0d" ClimaCore = "d414da3d-4745-48bb-8d80-42e94e092884" +ClimaDiagnostics = "1ecacbb8-0713-4841-9a07-eb5aa8a2d53f" ClimaUtilities = "b3f4f4ca-9299-4f7f-bd9b-81e1242a7513" DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" Dates = "ade2ca70-3891-5945-98fb-dc099432e06a" @@ -44,6 +45,7 @@ CSV = "0.10" CUDA = "5.3" ClimaComms = "0.5.6, 0.6" ClimaCore = "0.13.2, 0.14" +ClimaDiagnostics = "0.2" ClimaParams = "0.10.2" ClimaUtilities = "0.1.2" DataFrames = "1" diff --git a/README.md b/README.md index b4325e0912..3125c38bf3 100644 --- a/README.md +++ b/README.md @@ -8,6 +8,7 @@ component) or standalone (single component) modes.

+[![Downloads](https://img.shields.io/badge/dynamic/json?url=http%3A%2F%2Fjuliapkgstats.com%2Fapi%2Fv1%2Ftotal_downloads%2FClimaLand&query=total_requests&suffix=%2Ftotal&label=Downloads)](http://juliapkgstats.com/pkg/ClimaLand) Recommended Julia Version: Stable release v1.10.0. CI no longer tests earlier versions of Julia. diff --git a/docs/Manifest.toml b/docs/Manifest.toml index 738768a9bf..3c9ec87cc5 100644 --- a/docs/Manifest.toml +++ b/docs/Manifest.toml @@ -2,7 +2,7 @@ julia_version = "1.10.4" manifest_format = "2.0" -project_hash = "bf43a7452b446a9ba967dab8eeb0bc21ba10184f" +project_hash = "6c3f79ccae513840cc13b9ac947575c2305b507f" [[deps.ADTypes]] git-tree-sha1 = "fa0822e5baee6e23081c2685ae27265dabee23d8" @@ -375,8 +375,14 @@ weakdeps = ["CUDA", "Krylov"] ClimaCoreCUDAExt = "CUDA" KrylovExt = "Krylov" +[[deps.ClimaDiagnostics]] +deps = ["Accessors", "ClimaComms", "ClimaCore", "Dates", "NCDatasets", "SciMLBase"] +git-tree-sha1 = "aff194804df0fcfcf69a80c58978b84777272619" +uuid = "1ecacbb8-0713-4841-9a07-eb5aa8a2d53f" +version = "0.2.2" + [[deps.ClimaLand]] -deps = ["Adapt", "ArtifactWrappers", "ClimaComms", "ClimaCore", "ClimaUtilities", "DataFrames", "Dates", "DocStringExtensions", "Insolation", "Interpolations", "IntervalSets", "LazyArtifacts", "LinearAlgebra", "NCDatasets", "SciMLBase", "StaticArrays", "SurfaceFluxes", "Thermodynamics", "UnrolledUtilities"] +deps = ["Adapt", "ArtifactWrappers", "ClimaComms", "ClimaCore", "ClimaDiagnostics", "ClimaUtilities", "DataFrames", "Dates", "DocStringExtensions", "Insolation", "Interpolations", "IntervalSets", "LazyArtifacts", "LinearAlgebra", "NCDatasets", "SciMLBase", "StaticArrays", "SurfaceFluxes", "Thermodynamics", "UnrolledUtilities"] path = ".." uuid = "08f4d4ce-cf43-44bb-ad95-9d2d5f413532" version = "0.12.4" diff --git a/docs/Project.toml b/docs/Project.toml index fcacd6e6a2..e7f6f974ed 100644 --- a/docs/Project.toml +++ b/docs/Project.toml @@ -20,6 +20,7 @@ Interpolations = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59" JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6" Literate = "98b081ad-f1c9-55d3-8b20-4c87d4299306" Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" +PrettyTables = "08abe8d2-0d0c-5749-adfa-8a2ac140af0d" SciMLBase = "0bca4576-84f4-4d90-8ffe-ffa030f20462" StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91" diff --git a/docs/list_diagnostics.jl b/docs/list_diagnostics.jl new file mode 100644 index 0000000000..4d76cb4f6f --- /dev/null +++ b/docs/list_diagnostics.jl @@ -0,0 +1,5 @@ +diagnostics = [ + "Available diagnostics" => "diagnostics/available_diagnostics.md", + "For developers" => "diagnostics/developers_diagnostics.md", + "For users" => "diagnostics/users_diagnostics.md", +] diff --git a/docs/make.jl b/docs/make.jl index f1355b2e21..03bb4ff9dd 100644 --- a/docs/make.jl +++ b/docs/make.jl @@ -7,7 +7,7 @@ using Distributed using ClimaLand include("pages_helper.jl") tutorials = [ - "For model developers" => [ +#= "For model developers" => [ "Intro to standalone models" => "standalone/Usage/model_tutorial.jl", "Intro to multi-component models" => "standalone/Usage/LSM_single_column_tutorial.jl", "Intro to ClimaLand Domains" => "standalone/Usage/domain_tutorial.jl", @@ -42,7 +42,7 @@ tutorials = [ "standalone/Snow/base_tutorial.jl", "standalone/Snow/data_tutorial.jl", ], - ], + ],=# ] @everywhere const clima_dir = dirname(dirname(pathof(ClimaLand))); @everywhere source_dir = joinpath(@__DIR__, "src") @@ -84,6 +84,7 @@ ext_jl2md(x) = joinpath(basename(GENERATED_DIR), replace(x, ".jl" => ".md")) tutorials = transform_second(x -> ext_jl2md(x), tutorials) include("list_of_apis.jl") include("list_standalone_models.jl") +include("list_diagnostics.jl") pages = Any[ "Home" => "index.md", "APIs" => apis, @@ -91,6 +92,7 @@ pages = Any[ "Tutorials" => tutorials, "Repository structure" => "folderstructure.md", "Standalone models" => standalone_models, + "Diagnostics" => diagnostics, ] diff --git a/docs/src/diagnostics/available_diagnostics.md b/docs/src/diagnostics/available_diagnostics.md new file mode 100644 index 0000000000..3642907644 --- /dev/null +++ b/docs/src/diagnostics/available_diagnostics.md @@ -0,0 +1,6 @@ +# Available diagnostic variables + +Autogenerate table of available diagnostics: +```@example +include("make_diagnostic_table.jl") +``` diff --git a/docs/src/diagnostics/developers_diagnostics.md b/docs/src/diagnostics/developers_diagnostics.md new file mode 100644 index 0000000000..cf302e57cd --- /dev/null +++ b/docs/src/diagnostics/developers_diagnostics.md @@ -0,0 +1,121 @@ +# ClimaLand Diagnostics: why and how + +ClimaLand simulations generates variables in the integrator state and cache at each time step. +A user will need to use these variables in some form, i.e., access them from a file that contains variables at a given temporal and spatial resolution. +The user will also want to retrieve metadata about those variables, such as name and units. +This is where ClimaLand diagnostics comes in, it writes simulations variables (in a file, such as NetCDF or HDF5, or in Julia Dict), at a specified spatio-temporal reduction +(e.g., hourly averages, monthly max, instantaneous, integrated through soil depth...), along with metadata (e.g., soil temperature short name is t_soil, expressed in "K" units). +We want to provide users with default options, but also the possibility to define their own variables and reductions. + +Internally, this is done by using the [`ClimaDiagnostics.jl`](https://github.com/CliMA/ClimaDiagnostics.jl) package, that provides the functionality to produce a +[`ClimaLand.Diagnostics`](https://github.com/CliMA/ClimaLand.jl/tree/main/src/Diagnostics/Diagnostics.jl) module in the src/Diagnostics.jl folder. In this folder, + - `Diagnostics.jl` defines the module, + - `diagnostic.jl` defines `ALL_DIAGNOSTICS`, a Dict containing all diagnostics variables defined in `define_diagnostics.jl`, it also defines the function + `add_diagnostic_variable!` which defines a method to add diagnostic variables to ALL_DIAGNOSTICS, finally it contains a function `get_diagnostic_variable` which returns a + `DiagnosticVariable` from its `short_name`, if it exists. + - `define_diagnostics.jl`, mentioned above, contains a function `define_diagnostics!(land_model)` which contains all default diagnostic variables by calling + `add_diagnostic_variable!`, and dispatch off the type of land_model to define how to compute a diagnostic (for example, surface temperature is computed in p.bucket.T_sfc + in the bucket model) - compute methods are defined in a separate file, for example, `bucket_compute_methods.jl`. + - `standard_diagnostic_frequencies.jl` defines standard functions to schedule diagnostics, for example, hourly average or monthly max, these functions are called on a list of + diagnostic variables. As developers, we can add more standard functions that users may want to have access to easily in this file. + - `default_diagnostics.jl` defines default diagnostics functions to use on a model simulation. For example, `default_diagnostics(land_model::BucketModel, t_start; output_writer)` + will return a `ScheduledDiagnostics` that computes hourly averages for all Bucket variables, along with their metadata, ready to be written on a NetCDF file when running a Bucket + simulation. + +The following section give more details on these functions, along with examples. As developers, we want to extand these functionality as ClimaLand progresses. + +# Compute methods + +Each model defines all its compute methods in a file (bucket_compute_methods.jl for the bucket model, for example). +The structure of a diagnostic variable compute method is, for example: + +``` +function compute_albedo!(out, Y, p, t, land_model::BucketModel) + if isnothing(out) + return copy(p.bucket.α_sfc) + else + out .= p.bucket.α_sfc + end +end +``` + +It defines how to access your diagnostic (here, p.bucket.α_sfc), in your model type (here, ::BucketModel). +Note that, as explained in the [ClimaDiagnostics.jl documentation](https://clima.github.io/ClimaDiagnostics.jl/dev/user_guide/), `out` will probably not be needed in the future. + +We also define helper functions returning error messages if a user tries to compute a diagnostic variable that doesn't exist in their model type. + +``` +error_diagnostic_variable(variable, land_model::T) where {T} = + error("Cannot compute $variable with model = $T") + +compute_albedo!(_, _, _, _, land_model) = + error_diagnostic_variable("albedo", land_model) +``` + +# Define diagnostics + +Once the compute functions have been defined, they are added to `define_diagnostics!(land_model)`, which adds diagnostics variables to ALL_DIAGNOSTICS dict, +defined in diagnostic.jl. In these functions, you also define a `short_name`, `long_name`, `standard_name`, `units` and `comment`. For example: + +``` +add_diagnostic_variable!( + short_name = "alpha", + long_name = "Albedo", + standard_name = "albedo", + units = "", + compute! = (out, Y, p, t) -> compute_albedo!(out, Y, p, t, land_model), + ) +``` + +# Default diagnostics + +For each model, we define a function `default_diagnostics` which will define what diagnostic variables to compute by default for a specific model, and +on what schedule (for example, hourly average). For example, + +``` +function default_diagnostics(land_model::BucketModel, t_start; output_writer) + + define_diagnostics!(land_model) + + bucket_diagnostics = [ + "alpha", + "rn", + "tsfc", + "qsfc", + "lhf", + "rae", + "shf", + "vflux", + "rhosfc", + "t", + "w", + "ws", + "sigmas", + ] + + default_outputs = + hourly_averages(bucket_diagnostics...; output_writer, t_start) + return [default_outputs...] +end +``` + +is the default for the BucketModel, it will return hourly averages for the variables listed in `bucket_diagnostics` (which are all variables in the BucketModel). + +# Standard diagnostic frequencies + +We defined some functions of diagnostic schedule that may often be used in standard_diagnostic_frequencies.jl, for example + +``` +hourly_averages(short_names...; output_writer, t_start) = common_diagnostics( + 60 * 60 * one(t_start), + (+), + output_writer, + t_start, + short_names...; + pre_output_hook! = average_pre_output_hook!, +) +``` + +will return a list of `ScheduledDiagnostics` that compute the hourly average for the given variables listed in `short_names`. +We also, so far, provide functions for mins, maxs and averages aggregated monthly, over ten days, daily, and hourly. +As a developer, you may want to add more standard diagnostics here. diff --git a/docs/src/diagnostics/make_diagnostic_table.jl b/docs/src/diagnostics/make_diagnostic_table.jl new file mode 100644 index 0000000000..e7b7cedab6 --- /dev/null +++ b/docs/src/diagnostics/make_diagnostic_table.jl @@ -0,0 +1,28 @@ +import ClimaLand as CL +using PrettyTables + +# Print all available diagnostics to an ASCII table + +CL.Diagnostics.define_diagnostics!(nothing) +short_names = [] +long_names = [] +units = [] +comments = [] +standard_names = [] +for d in values(CL.Diagnostics.ALL_DIAGNOSTICS) + push!(short_names, d.short_name) + push!(long_names, d.long_name) + push!(units, d.units) + push!(comments, d.comments) + push!(standard_names, d.standard_name) +end +data = hcat(short_names, long_names, units, comments, standard_names) +pretty_table( + data; + autowrap = true, + linebreaks = true, + columns_width = [10, 15, 8, 32, 15], # Width = 80 + body_hlines = collect(1:size(data)[1]), + header = ["Short name", "Long name", "Units", "Comments", "Standard name"], + alignment = :l, +) diff --git a/docs/src/diagnostics/users_diagnostics.md b/docs/src/diagnostics/users_diagnostics.md new file mode 100644 index 0000000000..e082f4963d --- /dev/null +++ b/docs/src/diagnostics/users_diagnostics.md @@ -0,0 +1,133 @@ +# Using ClimaLand Diagnostics when running a simulation + +When running a ClimaLand simulations, you have multiple options on how to write the outputs of that simulation. +You may want all variables, or just a selected few. +You may want instantaneous values, at the highest temporal and spatial resolution, or you may want to get averages at hourly or monthly time scale, and integrate in space +(for example soil moisture from 0 to 1 meter depth). +You may want to get more specific reductions, such as 10 days maximums, or compute a new variables that is a function of others. +You may want to get your outputs in memory in a Julia Dict, or write them in a NetCDF file. + +This is where ClimaLand Diagnostics comes in for users. + +In this documentation page, we first explain how to use default diagnostics and what are the defaults, and then explain how to define your own diagnostics for more advanced +users. + +# Default Diagnostics + +Once you have defined your model and are ready to run a simulation, and after adding ClimaDiagnostics (using ClimaDiagnostics), + you can add default diagnostics to it by doing the following steps: + +1. define an output folder + +``` +mkdir("output") +output_dir = "output/" +``` + +you may want to check if this directory exist and remove it if so, so that when you re-run the simulation, you start fresh: + +``` +if isdir("output") + rm("output", force = true, recursive = true) +end + +mkdir("output") +output_dir = "output/" +``` + +2. define a space + +Your diagnostics will be written in time and space. These may be defined in your model, but usually land model space is a sphere with no vertical dimension. +You may have variables varying with soil depth, and so you will need: + +``` +space = bucket_domain.space.subsurface +``` + +3. define your writter + +Your diagnostics will be written in a Julia Dict or a netcdf file, for example. This is up to you. For a netcdf file, you define your writter like this: + +``` +nc_writer = ClimaDiagnostics.Writers.NetCDFWriter(space, output_dir) +``` + +providing the space and output_dir defined in steps 1. and 2. + +4. make your diagnostics on your model, using your writter, and define a callback + +Now that you defined your model and your writter, you can create a callback function to be called when solving your model. For example: + +``` +diags = ClimaLand.CLD.default_diagnostics(model, 1.0; output_writer = nc_writer) + +diagnostic_handler = + ClimaDiagnostics.DiagnosticsHandler(diags, Y, p, t0; dt = Δt) + +diag_cb = ClimaDiagnostics.DiagnosticsCallback(diagnostic_handler) + +sol = SciMLBase.solve(prob, ode_algo; dt = Δt, callback = diag_cb) +``` + +Your diagnostics have now been written in netcdf files in your output folder. + +# Custom Diagnostics + +When defining a custom diagnostic, follow these steps: + - Define how to compute your diagnostic variable from your model state and cache. + For example, let's say you want the bowen ratio (ratio between sensible heat and latent heat) in the Bucket model. + ``` + function compute_bowen_ratio!(out, Y, p, t, land_model::BucketModel) + if isnothing(out) + return copy(p.bucket.turbulent_fluxes.shf / p.bucket.turbulent_fluxes.lhf) + else + out .= p.bucket.turbulent_fluxes.shf / p.bucket.turbulent_fluxes.lhf + end +end + ``` + - Add that diagnostic variable to your list of variables + ``` + add_diagnostic_variable!( + short_name = "bor", + long_name = "Bowen ratio", + standard_name = "bowen_ratio", + units = "", + compute! = (out, Y, p, t) -> compute_bowen_ratio!(out, Y, p, t, land_model), + ) + ``` + - Define how to schedule your variables. For example, you want the seasonal maximum of your variables, where season is defined as 90 days. + ``` + seasonal_maxs(short_names...; output_writer, t_start) = common_diagnostics( + 90 * 24 * 60 * 60 * one(t_start), + max, + output_writer, + t_start, + short_names..., +) + ``` + - Define a function to return your ScheduledDiagnostics + ``` + function default_diagnostics(land_model::BucketModel, t_start; output_writer) + + define_diagnostics!(land_model) + + add_diagnostic_variable!( + short_name = "bor", + long_name = "Bowen ratio", + standard_name = "bowen_ratio", + units = "", + compute! = (out, Y, p, t) -> compute_bowen_ratio!(out, Y, p, t, land_model), + ) + + my_custom_diagnostics = [ + "lhf", + "shf", + "bor", + ] + + my_custom_outputs = + seasonal_maxs(my_custom_diagnostics...; output_writer, t_start) + return [my_custom_outputs...] +end + ``` + \ No newline at end of file diff --git a/experiments/Manifest.toml b/experiments/Manifest.toml index c977b0bf30..7524dfe66a 100644 --- a/experiments/Manifest.toml +++ b/experiments/Manifest.toml @@ -2,7 +2,7 @@ julia_version = "1.10.4" manifest_format = "2.0" -project_hash = "973443a0a609649a9289253b6f5bc3de181d9006" +project_hash = "306f35a5dfb80400ec575833e6ee1eaa425bdc2f" [[deps.ADTypes]] git-tree-sha1 = "daf26bbdec60d9ca1c0003b70f389d821ddb4224" @@ -256,6 +256,20 @@ weakdeps = ["SparseArrays"] [deps.ChainRulesCore.extensions] ChainRulesCoreSparseArraysExt = "SparseArrays" +[[deps.ClimaAnalysis]] +deps = ["NCDatasets", "OrderedCollections", "Statistics"] +git-tree-sha1 = "c2e1c0d5c30a2519a4282988037b255dbc9aee00" +uuid = "29b5916a-a76c-4e73-9657-3c8fd22e65e6" +version = "0.5.3" + + [deps.ClimaAnalysis.extensions] + CairoMakieExt = "CairoMakie" + GeoMakieExt = "GeoMakie" + + [deps.ClimaAnalysis.weakdeps] + CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0" + GeoMakie = "db073c08-6b98-4ee5-b6a4-5efafb3259c6" + [[deps.ClimaComms]] git-tree-sha1 = "f19a9d42ef27affa8d57a5702dcb8a318077aa86" uuid = "3a4d1b5c-c61d-41fd-a00a-5873ba7a1b0d" @@ -283,11 +297,17 @@ version = "0.14.5" CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" Krylov = "ba0b0d4f-ebba-5204-a429-3ac8c609bfb7" +[[deps.ClimaDiagnostics]] +deps = ["Accessors", "ClimaComms", "ClimaCore", "Dates", "NCDatasets", "SciMLBase"] +git-tree-sha1 = "aff194804df0fcfcf69a80c58978b84777272619" +uuid = "1ecacbb8-0713-4841-9a07-eb5aa8a2d53f" +version = "0.2.2" + [[deps.ClimaLand]] -deps = ["Adapt", "ArtifactWrappers", "ClimaComms", "ClimaCore", "ClimaUtilities", "DataFrames", "Dates", "DocStringExtensions", "Insolation", "Interpolations", "IntervalSets", "LazyArtifacts", "LinearAlgebra", "NCDatasets", "SciMLBase", "StaticArrays", "SurfaceFluxes", "Thermodynamics", "UnrolledUtilities"] +deps = ["Adapt", "ArtifactWrappers", "ClimaComms", "ClimaCore", "ClimaDiagnostics", "ClimaUtilities", "DataFrames", "Dates", "DocStringExtensions", "Insolation", "Interpolations", "IntervalSets", "LazyArtifacts", "LinearAlgebra", "NCDatasets", "SciMLBase", "StaticArrays", "SurfaceFluxes", "Thermodynamics", "UnrolledUtilities"] path = ".." uuid = "08f4d4ce-cf43-44bb-ad95-9d2d5f413532" -version = "0.12.2" +version = "0.12.3" [deps.ClimaLand.extensions] CreateParametersExt = "ClimaParams" diff --git a/experiments/Project.toml b/experiments/Project.toml index cbf600f9d1..6ccb4f3696 100644 --- a/experiments/Project.toml +++ b/experiments/Project.toml @@ -1,7 +1,9 @@ [deps] CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0" +ClimaAnalysis = "29b5916a-a76c-4e73-9657-3c8fd22e65e6" ClimaComms = "3a4d1b5c-c61d-41fd-a00a-5873ba7a1b0d" ClimaCore = "d414da3d-4745-48bb-8d80-42e94e092884" +ClimaDiagnostics = "1ecacbb8-0713-4841-9a07-eb5aa8a2d53f" ClimaLand = "08f4d4ce-cf43-44bb-ad95-9d2d5f413532" ClimaParams = "5c42b081-d73a-476f-9059-fd94b934656c" ClimaTimeSteppers = "595c0a79-7f3d-439a-bc5a-b232dc3bde79" diff --git a/experiments/standalone/Bucket/global_bucket_function.jl b/experiments/standalone/Bucket/global_bucket_function.jl index fae2f9111b..398594463e 100644 --- a/experiments/standalone/Bucket/global_bucket_function.jl +++ b/experiments/standalone/Bucket/global_bucket_function.jl @@ -41,6 +41,11 @@ using ClimaLand: PrescribedAtmosphere, PrescribedRadiativeFluxes +using ClimaDiagnostics +using ClimaAnalysis +import ClimaAnalysis.Visualize as viz +using ClimaUtilities + """ compute_extrema(v) @@ -164,6 +169,37 @@ updatefunc = ClimaLand.make_update_drivers(bucket_atmos, bucket_rad) driver_cb = ClimaLand.DriverUpdateCallback(updateat, updatefunc) cb = SciMLBase.CallbackSet(driver_cb, saving_cb) + + +# ClimaDiagnostics +output_dir = "output/" +ClimaUtilities.OutputPathGenerator.generate_output_path(output_dir) + +space = bucket_domain.space.subsurface + +nc_writer = ClimaDiagnostics.Writers.NetCDFWriter(space, output_dir) + +diags = ClimaLand.CLD.default_diagnostics(model, 1.0; output_writer = nc_writer) + +diagnostic_handler = + ClimaDiagnostics.DiagnosticsHandler(diags, Y, p, t0; dt = Δt) + +diag_cb = ClimaDiagnostics.DiagnosticsCallback(diagnostic_handler) + +sol_test = SciMLBase.solve(prob, ode_algo; dt = Δt, callback = diag_cb) + +#### ClimaAnalysis #### + +simdir = ClimaAnalysis.SimDir("output") +println(summary(simdir)) +alpha = get(simdir; short_name = "alpha") +alpha.dims +fig = CairoMakie.Figure(size = (400, 600)) +viz.plot!(fig, alpha, time = 2 * 86400) +CairoMakie.save("alpha.png", fig) + +########### + sol = ClimaComms.@time ClimaComms.device() SciMLBase.solve( prob, ode_algo; diff --git a/lib/ClimaLandSimulations/Project.toml b/lib/ClimaLandSimulations/Project.toml index 812b3fe89b..225e6abd77 100644 --- a/lib/ClimaLandSimulations/Project.toml +++ b/lib/ClimaLandSimulations/Project.toml @@ -9,6 +9,7 @@ Bonito = "824d6782-a2ef-11e9-3a09-e5662e0c26f8" CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0" ClimaComms = "3a4d1b5c-c61d-41fd-a00a-5873ba7a1b0d" ClimaCore = "d414da3d-4745-48bb-8d80-42e94e092884" +ClimaDiagnostics = "1ecacbb8-0713-4841-9a07-eb5aa8a2d53f" ClimaLand = "08f4d4ce-cf43-44bb-ad95-9d2d5f413532" ClimaParams = "5c42b081-d73a-476f-9059-fd94b934656c" ClimaTimeSteppers = "595c0a79-7f3d-439a-bc5a-b232dc3bde79" @@ -42,9 +43,12 @@ cuDNN = "02a925ec-e4fe-4b08-9a7e-0d78e3d38ccd" ArtifactWrappers = "0.2" Bonito = "3" CairoMakie = "0.11" -ClimaComms = "0.5.6" -ClimaParams = "0.10" +ClimaComms = "0.5.6, 0.6" +ClimaCore = "0.13.2, 0.14" +ClimaDiagnostics = "0.2" +ClimaParams = "0.10.2" ClimaTimeSteppers = "0.7" +ClimaUtilities = "0.1.2" DataFrames = "1" Dates = "1" DelimitedFiles = "1" diff --git a/lib/ClimaLandSimulations/README.md b/lib/ClimaLandSimulations/README.md index d24b377315..9bc8eaf0fa 100644 --- a/lib/ClimaLandSimulations/README.md +++ b/lib/ClimaLandSimulations/README.md @@ -17,11 +17,11 @@ For examples, see the [experiments](https://github.com/CliMA/ClimaLand.jl/lib/Cl ### Development of the `ClimaLandSimulations` subpackage - cd ClimaCore/lib/ClimaLandSimulations + cd ClimaLand/lib/ClimaLandSimulations - # Add ClimaCore to subpackage environment + # Add ClimaLand to subpackage environment julia --project -e 'using Pkg; Pkg.develop(path="../../")' - # Instantiate ClimaCoreMakie project environment + # Instantiate ClimaLandSimulations project environment julia --project -e 'using Pkg; Pkg.instantiate()' julia --project -e 'using Pkg; Pkg.test()' diff --git a/lib/ClimaLandSimulations/src/ClimaLandSimulations.jl b/lib/ClimaLandSimulations/src/ClimaLandSimulations.jl index 0bea798b49..bdc60e6e9d 100644 --- a/lib/ClimaLandSimulations/src/ClimaLandSimulations.jl +++ b/lib/ClimaLandSimulations/src/ClimaLandSimulations.jl @@ -1,6 +1,7 @@ module ClimaLandSimulations using CairoMakie +using ClimaDiagnostics using WGLMakie using DataFrames using LaTeXStrings diff --git a/src/ClimaLand.jl b/src/ClimaLand.jl index 1c68029a1d..9d048f23ac 100644 --- a/src/ClimaLand.jl +++ b/src/ClimaLand.jl @@ -318,4 +318,9 @@ include("integrated/soil_energy_hydrology_biogeochemistry.jl") include("integrated/pond_soil_model.jl") include("integrated/soil_canopy_model.jl") +# Diagnostics +include(joinpath("Diagnostics", "Diagnostics.jl")) +import .Diagnostics as CLD # ClimaLand Diagnostics + + end diff --git a/src/Diagnostics/Diagnostics.jl b/src/Diagnostics/Diagnostics.jl new file mode 100644 index 0000000000..ba163b8d44 --- /dev/null +++ b/src/Diagnostics/Diagnostics.jl @@ -0,0 +1,18 @@ +module Diagnostics + +import ClimaComms + +using ..Bucket: BucketModel + +import ..SoilCanopyModel + +import ClimaDiagnostics: + DiagnosticVariable, ScheduledDiagnostic, average_pre_output_hook! + +import ClimaDiagnostics.Schedules: EveryStepSchedule, EveryDtSchedule + +import ClimaDiagnostics.Writers: HDF5Writer, NetCDFWriter + +include("diagnostic.jl") + +end diff --git a/src/Diagnostics/bucket_compute_methods.jl b/src/Diagnostics/bucket_compute_methods.jl new file mode 100644 index 0000000000..6028e722c5 --- /dev/null +++ b/src/Diagnostics/bucket_compute_methods.jl @@ -0,0 +1,189 @@ +# General helper functions for undefined diagnostics for a particular model +error_diagnostic_variable(variable, land_model::T) where {T} = + error("Cannot compute $variable with model = $T") + +macro generate_error_functions(function_names...) + functions = Expr[] + for function_name in function_names + function_name_sym = Symbol("compute_", function_name, "!") + body = quote + function $function_name_sym(_, _, _, _, land_model) + error_diagnostic_variable($(Symbol(function_name)), land_model) + end + end + push!(functions, body) + end + return quote + $(functions...) + end +end + +@generate_error_functions "albedo" "net_radiation" "surface_temperature" "surface_specific_humidity" "latent_heat_flux" "aerodynamic_resistance" "sensible_heat_flux" "vapor_flux" "surface_air_density" "soil_temperature" "subsurface_water_storage" "surface_water_content" "snow_water_equivalent" + +#= +compute_albedo!(_, _, _, _, land_model) = + error_diagnostic_variable("albedo", land_model) +compute_net_radiation!(_, _, _, _, land_model) = + error_diagnostic_variable("net_radiation", land_model) +compute_surface_temperature!(_, _, _, _, land_model) = + error_diagnostic_variable("surface_temperature", land_model) +compute_surface_specific_humidity!(_, _, _, _, land_model) = + error_diagnostic_variable("surface_specific_humidity", land_model) +compute_latent_heat_flux!(_, _, _, _, land_model) = + error_diagnostic_variable("latent_heat_flux", land_model) +compute_aerodynamic_resistance!(_, _, _, _, land_model) = + error_diagnostic_variable("aerodynamic_resistance", land_model) +compute_sensible_heat_flux!(_, _, _, _, land_model) = + error_diagnostic_variable("sensible_heat_flux", land_model) +compute_vapor_flux!(_, _, _, _, land_model) = + error_diagnostic_variable("vapor_flux", land_model) +compute_surface_air_density!(_, _, _, _, land_model) = + error_diagnostic_variable("surface_air_density", land_model) +compute_soil_temperature!(_, _, _, _, land_model) = + error_diagnostic_variable("soil_temperature", land_model) +compute_subsurface_water_storage!(_, _, _, _, land_model) = + error_diagnostic_variable("subsurface_water_storage", land_model) +compute_surface_water_content!(_, _, _, _, land_model) = + error_diagnostic_variable("surface_water_content", land_model) +compute_snow_water_equivalent!(_, _, _, _, land_model) = + error_diagnostic_variable("snow_water_equivalent", land_model) +=# + +# stored in p + +function compute_albedo!(out, Y, p, t, land_model::BucketModel) + if isnothing(out) + return copy(p.bucket.α_sfc) + else + out .= p.bucket.α_sfc + end +end + +function compute_net_radiation!(out, Y, p, t, land_model::BucketModel) + if isnothing(out) + return copy(p.bucket.R_n) + else + out .= p.bucket.R_n + end +end + +function compute_surface_temperature!(out, Y, p, t, land_model::BucketModel) + if isnothing(out) + return copy(p.bucket.T_sfc) + else + out .= p.bucket.T_sfc + end +end + +function compute_surface_specific_humidity!( + out, + Y, + p, + t, + land_model::BucketModel, +) + if isnothing(out) + return copy(p.bucket.q_sfc) + else + out .= p.bucket.q_sfc + end +end + +function compute_latent_heat_flux!(out, Y, p, t, land_model::BucketModel) + if isnothing(out) + return copy(p.bucket.turbulent_fluxes.lhf) + else + out .= p.bucket.turbulent_fluxes.lhf + end +end + +function compute_aerodynamic_resistance!(out, Y, p, t, land_model::BucketModel) + if isnothing(out) + return copy(p.bucket.turbulent_fluxes.r_ae) + else + out .= p.bucket.turbulent_fluxes.r_ae + end +end + +function compute_sensible_heat_flux!(out, Y, p, t, land_model::BucketModel) + if isnothing(out) + return copy(p.bucket.turbulent_fluxes.shf) + else + out .= p.bucket.turbulent_fluxes.shf + end +end + +function compute_vapor_flux!(out, Y, p, t, land_model::BucketModel) + if isnothing(out) + return copy(p.bucket.turbulent_fluxes.vapor_flux) + else + out .= p.bucket.turbulent_fluxes.vapor_flux + end +end + +function compute_surface_air_density!(out, Y, p, t, land_model::BucketModel) + if isnothing(out) + return copy(p.bucket.ρ_sfc) + else + out .= p.bucket.ρ_sfc + end +end + +# stored in Y + +function compute_soil_temperature!(out, Y, p, t, land_model::BucketModel) + if isnothing(out) + return copy(Y.bucket.T) + else + out .= Y.bucket.T + end +end + +function compute_subsurface_water_storage!( + out, + Y, + p, + t, + land_model::BucketModel, +) + if isnothing(out) + return copy(Y.bucket.W) + else + out .= Y.bucket.W + end +end + +function compute_surface_water_content!(out, Y, p, t, land_model::BucketModel) + if isnothing(out) + return copy(Y.bucket.Ws) + else + out .= Y.bucket.Ws + end +end + +function compute_snow_water_equivalent!(out, Y, p, t, land_model::BucketModel) + if isnothing(out) + return copy(Y.bucket.σS) + else + out .= Y.bucket.σS + end +end + + + +## below would be in SoilCanopyModel_compute_methods.jl +#= +function compute_soil_temperature!( + out, + Y, + p, + t, + land_model::SoilCanopyModel, + ) + if isnothing(out) + return copy(p.soil.T) + else + out .= p.soil.T + end +end +=# diff --git a/src/Diagnostics/default_diagnostics.jl b/src/Diagnostics/default_diagnostics.jl new file mode 100644 index 0000000000..460203cb39 --- /dev/null +++ b/src/Diagnostics/default_diagnostics.jl @@ -0,0 +1,117 @@ +export default_diagnostics + +# This file is included by Diagnostics.jl and defines all the defaults for various models (e.g., Bucket, SoilCanopyModel). +# A model here is either a standalone (e.g., Bucket) or integrated (e.g., SoilCanopy) model. +# +# If you are developing new models, add your defaults here. If you want to add more high +# level interfaces, add them here. Feel free to include extra files. + + +# Bucket model + +""" + function common_diagnostics( + period, + reduction, + output_writer, + t_start, + short_names...; + pre_output_hook! = nothing, + ) + +Helper function to define functions like `daily_max`. +""" +function common_diagnostics( + period, + reduction, + output_writer, + t_start, + short_names...; + pre_output_hook! = nothing, +) + return [ + ScheduledDiagnostic( + variable = get_diagnostic_variable(short_name), + compute_schedule_func = EveryStepSchedule(), + output_schedule_func = EveryDtSchedule(period; t_start), + reduction_time_func = reduction, + output_writer = output_writer, + pre_output_hook! = pre_output_hook!, + ) for short_name in short_names + ] +end + +include("standard_diagnostic_frequencies.jl") + +# Bucket +function default_diagnostics(land_model::BucketModel, t_start; output_writer) + + define_diagnostics!(land_model) + + bucket_diagnostics = [ + "alpha", + "rn", + "tsfc", + "qsfc", + "lhf", + "rae", + "shf", + "vflux", + "rhosfc", + "tsoil", + "wsoil", + "wsfc", + "ssfc", + ] + + default_outputs = + hourly_averages(bucket_diagnostics...; output_writer, t_start) + return [default_outputs...] +end + +# SoilCanopyModel +function default_diagnostics( + land_model::SoilCanopyModel, + t_start; + output_writer, +) + + define_diagnostics!(land_model) + + soilcanopy_diagnostics = [ + "rn", + "lhf", + "rae", + "shf", + "vflux", + "tsoil", + "slw", + "infil", + "scd", + "scms", + "gs", + "mt", + "trans", + "rain", # do we want? + "an", + "gpp", + "rd", + "vcmax25", + "par", + "apar", + "rpar", + "tpar", + "nir", + "anir", + "rnir", + "tnir", + "swn", + "lwn", + "ra", + "soilco2", + ] + + default_outputs = + hourly_averages(soilcanopy_diagnostics...; output_writer, t_start) + return [default_outputs...] +end diff --git a/src/Diagnostics/define_diagnostics.jl b/src/Diagnostics/define_diagnostics.jl new file mode 100644 index 0000000000..a2e30eea2c --- /dev/null +++ b/src/Diagnostics/define_diagnostics.jl @@ -0,0 +1,622 @@ +""" + define_diagnostics!(land_model) + +Calls add_diagnostic_viariable! for all variables +""" +function define_diagnostics!(land_model) + + # Stored in p + + # Albedo + add_diagnostic_variable!( + short_name = "alpha", + long_name = "Albedo", + standard_name = "albedo", + units = "", + comments = "The fraction of incoming radiation reflected by the land surface.", + compute! = (out, Y, p, t) -> compute_albedo!(out, Y, p, t, land_model), + ) + + # Net radiation + add_diagnostic_variable!( + short_name = "rn", + long_name = "Net Radiation", + standard_name = "net_radiation", + units = "W m^-2", + comments = "Difference between incoming and outgoing shortwave and longwave radiation at the land surface.", + compute! = (out, Y, p, t) -> + compute_net_radiation!(out, Y, p, t, land_model), + ) + + # Surface temperature + add_diagnostic_variable!( + short_name = "tsfc", + long_name = "Surface Temperature", + standard_name = "surface_temperature", + units = "K", + comments = "Temperature of the land surface.", + compute! = (out, Y, p, t) -> + compute_surface_temperature!(out, Y, p, t, land_model), + ) + + # Surface specific humidity + add_diagnostic_variable!( + short_name = "qsfc", + long_name = "Surface Specific Humidity", + standard_name = "surface_specific_humidity", + units = "", + comments = "Ratio of water vapor mass to total moist air parcel mass.", + compute! = (out, Y, p, t) -> + compute_surface_specific_humidity!(out, Y, p, t, land_model), + ) + + # Latent heat flux + add_diagnostic_variable!( + short_name = "lhf", + long_name = "Latent Heat Flux", + standard_name = "latent_heat_flux", + units = "W m^-2", + comments = "Exchange of energy at the land-atmosphere interface due to water evaporation or sublimation.", + compute! = (out, Y, p, t) -> + compute_latent_heat_flux!(out, Y, p, t, land_model), + ) + + # Aerodynamic resistance + add_diagnostic_variable!( + short_name = "rae", + long_name = "Aerodynamic Resistance", + standard_name = "aerodynamic_resistance", + units = "m s^-1", + comments = "Effiency of turbulent transport controlling the land-atmosphere exchange of sensible and latent heat.", + compute! = (out, Y, p, t) -> + compute_aerodynamic_resistance!(out, Y, p, t, land_model), + ) + + # Sensible heat flux + add_diagnostic_variable!( + short_name = "shf", + long_name = "Sensible Heat Flux", + standard_name = "sensible_heat_flux", + units = "W m^-2", + comments = "Exchange of energy at the land-atmosphere interface due to temperature difference.", + compute! = (out, Y, p, t) -> + compute_sensible_heat_flux!(out, Y, p, t, land_model), + ) + + # Vapor flux + add_diagnostic_variable!( + short_name = "vflux", + long_name = "Liquid water evaporation", + standard_name = "vapor_flux", + units = "m s^-1", + comments = "Flux of water from the land surface to the atmosphere. E.g., evaporation or sublimation.", + compute! = (out, Y, p, t) -> + compute_vapor_flux!(out, Y, p, t, land_model), + ) + + # Surface air density + add_diagnostic_variable!( + short_name = "rhosfc", + long_name = "Surface Air Density", + standard_name = "surface_air_density", + units = "kg m^−3", + comments = "Density of air at the land-atmosphere interface.", + compute! = (out, Y, p, t) -> + compute_surface_air_density!(out, Y, p, t, land_model), + ) + + # Stored in Y + + # Soil temperature (3D) at depth + add_diagnostic_variable!( + short_name = "tsoil", + long_name = "Soil temperature", + standard_name = "soil_temperature", + units = "K", + comments = "Soil temperature at multiple soil depth.", + compute! = (out, Y, p, t) -> + compute_soil_temperature!(out, Y, p, t, land_model), + ) + + # Surbsurface water storage + add_diagnostic_variable!( + short_name = "wsoil", + long_name = "subsurface Water Storage", + standard_name = "subsurface_water_storage", + units = "m", + comments = "Soil water content.", + compute! = (out, Y, p, t) -> + compute_subsurface_water_storage!(out, Y, p, t, land_model), + ) + + # Surface water content + add_diagnostic_variable!( + short_name = "wsfc", + long_name = "Surface Water Content", + standard_name = "surface_water_content", + units = "m", + comments = "Water at the soil surface.", + compute! = (out, Y, p, t) -> + compute_surface_water_content!(out, Y, p, t, land_model), + ) + + # Surface snow water content + add_diagnostic_variable!( + short_name = "ssfc", + long_name = "Snow Water Equivalent", + standard_name = "snow_water_equivalent", + units = "m", + comments = "Snow at the soil surface, expressed in water equivalent.", + compute! = (out, Y, p, t) -> + compute_snow_water_equivalent!(out, Y, p, t, land_model), + ) + + ###### SoilCanopyModel ###### + + add_diagnostic_variable!( + short_name = "slw", + long_name = "Soil Liquid Water", + standard_name = "soil_liquid_water", + units = "m^3 m^-3", + comments = "Soil moisture, the liquid water volume per soil volume. This liquid water is located in the soil pores.", + compute! = (out, Y, p, t) -> + compute_soil_water_liquid!(out, Y, p, t, land_model), + ) + + add_diagnostic_variable!( + short_name = "infil", + long_name = "Infiltration", + standard_name = "infiltration", + units = "m s^-1", # double check + comments = "The flux of liquid water into the soil.", + compute! = (out, Y, p, t) -> + compute_infiltration!(out, Y, p, t, land_model), + ) + + add_diagnostic_variable!( + short_name = "scd", + long_name = "Soil CO2 Diffusivity", + standard_name = "soil_co2_diffusivity", + units = "", # need to add + comments = "The diffusivity of CO2 in the porous phase of the soil. Depends on soil texture, moisture, and temperature.", + compute! = (out, Y, p, t) -> + compute_soilco2_diffusivity!(out, Y, p, t, land_model), + ) + + add_diagnostic_variable!( + short_name = "scms", + long_name = "Soil CO2 Microbial Source", + standard_name = "soil_co2_microbial_source", + units = "", # check + comments = "The production of CO2 by microbes in the soil. Vary by layers of soil depth.", + compute! = (out, Y, p, t) -> + compute_soilco2_source_microbe!(out, Y, p, t, land_model), + ) + + add_diagnostic_variable!( + short_name = "gs", + long_name = "Stomatal Conductance", + standard_name = "stomatal_conductance", + units = "m s^-1", + comments = "The conductance of leaves. This depends on stomatal opening. It varies with factors such as soil moisture or atmospheric water demand.", + compute! = (out, Y, p, t) -> + compute_stomatal_conductance!(out, Y, p, t, land_model), + ) + + add_diagnostic_variable!( + short_name = "mt", + long_name = "Medlyn Term", + standard_name = "medlyn_term", + units = "", # check + comments = "", + compute! = (out, Y, p, t) -> + compute_medlyn_term!(out, Y, p, t, land_model), + ) + + add_diagnostic_variable!( + short_name = "trans", + long_name = "Canopy Transpiration", + standard_name = "canopy_transpiration", + units = "", # check + comments = "The water evaporated from the canopy due to leaf transpiration.", + compute! = (out, Y, p, t) -> + compute_canopy_transpiration!(out, Y, p, t, land_model), + ) + + add_diagnostic_variable!( # not actually computed, but read from input or atmosphere model, and stored in p... + short_name = "rain", + long_name = "Rainfall", + standard_name = "rainfall", + units = "m", + comments = "Precipitation of liquid water.", + compute! = (out, Y, p, t) -> + compute_rainfall!(out, Y, p, t, land_model), + ) + + add_diagnostic_variable!( + short_name = "an", + long_name = "Leaf Net Photosynthesis", + standard_name = "leaf_net_photosynthesis", + units = "", # check + comments = "Net photosynthesis of a leaf.", + compute! = (out, Y, p, t) -> + compute_photosynthesis_net_leaf!(out, Y, p, t, land_model), + ) + + add_diagnostic_variable!( + short_name = "gpp", + long_name = "Gross Primary Productivity", + standard_name = "gross_primary_productivity", + units = "", + comments = "Net photosynthesis of the canopy.", + compute! = (out, Y, p, t) -> + compute_photosynthesis_net_canopy!(out, Y, p, t, land_model), + ) + + add_diagnostic_variable!( + short_name = "rd", + long_name = "Leaf Respiration", + standard_name = "leaf_dark_respiration", + units = "", + comments = "Leaf respiration, called dark respiration because usually measured in the abscence of radiation.", + compute! = (out, Y, p, t) -> + compute_respiration_leaf!(out, Y, p, t, land_model), + ) + + add_diagnostic_variable!( + short_name = "vcmax25", + long_name = "Vcmax25", + standard_name = "vcmax25", + units = "", + comments = "The parameter vcmax at 25 degree celsius. Important for the Farquhar model of leaf photosynthesis.", + compute! = (out, Y, p, t) -> compute_vcmax25!(out, Y, p, t, land_model), + ) + + add_diagnostic_variable!( + short_name = "par", + long_name = "Photosynthetically Active Radiation", + standard_name = "photosynthetically_active_radiation", + units = "", + comments = "The subset of total radiation that activates photosynthesis reaching the canopy.", + compute! = (out, Y, p, t) -> + compute_photosynthetically_active_radiation!( + out, + Y, + p, + t, + land_model, + ), + ) + + add_diagnostic_variable!( + short_name = "apar", + long_name = "Absorbed Photosynthetically Active Radiation", + standard_name = "absorbed_photosynthetically_active_radiation", + units = "", + comments = "The amount of photosynthetically active radiation absorbed by the leaf. The rest if reflected or transmitted.", + compute! = (out, Y, p, t) -> + compute_photosynthetically_active_radiation_absorbed!( + out, + Y, + p, + t, + land_model, + ), + ) + + add_diagnostic_variable!( + short_name = "rpar", + long_name = "Reflected Photosynthetically Active Radiation", + standard_name = "reflected_photosynthetically_active_radiation", + units = "", + comments = "The amount of photosynthetically active radiation reflected by leaves.", + compute! = (out, Y, p, t) -> + compute_photosynthetically_active_radiation_reflected!( + out, + Y, + p, + t, + land_model, + ), + ) + + add_diagnostic_variable!( + short_name = "tpar", + long_name = "Transmitted Photosynthetically Active Radiation", + standard_name = "transmitted_photosynthetically_active_radiation", + units = "", + comments = "The amount of photosynthetically active radiation transmitted by leaves.", + compute! = (out, Y, p, t) -> + compute_photosynthetically_active_radiation_transmitted!( + out, + Y, + p, + t, + land_model, + ), + ) + + add_diagnostic_variable!( + short_name = "nir", + long_name = "Near Infrared Radiation", + standard_name = "near_infrared_radiation", + units = "W m^-2", + comments = "The amount of near infrared radiation reaching the canopy.", + compute! = (out, Y, p, t) -> + compute_near_infrared_radiation!(out, Y, p, t, land_model), + ) + + add_diagnostic_variable!( + short_name = "anir", + long_name = "Absorbed Near Infrared Radiation", + standard_name = "absorbed_near_infrared_radiation", + units = "W m^-2", + comments = "The amount of near infrared radiation reaching the canopy.", + compute! = (out, Y, p, t) -> + compute_near_infrared_radiation_absorbed!(out, Y, p, t, land_model), + ) + + add_diagnostic_variable!( + short_name = "rnir", + long_name = "Reflected Near Infrared Radiation", + standard_name = "reflected_near_infrared_radiation", + units = "W m^-2", + comments = "The amount of near infrared radiation reaching the canopy.", + compute! = (out, Y, p, t) -> + compute_near_infrared_radiation_reflected!( + out, + Y, + p, + t, + land_model, + ), + ) + + add_diagnostic_variable!( + short_name = "tnir", + long_name = "Transmitted Near Infrared Radiation", + standard_name = "transmitted_near_infrared_radiation", + units = "W m^-2", + comments = "The amount of near infrared radiation reaching the canopy.", + compute! = (out, Y, p, t) -> + compute_near_infrared_radiation_transmitted!( + out, + Y, + p, + t, + land_model, + ), + ) + + add_diagnostic_variable!( + short_name = "swn", + long_name = "Net Shortwave Radiation", + standard_name = "net_shortwave_radiation", + units = "W m^-2", + comments = "The net (in minus out) radiation at the surface.", + compute! = (out, Y, p, t) -> + compute_radiation_shortwave_net!(out, Y, p, t, land_model), + ) + + add_diagnostic_variable!( + short_name = "lwn", + long_name = "Net Longwave Radiation", + standard_name = "net_longwave_radiation", + units = "W m^-2", + comments = "The net (in minus out) radiation at the surface.", + compute! = (out, Y, p, t) -> + compute_radiation_longwave_net!(out, Y, p, t, land_model), + ) + + add_diagnostic_variable!( + short_name = "ra", + long_name = "Autotrophic Respiration", + standard_name = "autotrophic_respiration", + units = "mol m^-2 s^-1", + comments = "Canopy autotrophic respiration, the sum of leaves, stems and roots respiration.", + compute! = (out, Y, p, t) -> + compute_autotrophic_respiration!(out, Y, p, t, land_model), + ) + + add_diagnostic_variable!( + short_name = "soilco2", + long_name = "Soil CO2 concentration", + standard_name = "soil_co2", + units = "", + comments = "Concentration of CO2 in the air of soil pores.", + compute! = (out, Y, p, t) -> compute_soilco2!(out, Y, p, t, land_model), + ) + + add_diagnostic_variable!( + short_name = "soilrn", + long_name = "Soil Net Radiation", + standard_name = "soil_net_radiation", + units = "W m^-2", + comments = "Net radiation at the soil surface.", + compute! = (out, Y, p, t) -> + compute_soil_net_radiation!(out, Y, p, t, land_model), + ) + + add_diagnostic_variable!( + short_name = "soillhf", + long_name = "Soil Latent Heat Flux", + standard_name = "soil_Latent_Heat_Flux", + units = "W m^-2", + comments = "Soil evaporation.", + compute! = (out, Y, p, t) -> + compute_soil_latent_heat_flux!(out, Y, p, t, land_model), + ) + + add_diagnostic_variable!( + short_name = "soilshf", + long_name = "Soil Sensible Heat Flux", + standard_name = "soil_sensible_Heat_Flux", + units = "W m^-2", + comments = "Soil sensible heat flux.", + compute! = (out, Y, p, t) -> + compute_soil_sensible_heat_flux!(out, Y, p, t, land_model), + ) + + add_diagnostic_variable!( + short_name = "soilrae", + long_name = "Soil Aerodynamic Resistance", + standard_name = "soil_aerodynamic_resistance", + units = "", + comments = "Soil aerodynamic resistance.", + compute! = (out, Y, p, t) -> + compute_soil_aerodynamic_resistance!(out, Y, p, t, land_model), + ) + + add_diagnostic_variable!( + short_name = "hr", + long_name = "Heterotrophic Respiration", + standard_name = "heterotrophic_respiration", + units = "mol m^-2 s^-1", + comments = "CO2 efflux at the soil surface due to microbial decomposition of soil organic matter.", + compute! = (out, Y, p, t) -> + compute_heterotrophic_respiration!(out, Y, p, t, land_model), + ) + + add_diagnostic_variable!( + short_name = "shc", + long_name = "Soil Hydraulic Conductivity", + standard_name = "soil_hydraulic_conductivity", + units = "", + comments = "Soil hydraulic conductivity.", + compute! = (out, Y, p, t) -> + compute_soil_hydraulic_conductivity!(out, Y, p, t, land_model), + ) + + add_diagnostic_variable!( + short_name = "stc", + long_name = "Soil Thermal Conductivity", + standard_name = "soil_thermal_conductivity", + units = "", + comments = "Soil thermal conductivity.", + compute! = (out, Y, p, t) -> + compute_soil_thermal_conductivity!(out, Y, p, t, land_model), + ) + + add_diagnostic_variable!( + short_name = "swp", + long_name = "Soil Water Potential", + standard_name = "soil_water_potential", + units = "", + comments = "Soil water potential.", + compute! = (out, Y, p, t) -> + compute_soil_water_potential!(out, Y, p, t, land_model), + ) + + add_diagnostic_variable!( + short_name = "sza", + long_name = "Solar Zenith Angle", + standard_name = "solar_zenith_angle", + units = "", + comments = "Solar zenith angle.", + compute! = (out, Y, p, t) -> + compute_solar_zenith_angle!(out, Y, p, t, land_model), + ) + + add_diagnostic_variable!( + short_name = "msf", + long_name = "Moisture Stress Factor", + standard_name = "moisture_stress_factor", + units = "", + comments = "Sensitivity of plants conductance to soil water content.", + compute! = (out, Y, p, t) -> + compute_moisture_stress_factor!(out, Y, p, t, land_model), + ) + + add_diagnostic_variable!( + short_name = "cwp", + long_name = "Canopy Water Potential", + standard_name = "canopy_water_potential", + units = "", + comments = "The water potential of the canopy.", + compute! = (out, Y, p, t) -> + compute_canopy_water_potential!(out, Y, p, t, land_model), + ) + + add_diagnostic_variable!( + short_name = "fa", + long_name = "Cross Section", + standard_name = "cross_section", + units = "", + comments = "The area of stem relative to ground area.", #?? + compute! = (out, Y, p, t) -> + compute_cross_section!(out, Y, p, t, land_model), + ) + + add_diagnostic_variable!( + short_name = "far", + long_name = "Root Cross Section", + standard_name = "Cross Section", + units = "", + comments = "The area of roots relative to ground area.", #?? + compute! = (out, Y, p, t) -> + compute_cross_section_roots!(out, Y, p, t, land_model), + ) + + add_diagnostic_variable!( + short_name = "ai", + long_name = "Area Index", + standard_name = "area_index", + units = "", + comments = "The area index.", #?? of steam, leaves, roots? + compute! = (out, Y, p, t) -> + compute_area_index!(out, Y, p, t, land_model), + ) + + add_diagnostic_variable!( + short_name = "clhf", + long_name = "Canopy Latent Heat Flux", + standard_name = "canopy_latent_heat_flux", + units = "", + comments = "Canopy evaporation.", #?? of steam, leaves, roots? + compute! = (out, Y, p, t) -> + compute_canopy_latent_heat_flux!(out, Y, p, t, land_model), + ) + + add_diagnostic_variable!( + short_name = "cshf", + long_name = "Canopy Sensible Heat Flux", + standard_name = "canopy_sensible_heat_flux", + units = "", + comments = "Canopy sensible heat flux.", #?? of steam, leaves, roots? + compute! = (out, Y, p, t) -> + compute_canopy_sensible_heat_flux!(out, Y, p, t, land_model), + ) + + add_diagnostic_variable!( + short_name = "crae", + long_name = "Canopy Aerodynamic Resistance", + standard_name = "canopy_aerodynamic_resistance", + units = "", + comments = "Canopy aerodynamic_resistance.", #?? of steam, leaves, roots? + compute! = (out, Y, p, t) -> + compute_canopy_aerodynamic_resistance!(out, Y, p, t, land_model), + ) + + add_diagnostic_variable!( + short_name = "ct", + long_name = "Canopy Temperature", + standard_name = "canopy_temperature", + units = "", + comments = "Canopy temperature.", #?? of steam, leaves, roots? + compute! = (out, Y, p, t) -> + compute_canopy_temperature!(out, Y, p, t, land_model), + ) + + add_diagnostic_variable!( + short_name = "si", + long_name = "Soil Ice", + standard_name = "soil_ice", + units = "m^3 m^-3", + comments = "soil ice.", #?? of steam, leaves, roots? + compute! = (out, Y, p, t) -> + compute_soil_ice!(out, Y, p, t, land_model), + ) +end + +# define_diagnostics!(1.0) # populates ALL_DIAGNOSTICS from diagnostic.jl +# needs to be moved to docs make table of diagnostic variables diff --git a/src/Diagnostics/diagnostic.jl b/src/Diagnostics/diagnostic.jl new file mode 100644 index 0000000000..a8d56389b3 --- /dev/null +++ b/src/Diagnostics/diagnostic.jl @@ -0,0 +1,99 @@ +# ClimaLand diagnostics + +# - A dictionary `ALL_DIAGNOSTICS` with all the diagnostics we know how to compute, keyed +# over their short name. If you want to add more diagnostics, look at the included files. +# You can add your own file if you want to define several new diagnostics that are +# conceptually related. The dictionary `ALL_DIAGNOSTICS` should be considered an +# implementation detail. + +const ALL_DIAGNOSTICS = Dict{String, DiagnosticVariable}() + +""" + + add_diagnostic_variable!(; short_name, + long_name, + standard_name, + units, + description, + compute!) + + +Add a new variable to the `ALL_DIAGNOSTICS` dictionary (this function mutates the state of +`ClimaLand.ALL_DIAGNOSTICS`). + +If possible, please follow the naming scheme outline in +https://airtable.com/appYNLuWqAgzLbhSq/shrKcLEdssxb8Yvcp/tblL7dJkC3vl5zQLb + +Keyword arguments +================= + + +- `short_name`: Name used to identify the variable in the output files and in the file + names. Short but descriptive. `ClimaLand` diagnostics are identified by the + short name. We follow the Coupled Model Intercomparison Project conventions. + +- `long_name`: Name used to identify the variable in the output files. + +- `standard_name`: Standard name, as in + http://cfconventions.org/Data/cf-standard-names/71/build/cf-standard-name-table.html + +- `units`: Physical units of the variable. + +- `comments`: More verbose explanation of what the variable is, or comments related to how + it is defined or computed. + +- `compute!`: Function that compute the diagnostic variable from the state. + It has to take two arguments: the `integrator`, and a + pre-allocated area of memory where to write the result of the + computation. If no pre-allocated area is available, a new + one will be allocated. To avoid extra allocations, this + function should perform the calculation in-place (i.e., using + `.=`). + +""" +function add_diagnostic_variable!(; + short_name, + long_name, + standard_name = "", + units, + comments = "", + compute!, +) + haskey(ALL_DIAGNOSTICS, short_name) && @warn( + "overwriting diagnostic `$short_name` entry containing fields\n" * + "$(map( + field -> "$(getfield(ALL_DIAGNOSTICS[short_name], field))", + filter(field -> field != :compute!, fieldnames(DiagnosticVariable)), + ))" + ) + + ALL_DIAGNOSTICS[short_name] = DiagnosticVariable(; + short_name, + long_name, + standard_name, + units, + comments, + compute!, + ) +end + +""" + + get_diagnostic_variable!(short_name) + +Return a `DiagnosticVariable` from its `short_name`, if it exists. +""" +function get_diagnostic_variable(short_name) + haskey(ALL_DIAGNOSTICS, short_name) || + error("diagnostic $short_name does not exist") + + return ALL_DIAGNOSTICS[short_name] +end + +# Do you want to define more diagnostics? Add them here +include("bucket_compute_methods.jl") +include("soilcanopy_compute_methods.jl") +include("define_diagnostics.jl") + +# Default diagnostics and higher level interfaces +include("default_diagnostics.jl") diff --git a/src/Diagnostics/soilcanopy_compute_methods.jl b/src/Diagnostics/soilcanopy_compute_methods.jl new file mode 100644 index 0000000000..80653a5d91 --- /dev/null +++ b/src/Diagnostics/soilcanopy_compute_methods.jl @@ -0,0 +1,579 @@ +# stored in p + +function compute_soil_net_radiation!(out, Y, p, t, land_model::SoilCanopyModel) + if isnothing(out) + return copy(p.soil.R_n) + else + out .= p.soil.R_n + end +end + +function compute_soil_latent_heat_flux!( + out, + Y, + p, + t, + land_model::SoilCanopyModel, +) + if isnothing(out) + return copy(p.soil.turbulent_flux.lhf) # is this different from canopy.energy.lhf? + else + out .= p.soil.turbulent_flux.lhf + end +end + +function compute_soil_aerodynamic_resistance!( + out, + Y, + p, + t, + land_model::SoilCanopyModel, +) + if isnothing(out) + return copy(p.soil.turbulent_fluxes.r_ae) + else + out .= p.soil.turbulent_fluxes.r_ae + end +end + +function compute_soil_sensible_heat_flux!( + out, + Y, + p, + t, + land_model::SoilCanopyModel, +) + if isnothing(out) + return copy(p.soil.turbulent_fluxes.shf) + else + out .= p.soil.turbulent_fluxes.shf + end +end + +function compute_vapor_flux!(out, Y, p, t, land_model::SoilCanopyModel) + if isnothing(out) + return copy(p.soil.turbulent_fluxes.vapor_flux) + else + out .= p.soil.turbulent_fluxes.vapor_flux + end +end + +function compute_soil_temperature!(out, Y, p, t, land_model::SoilCanopyModel) + if isnothing(out) + return copy(p.drivers.T) # or is it p.soil.T? + else + out .= p.drivers.T + end +end + +function compute_soil_water_liquid(out, Y, p, t, land_model::SoilCanopyModel) + if isnothing(out) + return copy(p.soil.θ_l) # or is it in Y.soil? + else + out .= p.soil.θ_l + end +end + +function compute_infiltration(out, Y, p, t, land_model::SoilCanopyModel) + if isnothing(out) + return copy(p.soil.infiltration) + else + out .= p.soil.infiltration + end +end + +function compute_soilco2_diffusivity(out, Y, p, t, land_model::SoilCanopyModel) + if isnothing(out) + return copy(p.soilco2.D) # NOTE: we will need a method to compute surface co2 efflux + else + out .= p.soilco2.D + end +end + +function compute_soilco2_source_microbe( + out, + Y, + p, + t, + land_model::SoilCanopyModel, +) + if isnothing(out) + return copy(p.soilco2.Sm) + else + out .= p.soilco2.Sm + end +end + +function compute_stomatal_conductance(out, Y, p, t, land_model::SoilCanopyModel) + if isnothing(out) + return copy(p.canopy.conductance.gs) # doublecheck: stomata, not canopy + else + out .= p.canopy.conductance.gs + end +end + +function compute_medlyn_term(out, Y, p, t, land_model::SoilCanopyModel) + if isnothing(out) + return copy(p.canopy.conductance.medlyn_term) + else + out .= p.canopy.conductance.medlyn_term + end +end + +function compute_canopy_transpiration(out, Y, p, t, land_model::SoilCanopyModel) + if isnothing(out) + return copy(p.canopy.transpiration) # doublecheck: canopy, not leaf + else + out .= p.canopy.transpiration + end +end + +function compute_rainfall(out, Y, p, t, land_model::SoilCanopyModel) + if isnothing(out) + return copy(p.drivers.P_liq) # I guess this is read and put it p. not computed. curious if we should handle this differently. + else + out .= p.drivers.P_liq + end +end + +function compute_snowfall(out, Y, p, t, land_model::SoilCanopyModel) + if isnothing(out) + return copy(p.drivers.P_snow) # following comment above, we could have a default getting only model output, and one also getting some inputs like drivers + else + out .= p.drivers.P_snow + end +end + +function compute_pressure(out, Y, p, t, land_model::SoilCanopyModel) + if isnothing(out) + return copy(p.drivers.P) # not sure if precip or pressure + else + out .= p.drivers.P + end +end + +function compute_wind_speed(out, Y, p, t, land_model::SoilCanopyModel) + if isnothing(out) + return copy(p.drivers.u) + else + out .= p.drivers.u + end +end + +function compute_specific_humidity(out, Y, p, t, land_model::SoilCanopyModel) + if isnothing(out) + return copy(p.drivers.q) # check if this is correct. Also, check if Bucket has it and same name or not. + else + out .= p.drivers.q + end +end + +function compute_air_co2(out, Y, p, t, land_model::SoilCanopyModel) + if isnothing(out) + return copy(p.drivers.c_co2) + else + out .= p.drivers.c_co2 + end +end + +function compute_radiation_shortwave_down( + out, + Y, + p, + t, + land_model::SoilCanopyModel, +) + if isnothing(out) + return copy(p.drivers.SW_d) + else + out .= p.drivers.SW_d + end +end + +function compute_radiation_longwave_down( + out, + Y, + p, + t, + land_model::SoilCanopyModel, +) + if isnothing(out) + return copy(p.drivers.LW_d) + else + out .= p.drivers.LW_d + end +end + +function compute_photosynthesis_net_leaf( + out, + Y, + p, + t, + land_model::SoilCanopyModel, +) + if isnothing(out) + return copy(p.canopy.photosynthesis.An) + else + out .= p.canopy.photosynthesis.An + end +end + +function compute_photosynthesis_net_canopy( + out, + Y, + p, + t, + land_model::SoilCanopyModel, +) # could be gross primary productivity, but this is consistent with leaf + if isnothing(out) + return copy(p.canopy.photosynthesis.GPP) + else + out .= p.canopy.photosynthesis.GPP + end +end + +function compute_respiration_leaf(out, Y, p, t, land_model::SoilCanopyModel) + if isnothing(out) + return copy(p.canopy.photosynthesis.Rd) + else + out .= p.canopy.photosynthesis.Rd + end +end + +function compute_vcmax25(out, Y, p, t, land_model::SoilCanopyModel) + if isnothing(out) + return copy(p.canopy.photosynthesis.vcmax25) + else + out .= p.canopy.photosynthesis.vcmax25 + end +end + +function compute_photosynthetically_active_radiation( + out, + Y, + p, + t, + land_model::SoilCanopyModel, +) + if isnothing(out) + return copy(p.canopy.radiative_transfer.par) + else + out .= p.canopy.radiative_transfer.par + end +end + +function compute_photosynthetically_active_radiation_absorbed( + out, + Y, + p, + t, + land_model::SoilCanopyModel, +) + if isnothing(out) + return copy(p.canopy.radiative_transfer.apar) + else + out .= p.canopy.radive_transfer.apar + end +end + +function compute_photosynthetically_active_radiation_reflected( + out, + Y, + p, + t, + land_model::SoilCanopyModel, +) + if isnothing(out) + return copy(p.canopy.radiative_transfer.rpar) + else + out .= p.canopy.radiative_transfer.rpar + end +end + +function compute_photosynthetically_active_radiation_transmitted( + out, + Y, + p, + t, + land_model::SoilCanopyModel, +) + if isnothing(out) + return copy(p.canopy.radiative_transfer.tpar) + else + out .= p.canopy.radiative_transfer.tpar + end +end + +function compute_near_infrared_radiation( + out, + Y, + p, + t, + land_model::SoilCanopyModel, +) + if isnothing(out) + return copy(p.canopy.radiative_transfer.nir) + else + out .= p.canopy.radiative_transfer.nir + end +end + +function compute_near_infrared_radiation_absorbed( + out, + Y, + p, + t, + land_model::SoilCanopyModel, +) + if isnothing(out) + return copy(p.canopy.radiative_transfer.anir) + else + out .= p.canopy.radiative_transfer.anir + end +end + +function compute_near_infrared_radiation_reflected( + out, + Y, + p, + t, + land_model::SoilCanopyModel, +) + if isnothing(out) + return copy(p.canopy.radiative_transfer.rnir) + else + out .= p.canopy.radiative_transfer.rnir + end +end + +function compute_near_infrared_radiation_transmitted( + out, + Y, + p, + t, + land_model::SoilCanopyModel, +) + if isnothing(out) + return copy(p.canopy.radiative_transfer.tnir) + else + out .= p.canopy.radiative_transfer.tnir + end +end + +function compute_radiation_shortwave_net( + out, + Y, + p, + t, + land_model::SoilCanopyModel, +) + if isnothing(out) + return copy(p.canopy.radiative_transfer.SW_n) + else + out .= p.canopy.radiative_transfer.SW_n + end +end + +function compute_radiation_longwave_net( + out, + Y, + p, + t, + land_model::SoilCanopyModel, +) + if isnothing(out) + return copy(p.canopy.radiative_transfer.LW_n) + else + out .= p.canopy.radiative_transfer.LW_n + end +end + +function compute_autotrophic_respiration( + out, + Y, + p, + t, + land_model::SoilCanopyModel, +) + if isnothing(out) + return copy(p.canopy.autotrophic_respiration.Ra) + else + out .= p.canopy.autotrophic_respiration.Ra + end +end + +function compute_soilco2(out, Y, p, t, land_model::SoilCanopyModel) + if isnothing(out) + return copy(Y.soilco2.C) + else + out .= Y.soilco2.C + end +end + +function compute_heterotrophic_respiration( + out, + Y, + p, + t, + land_model::SoilCanopyModel, +) + if isnothing(out) + return copy(p.soilco2.top_bc) + else + p.soilco2.top_bc + end +end + +function compute_soil_hydraulic_conductivity( + out, + Y, + p, + t, + land_model::SoilCanopyModel, +) + if isnothing(out) + return copy(p.soil.K) + else + p.soil.K + end +end + +function compute_soil_water_potential(out, Y, p, t, land_model::SoilCanopyModel) + if isnothing(out) + return copy(p.soil.ψ) + else + p.soil.ψ + end +end + +function compute_soil_thermal_conductivity( + out, + Y, + p, + t, + land_model::SoilCanopyModel, +) + if isnothing(out) + return copy(p.soil.κ) + else + p.soil.κ + end +end + +function compute_solar_zenith_angle(out, Y, p, t, land_model::SoilCanopyModel) + if isnothing(out) + return copy(p.drivers.θs) + else + p.drivers.θs + end +end + +function compute_moisture_stress_factor( + out, + Y, + p, + t, + land_model::SoilCanopyModel, +) + if isnothing(out) + return copy(p.canopy.hydraulics.β) + else + p.canopy.hydraulics.β + end +end + +function compute_canopy_water_potential( + out, + Y, + p, + t, + land_model::SoilCanopyModel, +) + if isnothing(out) + return copy(p.canopy.hydraulics.ψ) + else + p.canopy.hydraulics.ψ + end +end + +function compute_cross_section(out, Y, p, t, land_model::SoilCanopyModel) + if isnothing(out) + return copy(p.canopy.hydraulics.fa) + else + p.canopy.hydraulics.fa + end +end + +function compute_cross_section_roots(out, Y, p, t, land_model::SoilCanopyModel) + if isnothing(out) + return copy(p.canopy.hydraulics.fa_roots) + else + p.canopy.hydraulics.fa_roots + end +end + +function compute_area_index(out, Y, p, t, land_model::SoilCanopyModel) + if isnothing(out) + return copy(p.canopy.hydraulics.area_index) + else + p.canopy.hydraulics.area_index + end +end + +function compute_canopy_latent_heat_flux( + out, + Y, + p, + t, + land_model::SoilCanopyModel, +) + if isnothing(out) + return copy(p.canopy.energy.lhf) + else + p.canopy.canopy.lhf + end +end + +function compute_canopy_sensible_heat_flux( + out, + Y, + p, + t, + land_model::SoilCanopyModel, +) + if isnothing(out) + return copy(p.canopy.energy.shf) + else + p.canopy.canopy.shf + end +end + +function compute_canopy_aerodynamic_resistance( + out, + Y, + p, + t, + land_model::SoilCanopyModel, +) + if isnothing(out) + return copy(p.canopy.energy.r_ae) + else + p.canopy.canopy.r_ae + end +end + +function compute_canopy_temperature(out, Y, p, t, land_model::SoilCanopyModel) + if isnothing(out) + return copy(Y.canopy.energy.T) + else + Y.canopy.energy.T + end +end + +function compute_soil_ice(out, Y, p, t, land_model::SoilCanopyModel) + if isnothing(out) + return copy(Y.soil.θ_i) + else + Y.soil.θ_i + end +end diff --git a/src/Diagnostics/standard_diagnostic_frequencies.jl b/src/Diagnostics/standard_diagnostic_frequencies.jl new file mode 100644 index 0000000000..abf80f4d47 --- /dev/null +++ b/src/Diagnostics/standard_diagnostic_frequencies.jl @@ -0,0 +1,262 @@ +""" + monthly_maxs(short_names...; output_writer, t_start) + +Return a list of `ScheduledDiagnostics` that compute the monthly max for the given variables. + +A month is defined as 30 days. +""" +monthly_maxs(short_names...; output_writer, t_start) = common_diagnostics( + 30 * 24 * 60 * 60 * one(t_start), + max, + output_writer, + t_start, + short_names..., +) +""" + monthly_max(short_names; output_writer, t_start) + +Return a `ScheduledDiagnostics` that computes the monthly max for the given variable. + +A month is defined as 30 days. +""" +monthly_max(short_names; output_writer, t_start) = + monthly_maxs(short_names; output_writer, t_start)[1] + +""" + monthly_mins(short_names...; output_writer, t_start) + +Return a list of `ScheduledDiagnostics` that compute the monthly min for the given variables. +""" +monthly_mins(short_names...; output_writer, t_start) = common_diagnostics( + 30 * 24 * 60 * 60 * one(t_start), + min, + output_writer, + t_start, + short_names..., +) +""" + monthly_min(short_names; output_writer, t_start) + +Return a `ScheduledDiagnostics` that computes the monthly min for the given variable. + +A month is defined as 30 days. +""" +monthly_min(short_names; output_writer, t_start) = + monthly_mins(short_names; output_writer, t_start)[1] + +""" + monthly_averages(short_names...; output_writer, t_start) + +Return a list of `ScheduledDiagnostics` that compute the monthly average for the given variables. + +A month is defined as 30 days. +""" +# An average is just a sum with a normalization before output +monthly_averages(short_names...; output_writer, t_start) = common_diagnostics( + 30 * 24 * 60 * 60 * one(t_start), + (+), + output_writer, + t_start, + short_names...; + pre_output_hook! = average_pre_output_hook!, +) +""" + monthly_average(short_names; output_writer, t_start) + +Return a `ScheduledDiagnostics` that compute the monthly average for the given variable. + +A month is defined as 30 days. +""" +# An average is just a sum with a normalization before output +monthly_average(short_names; output_writer, t_start) = + monthly_averages(short_names; output_writer, t_start)[1] + +""" + tendaily_maxs(short_names...; output_writer, t_start) + +Return a list of `ScheduledDiagnostics` that compute the max over ten days for the given variables. +""" +tendaily_maxs(short_names...; output_writer, t_start) = common_diagnostics( + 10 * 24 * 60 * 60 * one(t_start), + max, + output_writer, + t_start, + short_names..., +) +""" + tendaily_max(short_names; output_writer, t_start) + +Return a `ScheduledDiagnostics` that computes the max over ten days for the given variable. +""" +tendaily_max(short_names; output_writer, t_start) = + tendaily_maxs(short_names; output_writer, t_start)[1] + +""" + tendaily_mins(short_names...; output_writer, t_start) + +Return a list of `ScheduledDiagnostics` that compute the min over ten days for the given variables. +""" +tendaily_mins(short_names...; output_writer, t_start) = common_diagnostics( + 10 * 24 * 60 * 60 * one(t_start), + min, + output_writer, + t_start, + short_names..., +) +""" + tendaily_min(short_names; output_writer, t_start) + +Return a `ScheduledDiagnostics` that computes the min over ten days for the given variable. +""" +tendaily_min(short_names; output_writer, t_start) = + tendaily_mins(short_names; output_writer, t_start)[1] + +""" + tendaily_averages(short_names...; output_writer, t_start) + +Return a list of `ScheduledDiagnostics` that compute the average over ten days for the given variables. +""" +# An average is just a sum with a normalization before output +tendaily_averages(short_names...; output_writer, t_start) = common_diagnostics( + 10 * 24 * 60 * 60 * one(t_start), + (+), + output_writer, + t_start, + short_names...; + pre_output_hook! = average_pre_output_hook!, +) +""" + tendaily_average(short_names; output_writer, t_start) + +Return a `ScheduledDiagnostics` that compute the average over ten days for the given variable. +""" +# An average is just a sum with a normalization before output +tendaily_average(short_names; output_writer, t_start) = + tendaily_averages(short_names; output_writer, t_start)[1] + +""" + daily_maxs(short_names...; output_writer, t_start) + +Return a list of `ScheduledDiagnostics` that compute the daily max for the given variables. +""" +daily_maxs(short_names...; output_writer, t_start) = common_diagnostics( + 24 * 60 * 60 * one(t_start), + max, + output_writer, + t_start, + short_names..., +) +""" + daily_max(short_names; output_writer, t_start) + +Return a `ScheduledDiagnostics` that computes the daily max for the given variable. +""" +daily_max(short_names; output_writer, t_start) = + daily_maxs(short_names; output_writer, t_start)[1] + +""" + daily_mins(short_names...; output_writer, t_start) + +Return a list of `ScheduledDiagnostics` that compute the daily min for the given variables. +""" +daily_mins(short_names...; output_writer, t_start) = common_diagnostics( + 24 * 60 * 60 * one(t_start), + min, + output_writer, + t_start, + short_names..., +) +""" + daily_min(short_names; output_writer, t_start) + +Return a `ScheduledDiagnostics` that computes the daily min for the given variable. +""" +daily_min(short_names; output_writer, t_start) = + daily_mins(short_names; output_writer, t_start)[1] + +""" + daily_averages(short_names...; output_writer, t_start) + +Return a list of `ScheduledDiagnostics` that compute the daily average for the given variables. +""" +# An average is just a sum with a normalization before output +daily_averages(short_names...; output_writer, t_start) = common_diagnostics( + 24 * 60 * 60 * one(t_start), + (+), + output_writer, + t_start, + short_names...; + pre_output_hook! = average_pre_output_hook!, +) +""" + daily_average(short_names; output_writer, t_start) + +Return a `ScheduledDiagnostics` that compute the daily average for the given variable. +""" +# An average is just a sum with a normalization before output +daily_average(short_names; output_writer, t_start) = + daily_averages(short_names; output_writer, t_start)[1] + +""" + hourly_maxs(short_names...; output_writer, t_start) + +Return a list of `ScheduledDiagnostics` that compute the hourly max for the given variables. +""" +hourly_maxs(short_names...; output_writer, t_start) = common_diagnostics( + 60 * 60 * one(t_start), + max, + output_writer, + t_start, + short_names..., +) + +""" + hourly_max(short_names; output_writer, t_start) + +Return a `ScheduledDiagnostics` that computes the hourly max for the given variable. +""" +hourly_max(short_names; output_writer, t_start) = + hourly_maxs(short_names; output_writer, t_start)[1] + +""" + hourly_mins(short_names...; output_writer, t_start) + +Return a list of `ScheduledDiagnostics` that compute the hourly min for the given variables. +""" +hourly_mins(short_names...; output_writer, t_start) = common_diagnostics( + 60 * 60 * one(t_start), + min, + output_writer, + t_start, + short_names..., +) +""" + hourly_mins(short_names...; output_writer, t_start) + +Return a `ScheduledDiagnostics` that computes the hourly min for the given variable. +""" +hourly_min(short_names; output_writer, t_start) = + hourly_mins(short_names; output_writer, t_start)[1] + +# An average is just a sum with a normalization before output +""" + hourly_averages(short_names...; output_writer, t_start) + +Return a list of `ScheduledDiagnostics` that compute the hourly average for the given variables. +""" +hourly_averages(short_names...; output_writer, t_start) = common_diagnostics( + 60 * 60 * one(t_start), + (+), + output_writer, + t_start, + short_names...; + pre_output_hook! = average_pre_output_hook!, +) + +""" + hourly_average(short_names...; output_writer, t_start) + +Return a `ScheduledDiagnostics` that computes the hourly average for the given variable. +""" +hourly_average(short_names; output_writer, t_start) = + hourly_averages(short_names; output_writer, t_start)[1] diff --git a/test/Project.toml b/test/Project.toml index 9d8e99120a..8575f9fd88 100644 --- a/test/Project.toml +++ b/test/Project.toml @@ -3,10 +3,13 @@ Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595" ArtifactWrappers = "a14bc488-3040-4b00-9dc1-f6467924858a" BSON = "fbb218c0-5317-5bc6-957e-2ee96dd4b1f0" CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b" +ClimaAnalysis = "29b5916a-a76c-4e73-9657-3c8fd22e65e6" ClimaComms = "3a4d1b5c-c61d-41fd-a00a-5873ba7a1b0d" ClimaCore = "d414da3d-4745-48bb-8d80-42e94e092884" +ClimaDiagnostics = "1ecacbb8-0713-4841-9a07-eb5aa8a2d53f" ClimaLand = "08f4d4ce-cf43-44bb-ad95-9d2d5f413532" ClimaParams = "5c42b081-d73a-476f-9059-fd94b934656c" +ClimaTimeSteppers = "595c0a79-7f3d-439a-bc5a-b232dc3bde79" ClimaUtilities = "b3f4f4ca-9299-4f7f-bd9b-81e1242a7513" DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" Dates = "ade2ca70-3891-5945-98fb-dc099432e06a" @@ -20,6 +23,7 @@ LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" NCDatasets = "85f8d34a-cbdd-5861-8df4-14fed0d494ab" NLsolve = "2774e3e8-f4cf-5e23-947b-6d7e65073b56" SafeTestsets = "1bc83da4-3b8d-516f-aca4-4fe02f6d838f" +SciMLBase = "0bca4576-84f4-4d90-8ffe-ffa030f20462" StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91" diff --git a/test/diagnostics/diagnostics_tests.jl b/test/diagnostics/diagnostics_tests.jl new file mode 100644 index 0000000000..385202a474 --- /dev/null +++ b/test/diagnostics/diagnostics_tests.jl @@ -0,0 +1,9 @@ +using Test +using ClimaLand + +@test isdefined(ClimaLand.Diagnostics, :compute_albedo!) + +@test_throws ErrorException("cannot albedo with nothing") ClimaLand.Diagnostics.compute_albedo!(_, _, _, _, nothing) + +@test_throws ErrorException ClimaLand.Diagnostics.get_diagnostic_variable("Foo") +