From 11f0ee124a894016520493025735980d9bea4856 Mon Sep 17 00:00:00 2001 From: gaelforget Date: Mon, 27 Jan 2025 17:59:46 -0500 Subject: [PATCH 1/6] update back to Oceananigans v0.95.8 --- examples/Oceananigans.jl | 191 +++++---------------------------------- src/Oceananigans.jl | 11 ++- 2 files changed, 32 insertions(+), 170 deletions(-) diff --git a/examples/Oceananigans.jl b/examples/Oceananigans.jl index e2a0acee..58b875e2 100644 --- a/examples/Oceananigans.jl +++ b/examples/Oceananigans.jl @@ -125,7 +125,7 @@ end # ╔═╡ 1b932395-501f-42ba-940c-9512bdace2b8 begin - T,S,w,νₑ=ClimateModels.Oceananigans.tz_slice(MC,nt=nt) + T,S,w,νₑ=ClimateModels.Oceananigans.tz_slice(MC,nt=nt,version=thisversion) xw, yw, zw, xT, yT, zT=ClimateModels.Oceananigans.read_grid(MC) md"""## Plot Time vs Depth @@ -151,9 +151,8 @@ PlutoUI = "7f904dfe-b85e-4ff6-b463-dae2292396a8" [compat] CairoMakie = "~0.13.1" -ClimateModels = "~0.3.7" JLD2 = "~0.4.46" -Oceananigans = "~0.90.14" +Oceananigans = "~0.95.8" PlutoUI = "~0.7.58" """ @@ -163,7 +162,7 @@ PLUTO_MANIFEST_TOML_CONTENTS = """ julia_version = "1.11.1" manifest_format = "2.0" -project_hash = "c5d52e0cba1e5c61dc2a01834177f8a2920d9a1f" +project_hash = "cdea4f24ce8c8f6e2e2867c67bffb0dd1bb4e67d" [[deps.AbstractFFTs]] deps = ["LinearAlgebra"] @@ -218,38 +217,6 @@ version = "0.4.2" uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f" version = "1.1.2" -[[deps.ArrayInterface]] -deps = ["Adapt", "LinearAlgebra"] -git-tree-sha1 = "017fcb757f8e921fb44ee063a7aafe5f89b86dd1" -uuid = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9" -version = "7.18.0" - - [deps.ArrayInterface.extensions] - ArrayInterfaceBandedMatricesExt = "BandedMatrices" - ArrayInterfaceBlockBandedMatricesExt = "BlockBandedMatrices" - ArrayInterfaceCUDAExt = "CUDA" - ArrayInterfaceCUDSSExt = "CUDSS" - ArrayInterfaceChainRulesCoreExt = "ChainRulesCore" - ArrayInterfaceChainRulesExt = "ChainRules" - ArrayInterfaceGPUArraysCoreExt = "GPUArraysCore" - ArrayInterfaceReverseDiffExt = "ReverseDiff" - ArrayInterfaceSparseArraysExt = "SparseArrays" - ArrayInterfaceStaticArraysCoreExt = "StaticArraysCore" - ArrayInterfaceTrackerExt = "Tracker" - - [deps.ArrayInterface.weakdeps] - BandedMatrices = "aae01518-5342-5314-be14-df237901396f" - BlockBandedMatrices = "ffab5731-97b5-5995-9138-79e8c1846df0" - CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" - CUDSS = "45b445bb-4962-46a0-9369-b4df9d0f772e" - ChainRules = "082447d4-558c-5d27-93f4-14fc19e9eca2" - ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" - GPUArraysCore = "46192b85-c4d5-4398-a991-12ede77f4527" - ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" - SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" - StaticArraysCore = "1e83bf80-4336-4d27-bf5d-d5a4f845583c" - Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" - [[deps.Artifacts]] uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" version = "1.11.0" @@ -413,10 +380,10 @@ weakdeps = ["SparseArrays"] ChainRulesCoreSparseArraysExt = "SparseArrays" [[deps.ClimateModels]] -deps = ["CFTime", "CSV", "DataDeps", "DataFrames", "Dataverse", "Dates", "Downloads", "Git", "Glob", "JLD2", "OrderedCollections", "Pkg", "Printf", "Random", "Statistics", "Suppressor", "TOML", "Test", "UUIDs"] -git-tree-sha1 = "57a75abae974e07d74467a990855995f4128e6f2" +deps = ["CFTime", "CSV", "DataDeps", "DataFrames", "Dataverse", "Dates", "Downloads", "Git", "Glob", "JLD2", "OffsetArrays", "OrderedCollections", "Pkg", "Printf", "Random", "Statistics", "Suppressor", "TOML", "Test", "UUIDs"] +git-tree-sha1 = "21a16d3f599e0e08298808dd7704027c73e16fb2" uuid = "f6adb021-9183-4f40-84dc-8cea6f651bb0" -version = "0.3.7" +version = "0.3.8" [deps.ClimateModels.extensions] ClimateModelsCondaExt = ["Conda"] @@ -482,11 +449,6 @@ git-tree-sha1 = "98d64d5b9e5263884276656a43c45424b3a645c2" uuid = "1fbeeb36-5f17-413c-809b-666fb144f157" version = "0.3.7" -[[deps.CommonWorldInvalidations]] -git-tree-sha1 = "ae52d1c52048455e85a387fbee9be553ec2b68d0" -uuid = "f70d9fcc-98c5-4d4a-abd7-e4cdeebd8ca8" -version = "1.0.0" - [[deps.Compat]] deps = ["TOML", "UUIDs"] git-tree-sha1 = "8ae8d32e09f0dcf42a36b90d4e17f5dd2e4c4215" @@ -530,10 +492,10 @@ uuid = "a8cc5b0e-0ffa-5ad4-8c14-923d3ee1735f" version = "4.1.1" [[deps.CubedSphere]] -deps = ["Elliptic", "FFTW", "Printf", "ProgressBars", "SpecialFunctions", "TaylorSeries"] -git-tree-sha1 = "049f692019f52ad3b043edf20ef25ebd7b38eb94" +deps = ["TaylorSeries"] +git-tree-sha1 = "10874d1500159336863decaef665ab54805be29c" uuid = "7445602f-e544-4518-8976-18f8e8ae6cdb" -version = "0.2.6" +version = "0.3.1" [[deps.DataAPI]] git-tree-sha1 = "abe83f3a2f1b857aac70ef8b269080af17764bbe" @@ -643,11 +605,6 @@ git-tree-sha1 = "e3290f2d49e661fbd94046d7e3726ffcb2d41053" uuid = "5ae413db-bbd1-5e63-b57d-d24a61df00f5" version = "2.2.4+0" -[[deps.Elliptic]] -git-tree-sha1 = "71c79e77221ab3a29918aaf6db4f217b89138608" -uuid = "b305315f-e792-5b7a-8f41-49f472929428" -version = "1.0.1" - [[deps.EnumX]] git-tree-sha1 = "bdb1942cd4c45e3c678fd11569d5cccd80976237" uuid = "4e289a0a-7415-4d19-859d-a7e5c4648b56" @@ -940,11 +897,6 @@ git-tree-sha1 = "b6d6bfdd7ce25b0f9b2f6b3dd56b2673a66c8770" uuid = "b5f81e59-6552-4d32-b1f0-c071b021bf89" version = "0.2.5" -[[deps.IfElse]] -git-tree-sha1 = "debdd00ffef04665ccbb3e150747a77560e8fad1" -uuid = "615f187c-cbe4-4ef1-ba3b-2fcf58d6d173" -version = "0.1.1" - [[deps.ImageAxes]] deps = ["AxisArrays", "ImageBase", "ImageCore", "Reexport", "SimpleTraits"] git-tree-sha1 = "e12629406c6c4442539436581041d372d69c55ba" @@ -1108,18 +1060,6 @@ git-tree-sha1 = "31e996f0a15c7b280ba9f76636b3ff9e2ae58c9a" uuid = "682c06a0-de6a-54ab-a142-c8b1cf79cde6" version = "0.21.4" -[[deps.JSON3]] -deps = ["Dates", "Mmap", "Parsers", "PrecompileTools", "StructTypes", "UUIDs"] -git-tree-sha1 = "1d322381ef7b087548321d3f878cb4c9bd8f8f9b" -uuid = "0f8b85d8-7281-11e9-16c2-39a750bddbf1" -version = "1.14.1" - - [deps.JSON3.extensions] - JSON3ArrowExt = ["ArrowTypes"] - - [deps.JSON3.weakdeps] - ArrowTypes = "31f734f8-188a-4ce0-8406-c8a06bd891cd" - [[deps.JpegTurbo]] deps = ["CEnum", "FileIO", "ImageCore", "JpegTurbo_jll", "TOML"] git-tree-sha1 = "fa6d0bcff8583bac20f1ffa708c3913ca605c611" @@ -1344,9 +1284,9 @@ uuid = "5ced341a-0733-55b8-9ab6-a4889d929147" version = "1.10.1+0" [[deps.MIMEs]] -git-tree-sha1 = "65f28ad4b594aebe22157d6fac869786a255b7eb" +git-tree-sha1 = "1833212fd6f580c20d4291da9c1b4e8a655b128e" uuid = "6c6e2e6c-3030-632d-7369-2d6c69616d65" -version = "0.1.4" +version = "1.0.0" [[deps.MKL_jll]] deps = ["Artifacts", "IntelOpenMP_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "oneTBB_jll"] @@ -1502,18 +1442,19 @@ uuid = "510215fc-4207-5dde-b226-833fc4488ee2" version = "0.5.5" [[deps.Oceananigans]] -deps = ["Adapt", "CUDA", "Crayons", "CubedSphere", "Dates", "Distances", "DocStringExtensions", "FFTW", "Glob", "IncompleteLU", "InteractiveUtils", "IterativeSolvers", "JLD2", "KernelAbstractions", "LinearAlgebra", "Logging", "MPI", "NCDatasets", "OffsetArrays", "OrderedCollections", "PencilArrays", "PencilFFTs", "Pkg", "Printf", "Random", "Rotations", "SeawaterPolynomials", "SparseArrays", "Statistics", "StructArrays"] -git-tree-sha1 = "3a5d2b1d9a237731f886a657e72e4a52a7f6fb2b" -repo-rev = "v0.90.14" -repo-url = "https://github.com/CliMA/Oceananigans.jl.git" +deps = ["Adapt", "CUDA", "Crayons", "CubedSphere", "Dates", "Distances", "DocStringExtensions", "FFTW", "GPUArrays", "Glob", "IncompleteLU", "InteractiveUtils", "IterativeSolvers", "JLD2", "KernelAbstractions", "LinearAlgebra", "Logging", "MPI", "NCDatasets", "OffsetArrays", "OrderedCollections", "Pkg", "Printf", "Random", "Rotations", "SeawaterPolynomials", "SparseArrays", "Statistics", "StructArrays"] +git-tree-sha1 = "863beb6566b19698cd473f9637b7721068542ac2" uuid = "9e8cae18-63c1-5223-a75c-80ca9d6e9a09" -version = "0.90.14" +version = "0.95.8" [deps.Oceananigans.extensions] OceananigansEnzymeExt = "Enzyme" + OceananigansMakieExt = ["MakieCore", "Makie"] [deps.Oceananigans.weakdeps] Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" + Makie = "ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a" + MakieCore = "20f20a25-4f0e-4fdf-b5d1-57303727442b" [[deps.OffsetArrays]] git-tree-sha1 = "5e1897147d1ff8d98883cda2be2187dcf57d8f0c" @@ -1604,12 +1545,6 @@ git-tree-sha1 = "67186a2bc9a90f9f85ff3cc8277868961fb57cbd" uuid = "f57f5aa1-a3ce-4bc8-8ab9-96f992907883" version = "0.4.3" -[[deps.PackageExtensionCompat]] -git-tree-sha1 = "fb28e33b8a95c4cee25ce296c817d89cc2e53518" -uuid = "65ce6f38-6b18-4e1d-a461-8949797d7930" -version = "1.0.2" -weakdeps = ["Requires", "TOML"] - [[deps.Packing]] deps = ["GeometryBasics"] git-tree-sha1 = "bc5bf2ea3d5351edf285a06b0016788a121ce92c" @@ -1634,28 +1569,6 @@ git-tree-sha1 = "8489905bcdbcfac64d1daa51ca07c0d8f0283821" uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0" version = "2.8.1" -[[deps.PencilArrays]] -deps = ["Adapt", "JSON3", "LinearAlgebra", "MPI", "OffsetArrays", "Random", "Reexport", "StaticArrayInterface", "StaticArrays", "StaticPermutations", "Strided", "TimerOutputs", "VersionParsing"] -git-tree-sha1 = "3d8a67ac2ea254cabea5d7b5118e78e6564dd75f" -uuid = "0e08944d-e94e-41b1-9406-dcf66b6a9d2e" -version = "0.19.6" - - [deps.PencilArrays.extensions] - PencilArraysAMDGPUExt = ["AMDGPU"] - PencilArraysDiffEqExt = ["DiffEqBase"] - PencilArraysHDF5Ext = ["HDF5"] - - [deps.PencilArrays.weakdeps] - AMDGPU = "21141c5a-9bdb-4563-92ae-f87d6854732e" - DiffEqBase = "2b5f629d-d688-5b77-993f-72d75c75574e" - HDF5 = "f67ccb44-e63f-5c2f-98bd-6dc0ccc4ba2f" - -[[deps.PencilFFTs]] -deps = ["AbstractFFTs", "FFTW", "LinearAlgebra", "MPI", "PencilArrays", "Reexport", "TimerOutputs"] -git-tree-sha1 = "b4ea498ce6d75e63f30c2181e7d9b90fb13b387b" -uuid = "4a48f351-57a6-4416-9ec4-c37015456aae" -version = "0.15.2" - [[deps.Pixman_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LLVMOpenMP_jll", "Libdl"] git-tree-sha1 = "35621f10a7531bc8fa58f74610b1bfb70a3cfc6b" @@ -1685,9 +1598,9 @@ version = "1.4.3" [[deps.PlutoUI]] deps = ["AbstractPlutoDingetjes", "Base64", "ColorTypes", "Dates", "FixedPointNumbers", "Hyperscript", "HypertextLiteral", "IOCapture", "InteractiveUtils", "JSON", "Logging", "MIMEs", "Markdown", "Random", "Reexport", "URIs", "UUIDs"] -git-tree-sha1 = "eba4810d5e6a01f612b948c9fa94f905b49087b0" +git-tree-sha1 = "7e71a55b87222942f0f9337be62e26b1f103d3e4" uuid = "7f904dfe-b85e-4ff6-b463-dae2292396a8" -version = "0.7.60" +version = "0.7.61" [[deps.PolygonOps]] git-tree-sha1 = "77b3d3605fc1cd0b42d95eba87dfcd2bf67d5ff6" @@ -1723,12 +1636,6 @@ deps = ["Unicode"] uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7" version = "1.11.0" -[[deps.ProgressBars]] -deps = ["Printf"] -git-tree-sha1 = "b437cdb0385ed38312d91d9c00c20f3798b30256" -uuid = "49802e3a-d2f1-5c88-81d8-b72133a6f568" -version = "1.5.1" - [[deps.ProgressMeter]] deps = ["Distributed", "Printf"] git-tree-sha1 = "8f6bc219586aef8baf0ff9a5fe16ee9c70cb65e4" @@ -1970,23 +1877,6 @@ git-tree-sha1 = "46e589465204cd0c08b4bd97385e4fa79a0c770c" uuid = "cae243ae-269e-4f55-b966-ac2d0dc13c15" version = "0.1.1" -[[deps.Static]] -deps = ["CommonWorldInvalidations", "IfElse", "PrecompileTools"] -git-tree-sha1 = "87d51a3ee9a4b0d2fe054bdd3fc2436258db2603" -uuid = "aedffcd0-7271-4cad-89d0-dc628f76c6d3" -version = "1.1.1" - -[[deps.StaticArrayInterface]] -deps = ["ArrayInterface", "Compat", "IfElse", "LinearAlgebra", "PrecompileTools", "Static"] -git-tree-sha1 = "96381d50f1ce85f2663584c8e886a6ca97e60554" -uuid = "0d7ed370-da01-4f52-bd93-41d350b8b718" -version = "1.8.0" -weakdeps = ["OffsetArrays", "StaticArrays"] - - [deps.StaticArrayInterface.extensions] - StaticArrayInterfaceOffsetArraysExt = "OffsetArrays" - StaticArrayInterfaceStaticArraysExt = "StaticArrays" - [[deps.StaticArrays]] deps = ["LinearAlgebra", "PrecompileTools", "Random", "StaticArraysCore"] git-tree-sha1 = "47091a0340a675c738b1304b58161f3b0839d454" @@ -2003,11 +1893,6 @@ git-tree-sha1 = "192954ef1208c7019899fbf8049e717f92959682" uuid = "1e83bf80-4336-4d27-bf5d-d5a4f845583c" version = "1.4.3" -[[deps.StaticPermutations]] -git-tree-sha1 = "193c3daa18ff3e55c1dae66acb6a762c4a3bdb0b" -uuid = "15972242-4b8f-49a0-b8a1-9ac0e7a1a45d" -version = "0.3.0" - [[deps.Statistics]] deps = ["LinearAlgebra"] git-tree-sha1 = "ae3bb1eb3bba077cd276bc5cfc337cc65c3075c0" @@ -2041,22 +1926,6 @@ weakdeps = ["ChainRulesCore", "InverseFunctions"] StatsFunsChainRulesCoreExt = "ChainRulesCore" StatsFunsInverseFunctionsExt = "InverseFunctions" -[[deps.Strided]] -deps = ["LinearAlgebra", "StridedViews", "TupleTools"] -git-tree-sha1 = "f9ce8284e6eec72a21de3603493eb5355fcf7f39" -uuid = "5e0ebb24-38b0-5f93-81fe-25c709ecae67" -version = "2.2.0" - -[[deps.StridedViews]] -deps = ["LinearAlgebra", "PackageExtensionCompat"] -git-tree-sha1 = "b60baf1998bcdccc57e1cc2c6703df1f619a3754" -uuid = "4db3bf67-4bd7-4b4e-b153-31dc3fb37143" -version = "0.3.2" -weakdeps = ["CUDA"] - - [deps.StridedViews.extensions] - StridedViewsCUDAExt = "CUDA" - [[deps.StringManipulation]] deps = ["PrecompileTools"] git-tree-sha1 = "a6b1675a536c5ad1a60e5a5153e1fee12eb146e3" @@ -2076,12 +1945,6 @@ weakdeps = ["Adapt", "GPUArraysCore", "SparseArrays", "StaticArrays"] StructArraysSparseArraysExt = "SparseArrays" StructArraysStaticArraysExt = "StaticArrays" -[[deps.StructTypes]] -deps = ["Dates", "UUIDs"] -git-tree-sha1 = "159331b30e94d7b11379037feeb9b690950cace8" -uuid = "856f2bd8-1eba-4b0a-8007-ebc267875bd4" -version = "1.11.0" - [[deps.StyledStrings]] uuid = "f489334b-da3d-4c2e-b8f0-e476e12c162b" version = "1.11.0" @@ -2125,9 +1988,9 @@ version = "1.10.0" [[deps.TaylorSeries]] deps = ["LinearAlgebra", "Markdown", "Requires", "SparseArrays"] -git-tree-sha1 = "90c9bc500f4c5cdd235c81503ec91b2048f06423" +git-tree-sha1 = "bb212ead98022455eed514cff0adfa5de8645258" uuid = "6aa5eb33-94cf-58f4-a9d0-e4b2c4fc25ea" -version = "0.17.8" +version = "0.18.1" [deps.TaylorSeries.extensions] TaylorSeriesIAExt = "IntervalArithmetic" @@ -2179,11 +2042,6 @@ git-tree-sha1 = "4d4ed7f294cda19382ff7de4c137d24d16adc89b" uuid = "981d1d27-644d-49a2-9326-4793e63143c3" version = "0.1.0" -[[deps.TupleTools]] -git-tree-sha1 = "41e43b9dc950775eac654b9f845c839cd2f1821e" -uuid = "9d95972d-f1c8-5527-a6e0-b4b365fa01f6" -version = "1.6.0" - [[deps.URIs]] git-tree-sha1 = "67db6cc7b3821e19ebe75791a9dd19c9b1188f2b" uuid = "5c2747f8-b7ea-4ff2-ba2e-563bfd36b1d4" @@ -2224,11 +2082,6 @@ weakdeps = ["LLVM"] [deps.UnsafeAtomics.extensions] UnsafeAtomicsLLVM = ["LLVM"] -[[deps.VersionParsing]] -git-tree-sha1 = "58d6e80b4ee071f5efd07fda82cb9fbe17200868" -uuid = "81def892-9a0e-5fdd-b105-ffc91e053289" -version = "1.3.0" - [[deps.WeakRefStrings]] deps = ["DataAPI", "InlineStrings", "Parsers"] git-tree-sha1 = "b1be2855ed9ed8eac54e5caff2afcdb442d52c23" @@ -2438,7 +2291,7 @@ version = "3.6.0+0" # ╔═╡ Cell order: # ╟─a5f3898b-5abe-4230-88a9-36c5c823b951 # ╟─bf064e23-c33f-4339-b2f1-290d8d0f1d87 -# ╟─87a6ef53-5c0c-46d4-b4ca-9ab2b76cba74 +# ╠═87a6ef53-5c0c-46d4-b4ca-9ab2b76cba74 # ╟─1b932395-501f-42ba-940c-9512bdace2b8 # ╟─09495b06-7850-48f6-8c1c-f64de540f4a2 # ╟─42495d5e-2c2b-4260-85d5-2d7c5f53e70d diff --git a/src/Oceananigans.jl b/src/Oceananigans.jl index c3f7629b..9d1aa13c 100644 --- a/src/Oceananigans.jl +++ b/src/Oceananigans.jl @@ -84,12 +84,21 @@ function zt_read(fil,t) return t,w,T,S,νₑ end -function xz_plot_prep(MC,i) +function xz_plot_prep(MC,i;version=0.9) fil=joinpath(pathof(MC),"daily_cycle.jld2") t,w,T,S,νₑ=xz_read(fil,i) xw, yw, zw, xT, yT, zT=read_grid(MC) tt="$(round(t/86400)) days" #tt=prettytime(t) + + if version>0.90 + nt=size(T,1) + T=view(OffsetArray(T, 1:nt, -2:53), 1:nt, 1:50) + S=view(OffsetArray(S, 1:nt, -2:53), 1:nt, 1:50) + W=view(OffsetArray(w, 1:nt, -2:54), 1:nt, 1:51) + νₑ=view(OffsetArray(νₑ, 1:nt, -2:53), 1:nt, 1:50) + end + (tt,w,T,S,νₑ,xw, yw, zw, xT, yT, zT) end From 95127924ee7c2696e8d175d4fb2339ff0a79b993 Mon Sep 17 00:00:00 2001 From: gaelforget Date: Mon, 27 Jan 2025 21:05:23 -0500 Subject: [PATCH 2/6] update NonhydrostaticModel call --- examples/Oceananigans.jl | 8 ++++++-- ext/ClimateModelsOceananigansExt.jl | 21 ++++++++++----------- 2 files changed, 16 insertions(+), 13 deletions(-) diff --git a/examples/Oceananigans.jl b/examples/Oceananigans.jl index 58b875e2..809c11e8 100644 --- a/examples/Oceananigans.jl +++ b/examples/Oceananigans.jl @@ -138,6 +138,9 @@ tz_fig=ClimateModels.plot_examples(:Oceananigans_tz,xw, yw, zw, xT, yT, zT,T,S,w #save(joinpath(pathof(MC),"tz_4days.png"), tz_fig) +# ╔═╡ ddc2651a-caa4-4eb4-b5f7-7123eb33674c +Pkg.status() + # ╔═╡ 00000000-0000-0000-0000-000000000001 PLUTO_PROJECT_TOML_CONTENTS = """ [deps] @@ -2291,12 +2294,12 @@ version = "3.6.0+0" # ╔═╡ Cell order: # ╟─a5f3898b-5abe-4230-88a9-36c5c823b951 # ╟─bf064e23-c33f-4339-b2f1-290d8d0f1d87 -# ╠═87a6ef53-5c0c-46d4-b4ca-9ab2b76cba74 +# ╟─87a6ef53-5c0c-46d4-b4ca-9ab2b76cba74 # ╟─1b932395-501f-42ba-940c-9512bdace2b8 # ╟─09495b06-7850-48f6-8c1c-f64de540f4a2 # ╟─42495d5e-2c2b-4260-85d5-2d7c5f53e70d # ╟─5ae22c8a-17d9-446e-b0cd-d4af7c9834c8 -# ╟─193a8750-39bd-451f-8e22-4af1b25be22b +# ╠═193a8750-39bd-451f-8e22-4af1b25be22b # ╟─2fd54b18-27e2-4e90-9d7d-a1057d393a78 # ╟─da276d16-9078-4433-85ed-80d502e78a86 # ╟─be6b4de1-1e6d-42b0-ba3e-12a9fa2c140d @@ -2304,5 +2307,6 @@ version = "3.6.0+0" # ╟─851a7116-a781-4f86-887f-99dcf0a21ea2 # ╟─cd09078c-61e1-11ec-1253-536acf09f901 # ╟─ab07d8e3-897f-4290-88f9-f1314dbeaa26 +# ╠═ddc2651a-caa4-4eb4-b5f7-7123eb33674c # ╟─00000000-0000-0000-0000-000000000001 # ╟─00000000-0000-0000-0000-000000000002 diff --git a/ext/ClimateModelsOceananigansExt.jl b/ext/ClimateModelsOceananigansExt.jl index 360eeca5..8760fd90 100644 --- a/ext/ClimateModelsOceananigansExt.jl +++ b/ext/ClimateModelsOceananigansExt.jl @@ -41,15 +41,14 @@ function Oceananigans_build_model(grid,BC,IC) buoyancy = SeawaterBuoyancy(equation_of_state=LinearEquationOfState(thermal_expansion=2e-4, haline_contraction=8e-4)) - model = NonhydrostaticModel( - advection = UpwindBiased(order=5), - timestepper = :RungeKutta3, - grid = grid, - tracers = (:T, :S), - coriolis = FPlane(f=1e-4), - buoyancy = buoyancy, - closure = AnisotropicMinimumDissipation(), - boundary_conditions = (u=BC.u, T=BC.T, S=BC.S)) + model = NonhydrostaticModel(; grid, buoyancy, + advection = UpwindBiased(order=5), + tracers = (:T, :S), + coriolis = FPlane(f=1e-4), + closure = AnisotropicMinimumDissipation(), + boundary_conditions = (u=BC.u, T=BC.T, S=BC.S)) + +# timestepper = :RungeKutta3, # initial conditions (as functions of x,y,z) set!(model, u=IC.u, w=IC.u, T=IC.T, S=IC.S) @@ -67,8 +66,8 @@ function Oceananigans_build_simulation(model,Nh,rundir) @printf("Iteration: %04d, time: %s, Δt: %s, max(|w|) = %.1e ms⁻¹, wall time: %s\n", iteration(sim),prettytime(sim),prettytime(sim.Δt), maximum(abs, sim.model.velocities.w),prettytime(sim.run_wall_time)) - simulation.callbacks[:progress] = Callback(progress_message, IterationInterval(1minute)) - + add_callback!(simulation, progress_message, IterationInterval(20)) + eddy_viscosity = (; νₑ = model.diffusivity_fields.νₑ) simulation.output_writers[:slices] = JLD2OutputWriter(model, merge(model.velocities, model.tracers, eddy_viscosity), From bee18d47dc89bd78e9bb9d6b363f6b553be48009 Mon Sep 17 00:00:00 2001 From: gaelforget Date: Tue, 28 Jan 2025 08:44:34 -0500 Subject: [PATCH 3/6] plot nt in test --- test/runtests.jl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/runtests.jl b/test/runtests.jl index d1849f8a..e26434e3 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -10,7 +10,7 @@ import Zarr, NetCDF, IniFile, Oceananigans run(MC) nt=ClimateModels.Oceananigans.nt_from_jld2(MC) - XZ=ClimateModels.Oceananigans.xz_plot_prep(MC,1) + XZ=ClimateModels.Oceananigans.xz_plot_prep(MC,nt) xz_fig=ClimateModels.plot_examples(:Oceananigans_xz,XZ...) T,S,w,νₑ=ClimateModels.Oceananigans.tz_slice(MC,nt=nt,version=version_Oceananigans) From 1b80f8b0cd03eaacc58aec955c6c297bfe2e2015 Mon Sep 17 00:00:00 2001 From: gaelforget Date: Sun, 31 Aug 2025 11:24:27 -0400 Subject: [PATCH 4/6] update deps --- Project.toml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Project.toml b/Project.toml index 305b59a1..5e3a1e98 100644 --- a/Project.toml +++ b/Project.toml @@ -44,7 +44,7 @@ ClimateModelsPyCallExt = ["PyCall"] ClimateModelsZarrExt = ["Zarr"] [compat] -CFTime = "0.1" +CFTime = "0.1, 0.2" CSV = "0.6, 0.7, 0.8, 0.9, 0.10" Conda = "1" DataDeps = "0.7" @@ -53,8 +53,8 @@ Dataverse = "0.2" Git = "1" Glob = "1" IniFile = "0.5" -JLD2 = "0.4, 0.5" -Makie = "0.21, 0.22" +JLD2 = "0.4, 0.5, 0.6" +Makie = "0.21, 0.22, 0.23, 0.24" NetCDF = "0.11, 0.12" Oceananigans = "0.95" OffsetArrays = "1" From f99d91b133f8f515bcbe3de5d9f840126304e992 Mon Sep 17 00:00:00 2001 From: gaelforget Date: Sun, 31 Aug 2025 11:24:58 -0400 Subject: [PATCH 5/6] update ci --- .github/workflows/ci.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index af87b4fe..1d9102e2 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -23,14 +23,14 @@ jobs: - x64 steps: - uses: actions/checkout@v2 - - uses: julia-actions/setup-julia@v1 + - uses: julia-actions/setup-julia@v2 with: version: ${{ matrix.version }} arch: ${{ matrix.arch }} - run: sudo apt-get update - run: sudo apt-get install libnetcdf-dev - run: sudo apt-get install libnetcdff-dev - - uses: actions/cache@v1 + - uses: actions/cache@v4 env: cache-name: cache-artifacts with: @@ -60,7 +60,7 @@ jobs: runs-on: ubuntu-latest steps: - uses: actions/checkout@v2 - - uses: julia-actions/setup-julia@v1 + - uses: julia-actions/setup-julia@v2 with: version: '1' - run: | From 7ec9da671c0dbae3f1ec58e819e07d8e2e8e4239 Mon Sep 17 00:00:00 2001 From: gaelforget Date: Sun, 31 Aug 2025 11:25:27 -0400 Subject: [PATCH 6/6] bump version --- Project.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Project.toml b/Project.toml index 5e3a1e98..3919baba 100644 --- a/Project.toml +++ b/Project.toml @@ -1,7 +1,7 @@ name = "ClimateModels" uuid = "f6adb021-9183-4f40-84dc-8cea6f651bb0" authors = ["gaelforget "] -version = "0.3.8" +version = "0.3.9" [deps] CFTime = "179af706-886a-5703-950a-314cd64e0468"