From e4a74d814c53e0956732d0902af5ba5a5bf93db6 Mon Sep 17 00:00:00 2001 From: Daniel Karrasch Date: Fri, 17 Mar 2023 10:35:15 +0100 Subject: [PATCH] Internal updates (#99) --- .github/workflows/ci.yml | 2 +- .github/workflows/docs.yml | 2 +- Project.toml | 11 +- docs/Manifest.toml | 757 +++++++++++++++++-------------- docs/Project.toml | 6 +- docs/examples/abc.jl | 3 +- docs/examples/bickley.jl | 3 +- docs/examples/ocean_flow.jl | 6 +- docs/examples/rot_double_gyre.jl | 4 +- docs/examples/standard_map.jl | 4 +- docs/examples/trajectories.jl | 4 +- docs/src/fem.md | 2 +- docs/src/index.md | 4 +- src/CoherentStructures.jl | 3 +- src/advection_diffusion.jl | 16 +- src/ellipticLCS.jl | 12 +- src/gridfunctions.jl | 20 +- src/plotting.jl | 4 +- src/pullbacktensors.jl | 6 +- src/util.jl | 23 + test/test_elliptic.jl | 4 +- test/test_fem.jl | 16 +- 22 files changed, 504 insertions(+), 408 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index aa871b2e..4eed81c0 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -23,7 +23,7 @@ jobs: - ubuntu-latest - macOS-latest steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v3 - uses: julia-actions/setup-julia@v1 with: version: ${{ matrix.version }} diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index f31130dd..09c1d6dc 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -11,7 +11,7 @@ jobs: docs: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v1 + - uses: actions/checkout@v3 - uses: julia-actions/setup-julia@latest - name: Install dependencies run: julia --project=docs -e 'using Pkg; Pkg.instantiate();' diff --git a/Project.toml b/Project.toml index 77a28b88..3960d09d 100644 --- a/Project.toml +++ b/Project.toml @@ -1,6 +1,6 @@ name = "CoherentStructures" uuid = "0c1513b4-3a13-56f1-9cd2-8312eaec88c4" -version = "0.4.11" +version = "0.4.12" [deps] ArnoldiMethod = "ec485272-7323-5ecc-a04f-4719b315124d" @@ -19,6 +19,7 @@ NearestNeighbors = "b8a86587-4115-5ab1-83bc-aa920d37bbce" OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed" ProgressMeter = "92933f4c-e287-5a05-a399-4b506db050ca" RecipesBase = "3cdcf5f2-1ef4-517c-9805-6587b60abb01" +SciMLBase = "0bca4576-84f4-4d90-8ffe-ffa030f20462" SharedArrays = "1a1011a3-84de-559e-8e89-a11a2f7dc383" SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" @@ -34,24 +35,24 @@ DiffEqBase = "6" Distances = "0.9, 0.10" Ferrite = "0.3" GeometricalPredicates = "0.3, 0.4" -Interpolations = "0.11, 0.12, 0.13" +Interpolations = "0.11, 0.12, 0.13, 0.14" IterativeSolvers = "0.7, 0.8, 0.9" -LinearMaps = "2, 3" +LinearMaps = "3.10" NearestNeighbors = "0.4.4" OrdinaryDiffEq = "6.2" ProgressMeter = "1" RecipesBase = "0.7, 0.8, 1" +SciMLBase = "1.63" StaticArrays = "1.1" Tensors = "1.8" VoronoiDelaunay = "0.4" julia = "1.6" [extras] -Arpack = "7d9fca2a-8960-54d3-9f78-7d1dccf2cb97" BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf" DiffEqDevTools = "f3b72e0c-5b89-59e1-b016-84e28bfd966d" Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40" [targets] -test = ["Arpack", "BenchmarkTools", "DiffEqDevTools", "Random", "Test"] +test = ["BenchmarkTools", "DiffEqDevTools", "Random", "Test"] diff --git a/docs/Manifest.toml b/docs/Manifest.toml index 2fe3bf33..c401ae41 100644 --- a/docs/Manifest.toml +++ b/docs/Manifest.toml @@ -1,7 +1,8 @@ # This file is machine-generated - editing it directly is not advised -julia_version = "1.7.3" +julia_version = "1.8.5" manifest_format = "2.0" +project_hash = "cd8f7fb55a46cc85563a7bd251c955493ea322fb" [[deps.ANSIColoredPrinters]] git-tree-sha1 = "574baf8110975760d391c710b6341da1afa48d8c" @@ -9,13 +10,14 @@ uuid = "a4c015fc-c6ff-483c-b24f-f7ea428134e9" version = "0.0.1" [[deps.Adapt]] -deps = ["LinearAlgebra"] -git-tree-sha1 = "af92965fb30777147966f58acb05da51c5616b5f" +deps = ["LinearAlgebra", "Requires"] +git-tree-sha1 = "cc37d689f599e8df4f464b2fa3870ff7db7492ef" uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e" -version = "3.3.3" +version = "3.6.1" [[deps.ArgTools]] uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f" +version = "1.1.1" [[deps.ArnoldiMethod]] deps = ["LinearAlgebra", "Random", "StaticArrays"] @@ -23,53 +25,41 @@ git-tree-sha1 = "62e51b39331de8911e4a7ff6f5aaf38a5f4cc0ae" uuid = "ec485272-7323-5ecc-a04f-4719b315124d" version = "0.2.0" -[[deps.Arpack]] -deps = ["Arpack_jll", "Libdl", "LinearAlgebra"] -git-tree-sha1 = "2ff92b71ba1747c5fdd541f8fc87736d82f40ec9" -uuid = "7d9fca2a-8960-54d3-9f78-7d1dccf2cb97" -version = "0.4.0" - -[[deps.Arpack_jll]] -deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "OpenBLAS_jll", "Pkg"] -git-tree-sha1 = "5ba6c757e8feccf03a1554dfaf3e26b3cfc7fd5e" -uuid = "68821587-b530-5797-8361-c406ea357684" -version = "3.5.1+1" - [[deps.ArrayInterface]] -deps = ["ArrayInterfaceCore", "Compat", "IfElse", "LinearAlgebra", "Static"] -git-tree-sha1 = "6ccb71b40b04ad69152f1f83d5925de13911417e" +deps = ["ArrayInterfaceCore", "Compat", "IfElse", "LinearAlgebra", "SnoopPrecompile", "Static"] +git-tree-sha1 = "dedc16cbdd1d32bead4617d27572f582216ccf23" uuid = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9" -version = "6.0.19" +version = "6.0.25" [[deps.ArrayInterfaceCore]] -deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] -git-tree-sha1 = "7d255eb1d2e409335835dc8624c35d97453011eb" +deps = ["LinearAlgebra", "SnoopPrecompile", "SparseArrays", "SuiteSparse"] +git-tree-sha1 = "e5f08b5689b1aad068e01751889f2f615c7db36d" uuid = "30b0a656-2188-435a-8636-2ec0e6a096e2" -version = "0.1.14" +version = "0.1.29" [[deps.ArrayInterfaceGPUArrays]] deps = ["Adapt", "ArrayInterfaceCore", "GPUArraysCore", "LinearAlgebra"] -git-tree-sha1 = "febba7add2873aecc0b6620b55969e73ec875bce" +git-tree-sha1 = "fc114f550b93d4c79632c2ada2924635aabfa5ed" uuid = "6ba088a2-8465-4c0a-af30-387133b534db" -version = "0.2.1" +version = "0.2.2" [[deps.ArrayInterfaceOffsetArrays]] deps = ["ArrayInterface", "OffsetArrays", "Static"] -git-tree-sha1 = "c49f6bad95a30defff7c637731f00934c7289c50" +git-tree-sha1 = "3d1a9a01976971063b3930d1aed1d9c4af0817f8" uuid = "015c0d05-e682-4f19-8f0a-679ce4c54826" -version = "0.1.6" +version = "0.1.7" [[deps.ArrayInterfaceStaticArrays]] -deps = ["Adapt", "ArrayInterface", "ArrayInterfaceStaticArraysCore", "LinearAlgebra", "Static", "StaticArrays"] -git-tree-sha1 = "efb000a9f643f018d5154e56814e338b5746c560" +deps = ["Adapt", "ArrayInterface", "ArrayInterfaceCore", "ArrayInterfaceStaticArraysCore", "LinearAlgebra", "Static", "StaticArrays"] +git-tree-sha1 = "f12dc65aef03d0a49650b20b2fdaf184928fd886" uuid = "b0d46f97-bff5-4637-a19a-dd75974142cd" -version = "0.1.4" +version = "0.1.5" [[deps.ArrayInterfaceStaticArraysCore]] -deps = ["Adapt", "ArrayInterfaceCore", "LinearAlgebra", "StaticArraysCore"] -git-tree-sha1 = "a1e2cf6ced6505cbad2490532388683f1e88c3ed" +deps = ["ArrayInterfaceCore", "LinearAlgebra", "StaticArraysCore"] +git-tree-sha1 = "01a9f8e6cfc2bfdd01d333f70b8014a04893103c" uuid = "dd5226c6-a4d4-4bc7-8575-46859f9c95b9" -version = "0.1.0" +version = "0.1.4" [[deps.Artifacts]] uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" @@ -89,11 +79,16 @@ version = "0.4.6" [[deps.Base64]] uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f" +[[deps.BitFlags]] +git-tree-sha1 = "43b1a4a8f797c1cddadf60499a8a077d4af2cd2d" +uuid = "d1d4a3ce-64b1-5f1a-9ba4-7e7e69966f35" +version = "0.1.7" + [[deps.BitTwiddlingConvenienceFunctions]] deps = ["Static"] -git-tree-sha1 = "eaee37f76339077f86679787a71990c4e465477f" +git-tree-sha1 = "0c5f81f47bbbcf4aea7b2959135713459170798b" uuid = "62783981-4cbd-42fc-bca8-16325de8dc4b" -version = "0.1.4" +version = "0.1.5" [[deps.Bzip2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -103,12 +98,12 @@ version = "1.0.8+0" [[deps.CPUSummary]] deps = ["CpuId", "IfElse", "Static"] -git-tree-sha1 = "b1a532a582dd18b34543366322d390e1560d40a9" +git-tree-sha1 = "2c144ddb46b552f72d7eafe7cc2f50746e41ea21" uuid = "2a0fbf3d-bb9c-48f3-b0a9-814d99fd7ab9" -version = "0.1.23" +version = "0.2.2" [[deps.Cairo_jll]] -deps = ["Artifacts", "Bzip2_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "JLLWrappers", "LZO_jll", "Libdl", "Pixman_jll", "Pkg", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Zlib_jll", "libpng_jll"] +deps = ["Artifacts", "Bzip2_jll", "CompilerSupportLibraries_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "JLLWrappers", "LZO_jll", "Libdl", "Pixman_jll", "Pkg", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Zlib_jll", "libpng_jll"] git-tree-sha1 = "4b859a208b2397a7a623a03449e4636bdb17bcf2" uuid = "83423d85-b0ee-5818-9007-b63ccbeb887a" version = "1.16.1+1" @@ -121,45 +116,45 @@ version = "0.5.1" [[deps.ChainRulesCore]] deps = ["Compat", "LinearAlgebra", "SparseArrays"] -git-tree-sha1 = "ff38036fb7edc903de4e79f32067d8497508616b" +git-tree-sha1 = "c6d890a52d2c4d55d326439580c3b8d0875a77d9" uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" -version = "1.15.2" +version = "1.15.7" [[deps.ChangesOfVariables]] deps = ["ChainRulesCore", "LinearAlgebra", "Test"] -git-tree-sha1 = "1e315e3f4b0b7ce40feded39c73049692126cf53" +git-tree-sha1 = "485193efd2176b88e6622a39a246f8c5b600e74e" uuid = "9e997f8a-9a97-42d5-a9f1-ce6bfc15e2c0" -version = "0.1.3" +version = "0.1.6" [[deps.CloseOpenIntervals]] deps = ["ArrayInterface", "Static"] -git-tree-sha1 = "5522c338564580adf5d58d91e43a55db0fa5fb39" +git-tree-sha1 = "d61300b9895f129f4bd684b2aff97cf319b6c493" uuid = "fb6a15b2-703c-40df-9091-08a04967cfa9" -version = "0.1.10" +version = "0.1.11" [[deps.Clustering]] -deps = ["Distances", "LinearAlgebra", "NearestNeighbors", "Printf", "SparseArrays", "Statistics", "StatsBase"] -git-tree-sha1 = "75479b7df4167267d75294d14b58244695beb2ac" +deps = ["Distances", "LinearAlgebra", "NearestNeighbors", "Printf", "Random", "SparseArrays", "Statistics", "StatsBase"] +git-tree-sha1 = "64df3da1d2a26f4de23871cd1b6482bb68092bd5" uuid = "aaaa29a8-35af-508c-8bc3-b662a17a0fe5" -version = "0.14.2" +version = "0.14.3" [[deps.CodecZlib]] deps = ["TranscodingStreams", "Zlib_jll"] -git-tree-sha1 = "ded953804d019afa9a3f98981d99b33e3db7b6da" +git-tree-sha1 = "9c209fb7536406834aa938fb149964b985de6c83" uuid = "944b1d66-785c-5afd-91f1-9de20f533193" -version = "0.7.0" +version = "0.7.1" [[deps.CoherentStructures]] -deps = ["ArnoldiMethod", "AxisArrays", "ColorTypes", "DiffEqBase", "Distances", "Distributed", "Ferrite", "GeometricalPredicates", "Interpolations", "IterativeSolvers", "LinearAlgebra", "LinearMaps", "NearestNeighbors", "OrdinaryDiffEq", "ProgressMeter", "RecipesBase", "SharedArrays", "SparseArrays", "StaticArrays", "Statistics", "Tensors", "VoronoiDelaunay"] +deps = ["ArnoldiMethod", "AxisArrays", "ColorTypes", "DiffEqBase", "Distances", "Distributed", "Ferrite", "GeometricalPredicates", "Interpolations", "IterativeSolvers", "LinearAlgebra", "LinearMaps", "NearestNeighbors", "OrdinaryDiffEq", "ProgressMeter", "RecipesBase", "SciMLBase", "SharedArrays", "SparseArrays", "StaticArrays", "Statistics", "Tensors", "VoronoiDelaunay"] path = ".." uuid = "0c1513b4-3a13-56f1-9cd2-8312eaec88c4" -version = "0.4.11" +version = "0.4.12" [[deps.ColorSchemes]] -deps = ["ColorTypes", "ColorVectorSpace", "Colors", "FixedPointNumbers", "Random"] -git-tree-sha1 = "1fd869cc3875b57347f7027521f561cf46d1fcd8" +deps = ["ColorTypes", "ColorVectorSpace", "Colors", "FixedPointNumbers", "Random", "SnoopPrecompile"] +git-tree-sha1 = "aa3edc8f8dea6cbfa176ee12f7c2fc82f0608ed3" uuid = "35d6a980-a343-548e-a6ea-1d62b119f2f4" -version = "3.19.0" +version = "3.20.0" [[deps.ColorTypes]] deps = ["FixedPointNumbers", "Random"] @@ -169,20 +164,20 @@ version = "0.11.4" [[deps.ColorVectorSpace]] deps = ["ColorTypes", "FixedPointNumbers", "LinearAlgebra", "SpecialFunctions", "Statistics", "TensorCore"] -git-tree-sha1 = "d08c20eef1f2cbc6e60fd3612ac4340b89fea322" +git-tree-sha1 = "600cc5508d66b78aae350f7accdb58763ac18589" uuid = "c3611d14-8923-5661-9e6a-0046d554d3a4" -version = "0.9.9" +version = "0.9.10" [[deps.Colors]] deps = ["ColorTypes", "FixedPointNumbers", "Reexport"] -git-tree-sha1 = "417b0ed7b8b838aa6ca0a87aadf1bb9eb111ce40" +git-tree-sha1 = "fc08e5930ee9a4e03f84bfb5211cb54e7769758a" uuid = "5ae59095-9a9b-59fe-a467-6f913c188581" -version = "0.12.8" +version = "0.12.10" [[deps.CommonSolve]] -git-tree-sha1 = "332a332c97c7071600984b3c31d9067e1a4e6e25" +git-tree-sha1 = "9441451ee712d1aec22edad62db1a9af3dc8d852" uuid = "38540f10-b2f7-11e9-35d8-d573e4eb0ff2" -version = "0.2.1" +version = "0.2.3" [[deps.CommonSubexpressions]] deps = ["MacroTools", "Test"] @@ -192,19 +187,20 @@ version = "0.3.0" [[deps.Compat]] deps = ["Base64", "Dates", "DelimitedFiles", "Distributed", "InteractiveUtils", "LibGit2", "Libdl", "LinearAlgebra", "Markdown", "Mmap", "Pkg", "Printf", "REPL", "Random", "SHA", "Serialization", "SharedArrays", "Sockets", "SparseArrays", "Statistics", "Test", "UUIDs", "Unicode"] -git-tree-sha1 = "9be8be1d8a6f44b96482c8af52238ea7987da3e3" +git-tree-sha1 = "550e3f8a429fd2f8a9da59f1589c5e268ddc97b3" uuid = "34da2185-b29b-5c13-b0c7-acf172513d20" -version = "3.45.0" +version = "3.46.1" [[deps.CompilerSupportLibraries_jll]] deps = ["Artifacts", "Libdl"] uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae" +version = "1.0.1+0" [[deps.ConstructionBase]] deps = ["LinearAlgebra"] -git-tree-sha1 = "59d00b3139a9de4eb961057eabb65ac6522be954" +git-tree-sha1 = "89a9db8d28102b094992472d333674bd1a83ce2a" uuid = "187b0558-2788-49d3-abe0-74a17ed4e7c9" -version = "1.4.0" +version = "1.5.1" [[deps.Contour]] git-tree-sha1 = "d05d9e7b7aedff4e5b51a029dced05cfb6125781" @@ -218,9 +214,9 @@ uuid = "adafc99b-e345-5852-983c-f28acb93d879" version = "0.3.1" [[deps.DataAPI]] -git-tree-sha1 = "fb5f5316dd3fd4c5e7c30a24d50643b73e37cd40" +git-tree-sha1 = "e8119c1a33d267e16108be441a287a6981ba1630" uuid = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a" -version = "1.10.0" +version = "1.14.0" [[deps.DataStructures]] deps = ["Compat", "InteractiveUtils", "OrderedCollections"] @@ -248,28 +244,28 @@ uuid = "b429d917-457f-4dbc-8f4c-0cc954292b1d" version = "0.4.0" [[deps.DiffEqBase]] -deps = ["ArrayInterfaceCore", "ChainRulesCore", "DataStructures", "Distributions", "DocStringExtensions", "FastBroadcast", "ForwardDiff", "FunctionWrappers", "LinearAlgebra", "Logging", "MuladdMacro", "NonlinearSolve", "Parameters", "Printf", "RecursiveArrayTools", "Reexport", "Requires", "SciMLBase", "Setfield", "SparseArrays", "StaticArrays", "Statistics", "ZygoteRules"] -git-tree-sha1 = "da9b5a3f2372682d5de7e08ce01ec008b79f81f8" +deps = ["ArrayInterfaceCore", "ChainRulesCore", "DataStructures", "Distributions", "DocStringExtensions", "EnumX", "FastBroadcast", "ForwardDiff", "FunctionWrappers", "FunctionWrappersWrappers", "LinearAlgebra", "Logging", "Markdown", "MuladdMacro", "Parameters", "PreallocationTools", "Printf", "RecursiveArrayTools", "Reexport", "Requires", "SciMLBase", "Setfield", "SparseArrays", "Static", "StaticArraysCore", "Statistics", "Tricks", "ZygoteRules"] +git-tree-sha1 = "81470904b958f3f24173fa013d4a54198842cb8d" uuid = "2b5f629d-d688-5b77-993f-72d75c75574e" -version = "6.93.0" +version = "6.119.0" [[deps.DiffResults]] -deps = ["StaticArrays"] -git-tree-sha1 = "c18e98cba888c6c25d1c3b048e4b3380ca956805" +deps = ["StaticArraysCore"] +git-tree-sha1 = "782dd5f4561f5d267313f23853baaaa4c52ea621" uuid = "163ba53b-c6d8-5494-b064-1a9d43ac40c5" -version = "1.0.3" +version = "1.1.0" [[deps.DiffRules]] deps = ["IrrationalConstants", "LogExpFunctions", "NaNMath", "Random", "SpecialFunctions"] -git-tree-sha1 = "28d605d9a0ac17118fe2c5e9ce0fbb76c3ceb120" +git-tree-sha1 = "a4ad7ef19d2cdc2eff57abbbe68032b1cd0bd8f8" uuid = "b552c78f-8df3-52c6-915a-8e097449b14b" -version = "1.11.0" +version = "1.13.0" [[deps.Distances]] deps = ["LinearAlgebra", "SparseArrays", "Statistics", "StatsAPI"] -git-tree-sha1 = "3258d0659f812acde79e8a74b11f17ac06d0ca04" +git-tree-sha1 = "49eba9ad9f7ead780bfb7ee319f962c811c6d3b2" uuid = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7" -version = "0.10.7" +version = "0.10.8" [[deps.Distributed]] deps = ["Random", "Serialization", "Sockets"] @@ -277,25 +273,26 @@ uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b" [[deps.Distributions]] deps = ["ChainRulesCore", "DensityInterface", "FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SparseArrays", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns", "Test"] -git-tree-sha1 = "429077fd74119f5ac495857fd51f4120baf36355" +git-tree-sha1 = "da9e1a9058f8d3eec3a8c9fe4faacfb89180066b" uuid = "31c24e10-a181-5473-b8eb-7969acd0382f" -version = "0.25.65" +version = "0.25.86" [[deps.DocStringExtensions]] deps = ["LibGit2"] -git-tree-sha1 = "b19534d1895d702889b219c382a6e18010797f0b" +git-tree-sha1 = "2fb1e02f2b635d0845df5d7c167fec4dd739b00d" uuid = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae" -version = "0.8.6" +version = "0.9.3" [[deps.Documenter]] deps = ["ANSIColoredPrinters", "Base64", "Dates", "DocStringExtensions", "IOCapture", "InteractiveUtils", "JSON", "LibGit2", "Logging", "Markdown", "REPL", "Test", "Unicode"] -git-tree-sha1 = "2498c3704e9cd26bf586a351473417881676bb2d" +git-tree-sha1 = "58fea7c536acd71f3eef6be3b21c0df5f3df88fd" uuid = "e30172f5-a6a5-5a46-863b-614d45cd2de4" -version = "0.27.21" +version = "0.27.24" [[deps.Downloads]] deps = ["ArgTools", "FileWatching", "LibCURL", "NetworkOptions"] uuid = "f43a241f-c20a-4ad4-852c-f6b1247861c6" +version = "1.6.0" [[deps.DualNumbers]] deps = ["Calculus", "NaNMath", "SpecialFunctions"] @@ -303,16 +300,10 @@ git-tree-sha1 = "5837a837389fccf076445fce071c8ddaea35a566" uuid = "fa6b7ba4-c1ee-5f82-b5fc-ecf0adba8f74" version = "0.6.8" -[[deps.EarCut_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "3f3a2501fa7236e9b911e0f7a588c657e822bb6d" -uuid = "5ae413db-bbd1-5e63-b57d-d24a61df00f5" -version = "2.2.3+0" - [[deps.EnumX]] -git-tree-sha1 = "1d2621e1a6246c5cf1116be0055686f305210b80" +git-tree-sha1 = "bdb1942cd4c45e3c678fd11569d5cccd80976237" uuid = "4e289a0a-7415-4d19-859d-a7e5c4648b56" -version = "1.0.2" +version = "1.0.4" [[deps.Expat_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -321,10 +312,15 @@ uuid = "2e619515-83b5-522b-bb60-26c02a35a201" version = "2.4.8+0" [[deps.ExponentialUtilities]] -deps = ["ArrayInterfaceCore", "GPUArraysCore", "GenericSchur", "LinearAlgebra", "Printf", "SparseArrays", "libblastrampoline_jll"] -git-tree-sha1 = "b40c9037e1a33990466bc5d224ced34b34eebdb0" +deps = ["Adapt", "ArrayInterfaceCore", "ArrayInterfaceGPUArrays", "GPUArraysCore", "GenericSchur", "LinearAlgebra", "Printf", "SnoopPrecompile", "SparseArrays", "libblastrampoline_jll"] +git-tree-sha1 = "eb58c1e1417a6580b983069f1491ff82c37def2c" uuid = "d4d017d3-3776-5f7e-afef-a10c40355c18" -version = "1.18.0" +version = "1.23.0" + +[[deps.ExprTools]] +git-tree-sha1 = "c1d06d129da9f55715c6c212866f5b1bddc5fa00" +uuid = "e2ba6199-217a-4e67-a87a-7c52f15ade04" +version = "0.1.9" [[deps.FFMPEG]] deps = ["FFMPEG_jll"] @@ -333,16 +329,16 @@ 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", "Pkg", "Zlib_jll", "libaom_jll", "libass_jll", "libfdk_aac_jll", "libvorbis_jll", "x264_jll", "x265_jll"] -git-tree-sha1 = "ccd479984c7838684b3ac204b716c89955c76623" +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 = "4.4.2+0" +version = "4.4.2+2" [[deps.FastBroadcast]] deps = ["ArrayInterface", "ArrayInterfaceCore", "LinearAlgebra", "Polyester", "Static", "StrideArraysCore"] -git-tree-sha1 = "21cdeff41e5a1822c2acd7fc7934c5f450588e00" +git-tree-sha1 = "4bef892787c972913d4d84e7255400759bb650e5" uuid = "7034ab61-46d4-4ed7-9d0f-46aef9175898" -version = "0.2.1" +version = "0.2.4" [[deps.FastClosures]] git-tree-sha1 = "acebe244d53ee1b461970f8910c235b259e772ef" @@ -351,36 +347,36 @@ version = "0.3.2" [[deps.FastLapackInterface]] deps = ["LinearAlgebra"] -git-tree-sha1 = "9c77a18eddbc4f7b5edbd2f1c28467ba4ba787bd" +git-tree-sha1 = "c1293a93193f0ae94be7cf338d33e162c39d8788" uuid = "29a986be-02c6-4525-aec4-84b980013641" -version = "1.1.0" +version = "1.2.9" [[deps.Ferrite]] -deps = ["EnumX", "LinearAlgebra", "NearestNeighbors", "Reexport", "SparseArrays", "Tensors", "WriteVTK"] -git-tree-sha1 = "ec47cd34e82e8ab1dc70024feb652386ee2c6406" +deps = ["EnumX", "LinearAlgebra", "NearestNeighbors", "Preferences", "Reexport", "SparseArrays", "Tensors", "WriteVTK"] +git-tree-sha1 = "7309be360f3be1929da64f5cc6b79428540e7921" uuid = "c061ca5d-56c9-439f-9c0e-210fe06d3992" -version = "0.3.7" +version = "0.3.12" [[deps.FileIO]] deps = ["Pkg", "Requires", "UUIDs"] -git-tree-sha1 = "9267e5f50b0e12fdfd5a2455534345c4cf2c7f7a" +git-tree-sha1 = "7be5f99f7d15578798f338f5433b6c432ea8037b" uuid = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549" -version = "1.14.0" +version = "1.16.0" [[deps.FileWatching]] uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" [[deps.FillArrays]] deps = ["LinearAlgebra", "Random", "SparseArrays", "Statistics"] -git-tree-sha1 = "246621d23d1f43e3b9c368bf3b72b2331a27c286" +git-tree-sha1 = "9dec0199898d4d5c1d1b257cbf2cc498afe03a2a" uuid = "1a297f60-69ca-5386-bcde-b61e274b549b" -version = "0.13.2" +version = "0.13.8" [[deps.FiniteDiff]] deps = ["ArrayInterfaceCore", "LinearAlgebra", "Requires", "Setfield", "SparseArrays", "StaticArrays"] -git-tree-sha1 = "cb8c5f0074153ace28ce5100714df4378ad885e0" +git-tree-sha1 = "04ed1f0029b6b3af88343e439b995141cb0d0b8d" uuid = "6a86dc24-6348-571c-b903-95158fe2bd41" -version = "2.14.0" +version = "2.17.0" [[deps.FixedPointNumbers]] deps = ["Statistics"] @@ -402,9 +398,9 @@ version = "0.4.2" [[deps.ForwardDiff]] deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "LinearAlgebra", "LogExpFunctions", "NaNMath", "Preferences", "Printf", "Random", "SpecialFunctions", "StaticArrays"] -git-tree-sha1 = "2f18915445b248731ec5db4e4a17e451020bf21e" +git-tree-sha1 = "00e252f4d706b3d55a8863432e742bf5717b498d" uuid = "f6369f11-7733-5829-9624-2563aa707210" -version = "0.10.30" +version = "0.10.35" [[deps.FreeType2_jll]] deps = ["Artifacts", "Bzip2_jll", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] @@ -419,9 +415,15 @@ uuid = "559328eb-81f9-559d-9380-de523a88c83c" version = "1.0.10+0" [[deps.FunctionWrappers]] -git-tree-sha1 = "241552bc2209f0fa068b6415b1942cc0aa486bcc" +git-tree-sha1 = "d62485945ce5ae9c0c48f124a84998d755bae00e" uuid = "069b7b12-0de2-55c6-9aab-29f3d0a68a2e" -version = "1.1.2" +version = "1.1.3" + +[[deps.FunctionWrappersWrappers]] +deps = ["FunctionWrappers"] +git-tree-sha1 = "b104d487b34566608f8b4e1c39fb0b10aa279ff8" +uuid = "77dc65aa-8811-40c2-897b-53d922fa7daf" +version = "0.1.3" [[deps.Future]] deps = ["Random"] @@ -429,31 +431,32 @@ uuid = "9fa8497b-333b-5362-9e8d-4d0656e87820" [[deps.GLFW_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libglvnd_jll", "Pkg", "Xorg_libXcursor_jll", "Xorg_libXi_jll", "Xorg_libXinerama_jll", "Xorg_libXrandr_jll"] -git-tree-sha1 = "51d2dfe8e590fbd74e7a842cf6d13d8a2f45dc01" +git-tree-sha1 = "d972031d28c8c8d9d7b41a536ad7bb0c2579caca" uuid = "0656b61e-2033-5cc2-a64a-77c0f6c09b89" -version = "3.3.6+0" +version = "3.3.8+0" [[deps.GMP_jll]] deps = ["Artifacts", "Libdl"] uuid = "781609d7-10c4-51f6-84f2-b8444358ff6d" +version = "6.2.1+2" [[deps.GPUArraysCore]] deps = ["Adapt"] -git-tree-sha1 = "4078d3557ab15dd9fe6a0cf6f65e3d4937e98427" +git-tree-sha1 = "1cd7f0af1aa58abc02ea1d872953a97359cb87fa" uuid = "46192b85-c4d5-4398-a991-12ede77f4527" -version = "0.1.0" +version = "0.1.4" [[deps.GR]] -deps = ["Base64", "DelimitedFiles", "GR_jll", "HTTP", "JSON", "Libdl", "LinearAlgebra", "Pkg", "Printf", "Random", "RelocatableFolders", "Serialization", "Sockets", "Test", "UUIDs"] -git-tree-sha1 = "037a1ca47e8a5989cc07d19729567bb71bfabd0c" +deps = ["Artifacts", "Base64", "DelimitedFiles", "Downloads", "GR_jll", "HTTP", "JSON", "Libdl", "LinearAlgebra", "Pkg", "Preferences", "Printf", "Random", "Serialization", "Sockets", "TOML", "Tar", "Test", "UUIDs", "p7zip_jll"] +git-tree-sha1 = "660b2ea2ec2b010bb02823c6d0ff6afd9bdc5c16" uuid = "28b8d3ca-fb5f-59d9-8090-bfdbd6d07a71" -version = "0.66.0" +version = "0.71.7" [[deps.GR_jll]] -deps = ["Artifacts", "Bzip2_jll", "Cairo_jll", "FFMPEG_jll", "Fontconfig_jll", "GLFW_jll", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Libtiff_jll", "Pixman_jll", "Pkg", "Qt5Base_jll", "Zlib_jll", "libpng_jll"] -git-tree-sha1 = "c8ab731c9127cd931c93221f65d6a1008dad7256" +deps = ["Artifacts", "Bzip2_jll", "Cairo_jll", "FFMPEG_jll", "Fontconfig_jll", "GLFW_jll", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Libtiff_jll", "Pixman_jll", "Qt5Base_jll", "Zlib_jll", "libpng_jll"] +git-tree-sha1 = "d5e1fd17ac7f3aa4c5287a61ee28d4f8b8e98873" uuid = "d2c73de3-f751-5644-a686-071e5b155ba9" -version = "0.66.0+0" +version = "0.71.7+0" [[deps.GenericSchur]] deps = ["LinearAlgebra", "Printf"] @@ -466,12 +469,6 @@ git-tree-sha1 = "6c9f24b54b8bf2e3496b5b3c25f5a0aebacd95d5" uuid = "fd0ad045-b25c-564e-8f9c-8ef5c5f21267" version = "0.4.2" -[[deps.GeometryBasics]] -deps = ["EarCut_jll", "IterTools", "LinearAlgebra", "StaticArrays", "StructArrays", "Tables"] -git-tree-sha1 = "83ea630384a13fc4f002b77690bc0afeb4255ac9" -uuid = "5c1252a2-5f33-56bf-86c9-59e7332b4326" -version = "0.4.2" - [[deps.Gettext_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "XML2_jll"] git-tree-sha1 = "9b02998aba7bf074d14de89f9d37ca24a1a0b046" @@ -479,10 +476,10 @@ uuid = "78b55507-aeef-58d4-861c-77aaff3498b1" version = "0.21.0+0" [[deps.Glib_jll]] -deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "a32d672ac2c967f3deb8a81d828afc739c838a06" +deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Pkg", "Zlib_jll"] +git-tree-sha1 = "d3b3624125c1474292d0d8ed0f65554ac37ddb23" uuid = "7746bdde-850d-59dc-9ae8-88ece973131d" -version = "2.68.3+2" +version = "2.74.0+2" [[deps.Graphite2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -492,9 +489,9 @@ version = "1.3.14+0" [[deps.Graphs]] deps = ["ArnoldiMethod", "Compat", "DataStructures", "Distributed", "Inflate", "LinearAlgebra", "Random", "SharedArrays", "SimpleTraits", "SparseArrays", "Statistics"] -git-tree-sha1 = "db5c7e27c0d46fd824d470a3c32a4fc6c935fa96" +git-tree-sha1 = "1cf1d7dcb4bc32d7b4a5add4232db3750c27ecb4" uuid = "86223c79-3864-5bf0-83f7-82e725a168b6" -version = "1.7.1" +version = "1.8.0" [[deps.Grisu]] git-tree-sha1 = "53bb909d1151e57e2484c3d1b53e19552b887fb2" @@ -502,10 +499,10 @@ uuid = "42e2da0e-8278-4e71-bc24-59509adca0fe" version = "1.0.2" [[deps.HTTP]] -deps = ["Base64", "CodecZlib", "Dates", "IniFile", "Logging", "LoggingExtras", "MbedTLS", "NetworkOptions", "Random", "SimpleBufferStream", "Sockets", "URIs", "UUIDs"] -git-tree-sha1 = "bd11d3220f89382f3116ed34c92badaa567239c9" +deps = ["Base64", "CodecZlib", "Dates", "IniFile", "Logging", "LoggingExtras", "MbedTLS", "NetworkOptions", "OpenSSL", "Random", "SimpleBufferStream", "Sockets", "URIs", "UUIDs"] +git-tree-sha1 = "37e4657cd56b11abe3d10cd4a1ec5fbdb4180263" uuid = "cd3eb016-35fb-5094-929b-558a96fad6f3" -version = "1.0.5" +version = "1.7.4" [[deps.HarfBuzz_jll]] deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "Graphite2_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Pkg"] @@ -515,9 +512,9 @@ version = "2.8.1+1" [[deps.HostCPUFeatures]] deps = ["BitTwiddlingConvenienceFunctions", "IfElse", "Libdl", "Static"] -git-tree-sha1 = "b7b88a4716ac33fe31d6556c02fc60017594343c" +git-tree-sha1 = "734fd90dd2f920a2f1921d5388dcebe805b262dc" uuid = "3e5b6fbb-0976-4d2c-9146-d79de83f2fb0" -version = "0.1.8" +version = "0.1.14" [[deps.HypergeometricFunctions]] deps = ["DualNumbers", "LinearAlgebra", "OpenLibm_jll", "SpecialFunctions", "Test"] @@ -537,9 +534,9 @@ uuid = "615f187c-cbe4-4ef1-ba3b-2fcf58d6d173" version = "0.1.1" [[deps.Inflate]] -git-tree-sha1 = "f5fc07d4e706b84f72d54eedcc1c13d92fb0871c" +git-tree-sha1 = "5cd07aab533df5170988219191dfad0519391428" uuid = "d25df0c9-e2be-5dd7-82c8-3ad0b3e990b9" -version = "0.1.2" +version = "0.1.3" [[deps.IniFile]] git-tree-sha1 = "f550e6e32074c939295eb5ea6de31849ac2c9625" @@ -551,27 +548,27 @@ deps = ["Markdown"] uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240" [[deps.Interpolations]] -deps = ["AxisAlgorithms", "ChainRulesCore", "LinearAlgebra", "OffsetArrays", "Random", "Ratios", "Requires", "SharedArrays", "SparseArrays", "StaticArrays", "WoodburyMatrices"] -git-tree-sha1 = "b7bc05649af456efc75d178846f47006c2c4c3c7" +deps = ["Adapt", "AxisAlgorithms", "ChainRulesCore", "LinearAlgebra", "OffsetArrays", "Random", "Ratios", "Requires", "SharedArrays", "SparseArrays", "StaticArrays", "WoodburyMatrices"] +git-tree-sha1 = "721ec2cf720536ad005cb38f50dbba7b02419a15" uuid = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59" -version = "0.13.6" +version = "0.14.7" [[deps.IntervalSets]] deps = ["Dates", "Random", "Statistics"] -git-tree-sha1 = "57af5939800bce15980bddd2426912c4f83012d8" +git-tree-sha1 = "16c0cc91853084cb5f58a78bd209513900206ce6" uuid = "8197267c-284f-5f27-9208-e0e47529a953" -version = "0.7.1" +version = "0.7.4" [[deps.InverseFunctions]] deps = ["Test"] -git-tree-sha1 = "b3364212fb5d870f724876ffcd34dd8ec6d98918" +git-tree-sha1 = "49510dfcb407e572524ba94aeae2fced1f3feb0f" uuid = "3587e190-3f89-42d0-90ee-14403ec27112" -version = "0.1.7" +version = "0.1.8" [[deps.IrrationalConstants]] -git-tree-sha1 = "7fd44fd4ff43fc60815f8e764c0f352b83c49151" +git-tree-sha1 = "630b497eafcc20001bba38a4651b327dcfc491d2" uuid = "92d709cd-6900-40b7-9082-c6be49f344b6" -version = "0.1.1" +version = "0.2.2" [[deps.IterTools]] git-tree-sha1 = "fa6287a4469f5e048d763df38279ee729fbd44e5" @@ -590,10 +587,16 @@ uuid = "82899510-4779-5014-852e-03e436cf321d" version = "1.0.0" [[deps.JLD2]] -deps = ["FileIO", "MacroTools", "Mmap", "OrderedCollections", "Pkg", "Printf", "Reexport", "TranscodingStreams", "UUIDs"] -git-tree-sha1 = "81b9477b49402b47fbe7f7ae0b252077f53e4a08" +deps = ["FileIO", "MacroTools", "Mmap", "OrderedCollections", "Pkg", "Printf", "Reexport", "Requires", "TranscodingStreams", "UUIDs"] +git-tree-sha1 = "42c17b18ced77ff0be65957a591d34f4ed57c631" uuid = "033835bb-8acc-5ee8-8aae-3f567f8a3819" -version = "0.4.22" +version = "0.4.31" + +[[deps.JLFzf]] +deps = ["Pipe", "REPL", "Random", "fzf_jll"] +git-tree-sha1 = "f377670cda23b6b7c1c0b3893e37451c5c1a2185" +uuid = "1019f520-868f-41f5-a6de-eb00f4b6a39c" +version = "0.1.5" [[deps.JLLWrappers]] deps = ["Preferences"] @@ -608,28 +611,28 @@ uuid = "682c06a0-de6a-54ab-a142-c8b1cf79cde6" version = "0.21.3" [[deps.JpegTurbo_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "b53380851c6e6664204efb2e62cd24fa5c47e4ba" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "6f2675ef130a300a112286de91973805fcc5ffbc" uuid = "aacddb02-875f-59d6-b918-886e6ef4fbf8" -version = "2.1.2+0" +version = "2.1.91+0" [[deps.KLU]] deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse_jll"] -git-tree-sha1 = "cae5e3dfd89b209e01bcd65b3a25e74462c67ee0" +git-tree-sha1 = "764164ed65c30738750965d55652db9c94c59bfe" uuid = "ef3ab10e-7fda-4108-b977-705223b18434" -version = "0.3.0" +version = "0.4.0" [[deps.Krylov]] deps = ["LinearAlgebra", "Printf", "SparseArrays"] -git-tree-sha1 = "7f0a89bd74c30aa7ff96c4bf1bc884c39663a621" +git-tree-sha1 = "dd90aacbfb622f898a97c2a4411ac49101ebab8a" uuid = "ba0b0d4f-ebba-5204-a429-3ac8c609bfb7" -version = "0.8.2" +version = "0.9.0" [[deps.KrylovKit]] -deps = ["LinearAlgebra", "Printf"] -git-tree-sha1 = "49b0c1dd5c292870577b8f58c51072bd558febb9" +deps = ["ChainRulesCore", "GPUArraysCore", "LinearAlgebra", "Printf"] +git-tree-sha1 = "1a5e1d9941c783b0119897d29f2eb665d876ecf3" uuid = "0b1a1467-8014-51b9-945f-bf0ae24f4b77" -version = "0.5.4" +version = "0.6.0" [[deps.LAME_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -655,24 +658,32 @@ uuid = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f" version = "1.3.0" [[deps.Latexify]] -deps = ["Formatting", "InteractiveUtils", "LaTeXStrings", "MacroTools", "Markdown", "Printf", "Requires"] -git-tree-sha1 = "46a39b9c58749eefb5f2dc1178cb8fab5332b1ab" +deps = ["Formatting", "InteractiveUtils", "LaTeXStrings", "MacroTools", "Markdown", "OrderedCollections", "Printf", "Requires"] +git-tree-sha1 = "2422f47b34d4b127720a18f86fa7b1aa2e141f29" uuid = "23fbe1c1-3f47-55db-b15f-69d7ec21a316" -version = "0.15.15" +version = "0.15.18" [[deps.LayoutPointers]] deps = ["ArrayInterface", "ArrayInterfaceOffsetArrays", "ArrayInterfaceStaticArrays", "LinearAlgebra", "ManualMemory", "SIMDTypes", "Static"] -git-tree-sha1 = "b67e749fb35530979839e7b4b606a97105fe4f1c" +git-tree-sha1 = "0ad6f0c51ce004dadc24a28a0dfecfb568e52242" uuid = "10f19ff3-798f-405d-979b-55457f8fc047" -version = "0.1.10" +version = "0.1.13" + +[[deps.Lazy]] +deps = ["MacroTools"] +git-tree-sha1 = "1370f8202dac30758f3c345f9909b97f53d87d3f" +uuid = "50d2b5c4-7a5e-59d5-8109-a42b560f39c0" +version = "0.15.1" [[deps.LibCURL]] deps = ["LibCURL_jll", "MozillaCACerts_jll"] uuid = "b27032c2-a3e7-50c8-80cd-2d36dbcbfd21" +version = "0.6.3" [[deps.LibCURL_jll]] deps = ["Artifacts", "LibSSH2_jll", "Libdl", "MbedTLS_jll", "Zlib_jll", "nghttp2_jll"] uuid = "deac9b47-8bc7-5906-a0fe-35ac56dc84c0" +version = "7.84.0+0" [[deps.LibGit2]] deps = ["Base64", "NetworkOptions", "Printf", "SHA"] @@ -681,6 +692,7 @@ uuid = "76f85450-5226-5b5a-8eaa-529ad045b433" [[deps.LibSSH2_jll]] deps = ["Artifacts", "Libdl", "MbedTLS_jll"] uuid = "29816b5a-b9ab-546f-933c-edad1886dfa8" +version = "1.10.2+0" [[deps.Libdl]] uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb" @@ -699,9 +711,9 @@ version = "1.8.7+0" [[deps.Libglvnd_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll", "Xorg_libXext_jll"] -git-tree-sha1 = "7739f837d6447403596a75d19ed01fd08d6f56bf" +git-tree-sha1 = "6f73d1dd803986947b2c750138528a999a6c7733" uuid = "7e76a0d4-f3c7-5321-8279-8d96eeed0f29" -version = "1.3.0+3" +version = "1.6.0+0" [[deps.Libgpg_error_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -711,9 +723,9 @@ version = "1.42.0+0" [[deps.Libiconv_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "42b62845d70a619f063a7da093d995ec8e15e778" +git-tree-sha1 = "c7cb1f5d892775ba13767a87c7ada0b980ea0a71" uuid = "94ce4f54-9a6c-5748-9c1c-f9c7231a4531" -version = "1.16.1+1" +version = "1.16.1+2" [[deps.Libmount_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -741,52 +753,52 @@ version = "0.9.0" [[deps.LineSearches]] deps = ["LinearAlgebra", "NLSolversBase", "NaNMath", "Parameters", "Printf"] -git-tree-sha1 = "f27132e551e959b3667d8c93eae90973225032dd" +git-tree-sha1 = "7bbea35cec17305fc70a0e5b4641477dc0789d9d" uuid = "d3d80556-e9d4-5f37-9878-2ab0fcc64255" -version = "7.1.1" +version = "7.2.0" [[deps.LinearAlgebra]] deps = ["Libdl", "libblastrampoline_jll"] uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" [[deps.LinearMaps]] -deps = ["LinearAlgebra", "SparseArrays", "Statistics"] -git-tree-sha1 = "d1b46faefb7c2f48fdec69e6f3cc34857769bc15" +deps = ["ChainRulesCore", "LinearAlgebra", "SparseArrays", "Statistics"] +git-tree-sha1 = "4af48c3585177561e9f0d24eb9619ad3abf77cc7" uuid = "7a12625a-238d-50fd-b39a-03d52299707e" -version = "3.8.0" +version = "3.10.0" [[deps.LinearSolve]] -deps = ["ArrayInterfaceCore", "DocStringExtensions", "FastLapackInterface", "GPUArraysCore", "IterativeSolvers", "KLU", "Krylov", "KrylovKit", "LinearAlgebra", "RecursiveFactorization", "Reexport", "SciMLBase", "Setfield", "SparseArrays", "SuiteSparse", "UnPack"] -git-tree-sha1 = "5011ab36cb55f2c849487f0a3edffba602c705c1" +deps = ["ArrayInterface", "DocStringExtensions", "FastLapackInterface", "GPUArraysCore", "IterativeSolvers", "KLU", "Krylov", "KrylovKit", "LinearAlgebra", "Preferences", "RecursiveFactorization", "Reexport", "SciMLBase", "SciMLOperators", "Setfield", "SnoopPrecompile", "SparseArrays", "Sparspak", "SuiteSparse", "UnPack"] +git-tree-sha1 = "d1fce810e9a4213607f0182cf25ffd6ce13e19b6" uuid = "7ed4a6bd-45f5-4d41-b270-4a48e9bafcae" -version = "1.22.1" +version = "1.37.0" [[deps.Literate]] deps = ["Base64", "IOCapture", "JSON", "REPL"] -git-tree-sha1 = "5b5ec7696d40868945c407f28a6672a230448b70" +git-tree-sha1 = "1c4418beaa6664041e0f9b48f0710f57bff2fcbe" uuid = "98b081ad-f1c9-55d3-8b20-4c87d4299306" -version = "2.13.4" +version = "2.14.0" [[deps.LogExpFunctions]] deps = ["ChainRulesCore", "ChangesOfVariables", "DocStringExtensions", "InverseFunctions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "09e4b894ce6a976c354a69041a04748180d43637" +git-tree-sha1 = "0a1b7c2863e44523180fdb3146534e265a91870b" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.15" +version = "0.3.23" [[deps.Logging]] uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" [[deps.LoggingExtras]] deps = ["Dates", "Logging"] -git-tree-sha1 = "5d4d2d9904227b8bd66386c1138cf4d5ffa826bf" +git-tree-sha1 = "cedb76b37bc5a6c702ade66be44f831fa23c681e" uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" -version = "0.4.9" +version = "1.0.0" [[deps.LoopVectorization]] -deps = ["ArrayInterface", "ArrayInterfaceCore", "ArrayInterfaceOffsetArrays", "ArrayInterfaceStaticArrays", "CPUSummary", "ChainRulesCore", "CloseOpenIntervals", "DocStringExtensions", "ForwardDiff", "HostCPUFeatures", "IfElse", "LayoutPointers", "LinearAlgebra", "OffsetArrays", "PolyesterWeave", "SIMDDualNumbers", "SIMDTypes", "SLEEFPirates", "SpecialFunctions", "Static", "ThreadingUtilities", "UnPack", "VectorizationBase"] -git-tree-sha1 = "adc9421494fd93e31a18a66e49d79615ad6b2efa" +deps = ["ArrayInterface", "ArrayInterfaceCore", "ArrayInterfaceOffsetArrays", "ArrayInterfaceStaticArrays", "CPUSummary", "ChainRulesCore", "CloseOpenIntervals", "DocStringExtensions", "ForwardDiff", "HostCPUFeatures", "IfElse", "LayoutPointers", "LinearAlgebra", "OffsetArrays", "PolyesterWeave", "SIMDTypes", "SLEEFPirates", "SnoopPrecompile", "SpecialFunctions", "Static", "ThreadingUtilities", "UnPack", "VectorizationBase"] +git-tree-sha1 = "9696a80c21a56b937e3fd89e972f8db5db3186e2" uuid = "bdcacae8-1622-11e9-2a5c-532679323890" -version = "0.12.120" +version = "0.12.150" [[deps.MPC_jll]] deps = ["Artifacts", "GMP_jll", "JLLWrappers", "Libdl", "MPFR_jll", "Pkg"] @@ -797,12 +809,13 @@ version = "1.2.1+0" [[deps.MPFR_jll]] deps = ["Artifacts", "GMP_jll", "Libdl"] uuid = "3a97d323-0669-5f0c-9066-3539efd106a3" +version = "4.1.1+1" [[deps.MacroTools]] deps = ["Markdown", "Random"] -git-tree-sha1 = "3d3e902b31198a27340d0bf00d6ac452866021cf" +git-tree-sha1 = "42324d08725e200c23d4dfb549e0d5d89dede2d2" uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09" -version = "0.5.9" +version = "0.5.10" [[deps.ManualMemory]] git-tree-sha1 = "bcaef4fc7a0cfe2cba636d84cda54b5e4e4ca3cd" @@ -815,41 +828,43 @@ uuid = "d6f4376e-aef5-505a-96c1-9c027394607a" [[deps.MbedTLS]] deps = ["Dates", "MbedTLS_jll", "MozillaCACerts_jll", "Random", "Sockets"] -git-tree-sha1 = "891d3b4e8f8415f53108b4918d0183e61e18015b" +git-tree-sha1 = "03a9b9718f5682ecb107ac9f7308991db4ce395b" uuid = "739be429-bea8-5141-9913-cc70e7f3736d" -version = "1.1.0" +version = "1.1.7" [[deps.MbedTLS_jll]] deps = ["Artifacts", "Libdl"] uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1" +version = "2.28.0+0" [[deps.Measures]] -git-tree-sha1 = "e498ddeee6f9fdb4551ce855a46f54dbd900245f" +git-tree-sha1 = "c13304c81eec1ed3af7fc20e75fb6b26092a1102" uuid = "442fdcdd-2543-5da2-b0f3-8c86c306513e" -version = "0.3.1" +version = "0.3.2" [[deps.Missings]] deps = ["DataAPI"] -git-tree-sha1 = "bf210ce90b6c9eed32d25dbcae1ebc565df2687f" +git-tree-sha1 = "f66bdc5de519e8f8ae43bdc598782d35a25b1272" uuid = "e1d29d7a-bbdc-5cf2-9ac0-f12de2c33e28" -version = "1.0.2" +version = "1.1.0" [[deps.Mmap]] uuid = "a63ad114-7e13-5084-954f-fe012c677804" [[deps.MozillaCACerts_jll]] uuid = "14a3606d-f60d-562e-9121-12d972cd8159" +version = "2022.2.1" [[deps.MuladdMacro]] -git-tree-sha1 = "c6190f9a7fc5d9d5915ab29f2134421b12d24a68" +git-tree-sha1 = "cac9cc5499c25554cba55cd3c30543cff5ca4fab" uuid = "46d2c3a1-f734-5fdb-9937-b9b9aeba4221" -version = "0.2.2" +version = "0.2.4" [[deps.NLSolversBase]] deps = ["DiffResults", "Distributed", "FiniteDiff", "ForwardDiff"] -git-tree-sha1 = "50310f934e55e5ca3912fb941dec199b49ca9b68" +git-tree-sha1 = "a0b464d183da839699f4c79e7606d9d186ec172c" uuid = "d41bc354-129a-5804-8e4c-c37616107c6c" -version = "7.8.2" +version = "7.8.3" [[deps.NLsolve]] deps = ["Distances", "LineSearches", "LinearAlgebra", "NLSolversBase", "Printf", "Reexport"] @@ -858,30 +873,32 @@ uuid = "2774e3e8-f4cf-5e23-947b-6d7e65073b56" version = "4.5.1" [[deps.NaNMath]] -git-tree-sha1 = "b086b7ea07f8e38cf122f5016af580881ac914fe" +deps = ["OpenLibm_jll"] +git-tree-sha1 = "0877504529a3e5c3343c6f8b4c0381e57e4387e4" uuid = "77ba4419-2d1f-58cd-9bb1-8ffee604a2e3" -version = "0.3.7" +version = "1.0.2" [[deps.NearestNeighbors]] deps = ["Distances", "StaticArrays"] -git-tree-sha1 = "0e353ed734b1747fc20cd4cba0edd9ac027eff6a" +git-tree-sha1 = "2c3726ceb3388917602169bed973dbc97f1b51a8" uuid = "b8a86587-4115-5ab1-83bc-aa920d37bbce" -version = "0.4.11" +version = "0.4.13" [[deps.NetworkOptions]] uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908" +version = "1.2.0" [[deps.NonlinearSolve]] -deps = ["ArrayInterfaceCore", "FiniteDiff", "ForwardDiff", "IterativeSolvers", "LinearAlgebra", "RecursiveArrayTools", "RecursiveFactorization", "Reexport", "SciMLBase", "Setfield", "StaticArrays", "UnPack"] -git-tree-sha1 = "932bbdc22e6a2e0bae8dec35d32e4c8cb6c50f98" +deps = ["ArrayInterface", "DiffEqBase", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "LinearSolve", "RecursiveArrayTools", "Reexport", "SciMLBase", "SimpleNonlinearSolve", "SnoopPrecompile", "SparseArrays", "SparseDiffTools", "StaticArraysCore", "UnPack"] +git-tree-sha1 = "3f856788ba532419c07ba2e0dc37b06e5d784992" uuid = "8913a72c-1f9b-4ce2-8d82-65094dcecaec" -version = "0.3.21" +version = "1.5.0" [[deps.OffsetArrays]] deps = ["Adapt"] -git-tree-sha1 = "1ea784113a6aa054c5ebd95945fa5e52c2f378e7" +git-tree-sha1 = "82d7c9e310fe55aa54996e6f7f94674e2a38fcb4" uuid = "6fe1bfb0-de20-5000-8ca7-80f57d26f881" -version = "1.12.7" +version = "1.12.9" [[deps.Ogg_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -892,16 +909,24 @@ version = "1.3.5+1" [[deps.OpenBLAS_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "Libdl"] uuid = "4536629a-c528-5b80-bd46-f80d51c5b363" +version = "0.3.20+0" [[deps.OpenLibm_jll]] deps = ["Artifacts", "Libdl"] uuid = "05823500-19ac-5b8b-9628-191a04bc5112" +version = "0.8.1+0" + +[[deps.OpenSSL]] +deps = ["BitFlags", "Dates", "MozillaCACerts_jll", "OpenSSL_jll", "Sockets"] +git-tree-sha1 = "6503b77492fd7fcb9379bf73cd31035670e3c509" +uuid = "4d8831e6-92b7-49fb-bdf8-b643e874388c" +version = "1.3.3" [[deps.OpenSSL_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "e60321e3f2616584ff98f0a4f18d98ae6f89bbb3" +git-tree-sha1 = "9ff31d101d987eb9d66bd8b176ac7c277beccd09" uuid = "458c3c95-2e84-50aa-8efc-19380b2a3a95" -version = "1.1.17+0" +version = "1.1.20+0" [[deps.OpenSpecFun_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Pkg"] @@ -921,22 +946,21 @@ uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d" version = "1.4.1" [[deps.OrdinaryDiffEq]] -deps = ["Adapt", "ArrayInterface", "ArrayInterfaceGPUArrays", "ArrayInterfaceStaticArrays", "DataStructures", "DiffEqBase", "DocStringExtensions", "ExponentialUtilities", "FastBroadcast", "FastClosures", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "LinearSolve", "Logging", "LoopVectorization", "MacroTools", "MuladdMacro", "NLsolve", "NonlinearSolve", "Polyester", "PreallocationTools", "RecursiveArrayTools", "Reexport", "SciMLBase", "SparseArrays", "SparseDiffTools", "StaticArrays", "UnPack"] -git-tree-sha1 = "062f233b13f04aa942bd3ca831791280f57874a3" +deps = ["Adapt", "ArrayInterface", "ArrayInterfaceCore", "ArrayInterfaceGPUArrays", "ArrayInterfaceStaticArrays", "ArrayInterfaceStaticArraysCore", "DataStructures", "DiffEqBase", "DocStringExtensions", "ExponentialUtilities", "FastBroadcast", "FastClosures", "FiniteDiff", "ForwardDiff", "FunctionWrappersWrappers", "LinearAlgebra", "LinearSolve", "Logging", "LoopVectorization", "MacroTools", "MuladdMacro", "NLsolve", "NonlinearSolve", "Polyester", "PreallocationTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLNLSolve", "SimpleNonlinearSolve", "SnoopPrecompile", "SparseArrays", "SparseDiffTools", "StaticArrays", "UnPack"] +git-tree-sha1 = "295b13e65001f8e08fb6a861bdf61ade8ffc460b" uuid = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed" -version = "6.18.1" +version = "6.44.1" -[[deps.PCRE_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "b2a7af664e098055a7529ad1a900ded962bca488" -uuid = "2f80f16e-611a-54ab-bc61-aa92de5b98fc" -version = "8.44.0+0" +[[deps.PCRE2_jll]] +deps = ["Artifacts", "Libdl"] +uuid = "efcefdf7-47ab-520b-bdef-62a2eaa19f15" +version = "10.40.0+0" [[deps.PDMats]] deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] -git-tree-sha1 = "cf494dca75a69712a72b80bc48f59dcf3dea63ec" +git-tree-sha1 = "67eae2738d63117a196f497d7db789821bce61d1" uuid = "90014a1f-27ba-587c-ab20-58faa44d9150" -version = "0.11.16" +version = "0.11.17" [[deps.Parameters]] deps = ["OrderedCollections", "UnPack"] @@ -945,10 +969,15 @@ uuid = "d96e819e-fc66-5662-9728-84c9c7592b0a" version = "0.12.3" [[deps.Parsers]] -deps = ["Dates"] -git-tree-sha1 = "0044b23da09b5608b4ecacb4e5e6c6332f833a7e" +deps = ["Dates", 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"c6c0f690d0cc7caddb74cef7aa847b824a16b256" +git-tree-sha1 = "0c03844e2231e12fda4d0086fd7cbe4098ee8dc5" uuid = "ea2cea3b-5b76-57ae-a6ef-0a8af62496e1" -version = "5.15.3+1" +version = "5.15.3+2" [[deps.QuadGK]] deps = ["DataStructures", "LinearAlgebra"] -git-tree-sha1 = "78aadffb3efd2155af139781b8a8df1ef279ea39" +git-tree-sha1 = "6ec7ac8412e83d57e313393220879ede1740f9ee" uuid = "1fd47b50-473d-5c70-9696-f719f8f3bcdc" -version = "2.4.2" +version = "2.8.2" [[deps.REPL]] deps = ["InteractiveUtils", "Markdown", "Sockets", "Unicode"] @@ -1044,27 +1074,28 @@ uuid = "c84ed2f1-dad5-54f0-aa8e-dbefe2724439" version = "0.4.3" [[deps.RecipesBase]] -git-tree-sha1 = "6bf3f380ff52ce0832ddd3a2a7b9538ed1bcca7d" +deps = ["SnoopPrecompile"] +git-tree-sha1 = "261dddd3b862bd2c940cf6ca4d1c8fe593e457c8" uuid = "3cdcf5f2-1ef4-517c-9805-6587b60abb01" -version = "1.2.1" +version = "1.3.3" [[deps.RecipesPipeline]] -deps = ["Dates", "NaNMath", "PlotUtils", "RecipesBase"] -git-tree-sha1 = 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-git-tree-sha1 = "bf3188feca147ce108c76ad82c2792c57abe7b1f" +git-tree-sha1 = "f65dcb5fa46aee0cf9ed6274ccbd597adc49aa7b" uuid = "79098fc4-a85e-5d69-aa6a-4863f24498fa" -version = "0.7.0" +version = "0.7.1" [[deps.Rmath_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "68db32dff12bb6127bac73c209881191bf0efbb7" +git-tree-sha1 = "6ed52fdd3382cf21947b15e8870ac0ddbff736da" uuid = "f50d1b31-88e8-58de-be2c-1cc44531875f" -version = "0.3.0+0" +version = "0.4.0+0" + +[[deps.RuntimeGeneratedFunctions]] +deps = ["ExprTools", "SHA", "Serialization"] +git-tree-sha1 = "50314d2ef65fce648975a8e80ae6d8409ebbf835" +uuid = "7e49a35a-f44a-4d26-94aa-eba1b4ca6b47" +version = "0.5.5" [[deps.SHA]] uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" +version = "0.7.0" [[deps.SIMD]] -git-tree-sha1 = "7dbc15af7ed5f751a82bf3ed37757adf76c32402" +deps = ["SnoopPrecompile"] +git-tree-sha1 = "8b20084a97b004588125caebf418d8cab9e393d1" uuid = "fdea26ae-647d-5447-a871-4b548cad5224" -version = "3.4.1" - 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["ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "Preferences", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "SnoopPrecompile", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "TruncatedStacktraces"] +git-tree-sha1 = "4848a0542bfa419b44b57d7e016cd82479a8a27c" uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462" -version = "1.42.4" +version = "1.91.0" + +[[deps.SciMLNLSolve]] +deps = ["DiffEqBase", "LineSearches", "NLsolve", "Reexport", "SciMLBase"] +git-tree-sha1 = "66c7f901dbcad51791136e2d90ee67240256ecde" +uuid = "e9a6253c-8580-4d32-9898-8661bb511710" +version = "0.1.3" + +[[deps.SciMLOperators]] +deps = ["ArrayInterfaceCore", "DocStringExtensions", "Lazy", "LinearAlgebra", "Setfield", "SparseArrays", "StaticArraysCore", "Tricks"] +git-tree-sha1 = 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"d75bda01f8c31ebb72df80a46c88b25d1c79c56d" +git-tree-sha1 = "ef28127915f4229c971eb43f3fc075dd3fe91880" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "2.1.7" +version = "2.2.0" [[deps.Static]] deps = ["IfElse"] -git-tree-sha1 = "46638763d3a25ad7818a15d441e0c3446a10742d" +git-tree-sha1 = "08be5ee09a7632c32695d954a602df96a877bf0d" uuid = "aedffcd0-7271-4cad-89d0-dc628f76c6d3" -version = "0.7.5" +version = "0.8.6" [[deps.StaticArrays]] deps = ["LinearAlgebra", "Random", "StaticArraysCore", "Statistics"] -git-tree-sha1 = "e972716025466461a3dc1588d9168334b71aafff" +git-tree-sha1 = "6aa098ef1012364f2ede6b17bf358c7f1fbe90d4" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.5.1" +version = "1.5.17" [[deps.StaticArraysCore]] -git-tree-sha1 = "66fe9eb253f910fe8cf161953880cfdaef01cdf0" +git-tree-sha1 = "6b7ba252635a5eff6a0b0664a41ee140a1c9e72a" uuid = "1e83bf80-4336-4d27-bf5d-d5a4f845583c" -version = "1.0.1" +version = "1.4.0" [[deps.Statistics]] deps = ["LinearAlgebra", "SparseArrays"] @@ -1210,21 +1273,21 @@ uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" [[deps.StatsAPI]] deps = ["LinearAlgebra"] -git-tree-sha1 = "2c11d7290036fe7aac9038ff312d3b3a2a5bf89e" +git-tree-sha1 = "f9af7f195fb13589dd2e2d57fdb401717d2eb1f6" uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0" -version = "1.4.0" +version = "1.5.0" [[deps.StatsBase]] deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] -git-tree-sha1 = "472d044a1c8df2b062b23f222573ad6837a615ba" +git-tree-sha1 = "d1bf48bfcc554a3761a133fe3a9bb01488e06916" uuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91" -version = "0.33.19" +version = "0.33.21" [[deps.StatsFuns]] deps = ["ChainRulesCore", "HypergeometricFunctions", "InverseFunctions", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"] -git-tree-sha1 = "5783b877201a82fc0014cbf381e7e6eb130473a4" +git-tree-sha1 = "f625d686d5a88bcd2b15cd81f18f98186fdc0c9a" uuid = "4c63d2b9-4356-54db-8cca-17b64c39e42c" -version = "1.0.1" +version = "1.3.0" [[deps.StreamMacros]] deps = ["DiffEqBase", "StaticArrays", "SymEngine"] @@ -1236,15 +1299,9 @@ version = "0.2.0" [[deps.StrideArraysCore]] deps = ["ArrayInterface", "CloseOpenIntervals", "IfElse", "LayoutPointers", "ManualMemory", "SIMDTypes", "Static", "ThreadingUtilities"] -git-tree-sha1 = "ac730bd978bf35f9fe45daa0bd1f51e493e97eb4" +git-tree-sha1 = "8114ba9c3694827838d45ea3c9f6b9ccb4182cf2" uuid = "7792a7ef-975c-4747-a70f-980b88e8d1da" -version = "0.3.15" - -[[deps.StructArrays]] -deps = ["Adapt", "DataAPI", "StaticArrays", "Tables"] -git-tree-sha1 = "ec47fb6069c57f1cee2f67541bf8f23415146de7" -uuid = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" -version = "0.6.11" +version = "0.4.7" [[deps.SuiteSparse]] deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"] @@ -1253,6 +1310,7 @@ uuid = "4607b0f0-06f3-5cda-b6b1-a6196a1729e9" [[deps.SuiteSparse_jll]] deps = ["Artifacts", "Libdl", "Pkg", "libblastrampoline_jll"] uuid = "bea87d4a-7f5b-5778-9afe-8cc45184846c" +version = "5.10.1+0" [[deps.SymEngine]] deps = ["Compat", "Libdl", "LinearAlgebra", "RecipesBase", "SpecialFunctions", "SymEngine_jll"] @@ -1266,9 +1324,16 @@ git-tree-sha1 = "3cd0f249ae20a0093f839738a2f2c1476d5581fe" uuid = "3428059b-622b-5399-b16f-d347a77089a4" version = "0.8.1+0" +[[deps.SymbolicIndexingInterface]] +deps = ["DocStringExtensions"] +git-tree-sha1 = "f8ab052bfcbdb9b48fad2c80c873aa0d0344dfe5" +uuid = "2efcf032-c050-4f8e-a9bb-153293bab1f5" +version = "0.2.2" + [[deps.TOML]] deps = ["Dates"] uuid = "fa267f1f-6049-4f14-aa54-33bafae1ed76" +version = "1.0.0" [[deps.TableTraits]] deps = ["IteratorInterfaceExtensions"] @@ -1278,13 +1343,14 @@ version = "1.0.1" [[deps.Tables]] deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "LinearAlgebra", "OrderedCollections", "TableTraits", "Test"] -git-tree-sha1 = "5ce79ce186cc678bbb5c5681ca3379d1ddae11a1" +git-tree-sha1 = "1544b926975372da01227b382066ab70e574a3ec" uuid = "bd369af6-aec1-5ad0-b16a-f7cc5008161c" -version = "1.7.0" +version = "1.10.1" [[deps.Tar]] deps = ["ArgTools", "SHA"] uuid = "a4e569a6-e804-4fa4-b0f3-eef7a1d5b13e" +version = "1.10.1" [[deps.TensorCore]] deps = ["LinearAlgebra"] @@ -1293,10 +1359,10 @@ uuid = "62fd8b95-f654-4bbd-a8a5-9c27f68ccd50" version = "0.1.1" [[deps.Tensors]] -deps = ["ForwardDiff", "LinearAlgebra", "SIMD", "StaticArrays", "Statistics"] -git-tree-sha1 = "d04564923243e1c306369fb6df9b6792fd0818c4" +deps = ["ForwardDiff", "LinearAlgebra", "SIMD", "SnoopPrecompile", "StaticArrays", "Statistics"] +git-tree-sha1 = "71f054343e85ab1eab12bf8336004309002ff82d" uuid = "48a634ad-e948-5137-8d70-aa71f2a747f4" -version = "1.11.0" +version = "1.13.1" [[deps.Test]] deps = ["InteractiveUtils", "Logging", "Random", "Serialization"] @@ -1304,32 +1370,37 @@ uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40" [[deps.ThreadingUtilities]] deps = ["ManualMemory"] -git-tree-sha1 = "f8629df51cab659d70d2e5618a430b4d3f37f2c3" +git-tree-sha1 = "c97f60dd4f2331e1a495527f80d242501d2f9865" uuid = "8290d209-cae3-49c0-8002-c8c24d57dab5" -version = "0.5.0" +version = "0.5.1" [[deps.TranscodingStreams]] deps = ["Random", "Test"] -git-tree-sha1 = "216b95ea110b5972db65aa90f88d8d89dcb8851c" +git-tree-sha1 = "94f38103c984f89cf77c402f2a68dbd870f8165f" uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa" -version = "0.9.6" - -[[deps.TreeViews]] -deps = ["Test"] -git-tree-sha1 = "8d0d7a3fe2f30d6a7f833a5f19f7c7a5b396eae6" -uuid = "a2a6695c-b41b-5b7d-aed9-dbfdeacea5d7" -version = "0.3.0" +version = "0.9.11" [[deps.TriangularSolve]] deps = ["CloseOpenIntervals", "IfElse", "LayoutPointers", "LinearAlgebra", "LoopVectorization", "Polyester", "Static", "VectorizationBase"] -git-tree-sha1 = "caf797b6fccbc0d080c44b4cb2319faf78c9d058" +git-tree-sha1 = "31eedbc0b6d07c08a700e26d31298ac27ef330eb" uuid = "d5829a12-d9aa-46ab-831f-fb7c9ab06edf" -version = "0.1.12" +version = "0.1.19" + +[[deps.Tricks]] +git-tree-sha1 = "6bac775f2d42a611cdfcd1fb217ee719630c4175" +uuid = "410a4b4d-49e4-4fbc-ab6d-cb71b17b3775" +version = "0.1.6" + +[[deps.TruncatedStacktraces]] +deps = ["InteractiveUtils", "MacroTools", "Preferences"] +git-tree-sha1 = "6901000d75a14520bdd067fe90b9392384eb04a7" +uuid = "781d530d-4396-4725-bb49-402e4bee1e77" +version = "1.2.0" [[deps.URIs]] -git-tree-sha1 = "97bbe755a53fe859669cd907f2d96aee8d2c1355" +git-tree-sha1 = "074f993b0ca030848b897beff716d93aca60f06a" uuid = "5c2747f8-b7ea-4ff2-ba2e-563bfd36b1d4" -version = "1.3.0" +version = "1.4.2" [[deps.UUIDs]] deps = ["Random", "SHA"] @@ -1350,15 +1421,15 @@ uuid = "1cfade01-22cf-5700-b092-accc4b62d6e1" version = "0.4.1" [[deps.Unzip]] -git-tree-sha1 = "34db80951901073501137bdbc3d5a8e7bbd06670" +git-tree-sha1 = "ca0969166a028236229f63514992fc073799bb78" uuid = "41fe7b60-77ed-43a1-b4f0-825fd5a5650d" -version = "0.1.2" +version = "0.2.0" [[deps.VectorizationBase]] deps = ["ArrayInterface", "CPUSummary", "HostCPUFeatures", "IfElse", "LayoutPointers", "Libdl", "LinearAlgebra", "SIMDTypes", "Static"] -git-tree-sha1 = "953ba1475022a4de16439857a8f79831abf5fa30" +git-tree-sha1 = "4c59c2df8d2676c4691a39fa70495a6db0c5d290" uuid = "3d5dd08c-fd9d-11e8-17fa-ed2836048c2f" -version = "0.21.42" +version = "0.21.58" [[deps.VertexSafeGraphs]] deps = ["Graphs"] @@ -1374,9 +1445,9 @@ version = "0.4.3" [[deps.Wayland_jll]] deps = ["Artifacts", "Expat_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Pkg", "XML2_jll"] -git-tree-sha1 = "3e61f0b86f90dacb0bc0e73a0c5a83f6a8636e23" +git-tree-sha1 = "ed8d92d9774b077c53e1da50fd81a36af3744c1c" uuid = "a2964d1f-97da-50d4-b82a-358c7fce9d89" -version = "1.19.0+0" +version = "1.21.0+0" [[deps.Wayland_protocols_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -1392,15 +1463,15 @@ version = "0.5.5" [[deps.WriteVTK]] deps = ["Base64", "CodecZlib", "FillArrays", "LightXML", "TranscodingStreams"] -git-tree-sha1 = "8c1e15c8c5b2b69648d2d5c89a1ede519199a0e6" +git-tree-sha1 = "49353f30da65f377cff0f934bb9f562a2c0441b9" uuid = "64499a7a-5c06-52f2-abe2-ccb03c286192" -version = "1.14.3" +version = "1.17.1" [[deps.XML2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "58443b63fb7e465a8a7210828c91c08b92132dff" +git-tree-sha1 = "93c41695bc1c08c46c5899f4fe06d6ead504bb73" uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a" -version = "2.9.14+0" +version = "2.10.3+0" [[deps.XSLT_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgcrypt_jll", "Libgpg_error_jll", "Libiconv_jll", "Pkg", "XML2_jll", "Zlib_jll"] @@ -1537,12 +1608,13 @@ version = "1.4.0+3" [[deps.Zlib_jll]] deps = ["Libdl"] uuid = "83775a58-1f1d-513f-b197-d71354ab007a" +version = "1.2.12+3" [[deps.Zstd_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "e45044cd873ded54b6a5bac0eb5c971392cf1927" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "c6edfe154ad7b313c01aceca188c05c835c67360" uuid = "3161d3a3-bdf6-5164-811a-617609db77b4" -version = "1.5.2+0" +version = "1.5.4+0" [[deps.ZygoteRules]] deps = ["MacroTools"] @@ -1550,6 +1622,12 @@ git-tree-sha1 = "8c1a8e4dfacb1fd631745552c8db35d0deb09ea0" uuid = "700de1a5-db45-46bc-99cf-38207098b444" version = "0.2.2" +[[deps.fzf_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "868e669ccb12ba16eaf50cb2957ee2ff61261c56" +uuid = "214eeab7-80f7-51ab-84ad-2988db7cef09" +version = "0.29.0+0" + [[deps.libaom_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] git-tree-sha1 = "3a2ea60308f0996d26f1e5354e10c24e9ef905d4" @@ -1565,6 +1643,7 @@ version = "0.15.1+0" [[deps.libblastrampoline_jll]] deps = ["Artifacts", "Libdl", "OpenBLAS_jll"] uuid = "8e850b90-86db-534c-a0d3-1478176c7d93" +version = "5.1.1+0" [[deps.libfdk_aac_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -1587,10 +1666,12 @@ version = "1.3.7+1" [[deps.nghttp2_jll]] deps = ["Artifacts", "Libdl"] uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d" +version = "1.48.0+0" [[deps.p7zip_jll]] deps = ["Artifacts", "Libdl"] uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0" +version = "17.4.0+0" [[deps.x264_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -1606,6 +1687,6 @@ version = "3.5.0+0" [[deps.xkbcommon_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Wayland_jll", "Wayland_protocols_jll", "Xorg_libxcb_jll", "Xorg_xkeyboard_config_jll"] -git-tree-sha1 = "ece2350174195bb31de1a63bea3a41ae1aa593b6" +git-tree-sha1 = "9ebfc140cc56e8c2156a15ceac2f0302e327ac0a" uuid = "d8fb68d0-12a3-5cfd-a85a-d49703b185fd" -version = "0.9.1+5" +version = "1.4.1+0" diff --git a/docs/Project.toml b/docs/Project.toml index 5d4242fe..e68b0031 100644 --- a/docs/Project.toml +++ b/docs/Project.toml @@ -1,5 +1,4 @@ [deps] -Arpack = "7d9fca2a-8960-54d3-9f78-7d1dccf2cb97" Clustering = "aaaa29a8-35af-508c-8bc3-b662a17a0fe5" CoherentStructures = "0c1513b4-3a13-56f1-9cd2-8312eaec88c4" Dates = "ade2ca70-3891-5945-98fb-dc099432e06a" @@ -18,14 +17,15 @@ StreamMacros = "1418a599-1564-4a75-98e9-b890cf8b552f" Tensors = "48a634ad-e948-5137-8d70-aa71f2a747f4" [compat] -Arpack = "0.4" Clustering = "0.13, 0.14" Distances = "0.10" Documenter = "0.24, 0.25, 0.26, 0.27" -Interpolations = "0.13" +Interpolations = "0.13, 0.14" JLD2 = "0.1.11, 0.2, 0.3, 0.4" Literate = "2.2.1" OrdinaryDiffEq = "6.2" Plots = "0.29, 1" StaticArrays = "1.1" +StreamMacros = "0.2" Tensors = "1.8" +julia = "1.6" diff --git a/docs/examples/abc.jl b/docs/examples/abc.jl index dfd811e2..1d2cd7b9 100644 --- a/docs/examples/abc.jl +++ b/docs/examples/abc.jl @@ -1,5 +1,4 @@ using CoherentStructures -using Arpack using Plots @@ -12,7 +11,7 @@ bdata = BoundaryData(abcctx, bdata_predicate) cgfun = x-> mean_diff_tensor(abcFlow, x, [0.0,1.0], 1.e-10, p=(√3,√2,1), tolerance=1.e-3) @time M = assembleMassMatrix(abcctx, bdata=bdata); @time K = assembleStiffnessMatrix(abcctx, cgfun, bdata=bdata) -@time λ, V = eigs(K, M, which=:SM, nev=10) #This takes really long! +@time λ, V = CoherentStructures.get_smallest_eigenpairs(K, M, 10) #This takes really long! plot_real_spectrum(λ) diff --git a/docs/examples/bickley.jl b/docs/examples/bickley.jl index fc15212a..8af04243 100644 --- a/docs/examples/bickley.jl +++ b/docs/examples/bickley.jl @@ -84,12 +84,11 @@ bdata = BoundaryData(ctx, predicate, []); # Using a FEM-based method to compute coherent structures: -using Arpack cgfun = x -> mean_diff_tensor(bickley, x, range(0.0, stop=40*3600*24, length=81), 1.e-8; tolerance=1e-5) K = assembleStiffnessMatrix(ctx, cgfun, bdata=bdata) M = assembleMassMatrix(ctx, bdata=bdata) -λ, v = eigs(K, M, which=:SM, nev= 10) +λ, v = CoherentStructures.get_smallest_eigenpairs(K, M, 10) import Plots fig_spectrum = plot_real_spectrum(λ) diff --git a/docs/examples/ocean_flow.jl b/docs/examples/ocean_flow.jl index 914382d3..b97a47a4 100644 --- a/docs/examples/ocean_flow.jl +++ b/docs/examples/ocean_flow.jl @@ -35,7 +35,7 @@ nprocs() == 1 && addprocs() # Next, we load and interpolate the velocity data sets. using JLD2 -xs, ys, ts, us, vs = load(OCEAN_FLOW_FILE, "Lon", "Lat", "Time", "UT", "VT") +xs, ys, ts, us, vs = load("docs/examples/Ocean_geostrophic_velocity.jld2", "Lon", "Lat", "Time", "UT", "VT") const uv = interpolateVF(xs, ys, ts, us, vs) # Now, we set up the computational problem. @@ -170,9 +170,7 @@ S = applyBCS(ctx, 0.5(S0 + S1), bdata); # We can now solve the eigenproblem. -using Arpack - -λ, v = eigs(S, M, which=:SM, nev=6); +λ, v = CoherentStructures.get_smallest_eigenpairs(S, M, 6); # We upsample the eigenfunctions and then cluster. diff --git a/docs/examples/rot_double_gyre.jl b/docs/examples/rot_double_gyre.jl index 0eccfec4..dbe618ae 100644 --- a/docs/examples/rot_double_gyre.jl +++ b/docs/examples/rot_double_gyre.jl @@ -41,14 +41,14 @@ end # # The following code demonstrates how to use these methods. -using CoherentStructures, Arpack +using CoherentStructures LL, UR = (0.0, 0.0), (1.0, 1.0) ctx, _ = regularTriangularGrid((50, 50), LL, UR) A = x -> mean_diff_tensor(rot_double_gyre, x, [0.0, 1.0], 1.e-10, tolerance= 1.e-4) K = assembleStiffnessMatrix(ctx, A) M = assembleMassMatrix(ctx) -λ, v = eigs(-K, M, which=:SM); +λ, v = CoherentStructures.get_smallest_eigenpairs(-K, M, 6); # This velocity field is given by the `rot_double_gyre` function. The third # argument to `mean_diff_tensor` is a vector of time instances at which we evaluate diff --git a/docs/examples/standard_map.jl b/docs/examples/standard_map.jl index 5713eb43..8ba9d09f 100644 --- a/docs/examples/standard_map.jl +++ b/docs/examples/standard_map.jl @@ -45,7 +45,7 @@ DISPLAY_PLOT(fig, standard_map_orbits) # Approximating the Dynamic Laplacian by FEM methods is straightforward: -using Arpack, CoherentStructures, Distances, Tensors +using CoherentStructures, Distances, Tensors Df(x) = Tensor{2,2}((1.0+a*cos(x[1]), a*cos(x[1]), 1.0, 1.0)) @@ -60,7 +60,7 @@ cg(x) = 0.5*(I + dott(inv(Df2(x)))) # avg. inv. Cauchy-Green tensor K = assembleStiffnessMatrix(ctx, cg, bdata=bd) M = assembleMassMatrix(ctx, bdata=bd) -λ, v = eigs(K, M, which=:SM) +λ, v = CoherentStructures.get_smallest_eigenpairs(K, M, 6) using Printf title = [ @sprintf("\\lambda = %.3f", λ[i]) for i = 1:4 ] diff --git a/docs/examples/trajectories.jl b/docs/examples/trajectories.jl index 4abb9887..e8c99c9f 100644 --- a/docs/examples/trajectories.jl +++ b/docs/examples/trajectories.jl @@ -196,9 +196,7 @@ ctx, _ = irregularDelaunayGrid(particles) S = adaptiveTOCollocationStiffnessMatrix(ctx, (i, ts) -> trajectories[i], ts; flow_map_mode=1) M = assembleMassMatrix(ctx) - -using Arpack -λ, V = eigs(S, M; which=:SM, nev=6) +λ, V = CoherentStructures.get_smallest_eigenpairs(S, M, 6) # We can plot the computed spectrum. diff --git a/docs/src/fem.md b/docs/src/fem.md index 089cc3d2..614e7667 100644 --- a/docs/src/fem.md +++ b/docs/src/fem.md @@ -292,5 +292,5 @@ plot_ftle ```julia const default_quadrature_order=5 -const default_solver = OrdinaryDiffEq.BS5() +const default_solver = OrdinaryDiffEq.Tsit5() ``` diff --git a/docs/src/index.md b/docs/src/index.md index e1a9ec71..785716fa 100644 --- a/docs/src/index.md +++ b/docs/src/index.md @@ -8,8 +8,8 @@ It has been developed in [Oliver Junge](https://www-m3.ma.tum.de/Allgemeines/OliverJunge)'s research group at TUM, Germany, by (in alphabetical order) * Alvaro de Diego ([@adediego](https://github.com/adediego)) -* [Oliver Junge](https://www-m3.ma.tum.de/Allgemeines/OliverJunge) ([@gaioguy](https://github.com/gaioguy)) -* [Daniel Karrasch](https://www-m3.ma.tum.de/Allgemeines/DanielKarrasch) ([@dkarrasch](https://github.com/dkarrasch)) +* [Oliver Junge](https://www.math.cit.tum.de/math/personen/professuren/junge-oliver/) ([@gaioguy](https://github.com/gaioguy)) +* Daniel Karrasch ([@dkarrasch](https://github.com/dkarrasch)) * Nathanael Schilling ([@natschil](https://github.com/natschil)) Contributions from colleagues in the field are most welcome via raising issues or, even better, via pull requests. diff --git a/src/CoherentStructures.jl b/src/CoherentStructures.jl index 35840a4c..6ff9e2e6 100644 --- a/src/CoherentStructures.jl +++ b/src/CoherentStructures.jl @@ -16,6 +16,7 @@ using Tensors: Vec, Tensor, SymmetricTensor, basevec, dott, tdot, otimes, unsafe using AxisArrays: AxisArray, ClosedInterval, axisvalues # using DiffEqBase: DiffEqBase, initialize!, isconstant, update_coefficients!, @.. +using SciMLBase using OrdinaryDiffEq: ODEProblem, ODEFunction, ContinuousCallback, terminate!, solve, Tsit5 # using OrdinaryDiffEq: OrdinaryDiffEqNewtonAlgorithm, DEFAULT_LINSOLVE, # alg_order, OrdinaryDiffEqMutableCache, alg_cache, @muladd, perform_step!, @unpack, @@ -30,7 +31,7 @@ using Interpolations: Interpolations, LinearInterpolation, CubicSplineInterpolat interpolate, scale, BSpline, Linear, Cubic, Natural, OnGrid, Free # import linear algebra related packages -using LinearMaps: LinearMap +using LinearMaps: LinearMap, FunctionMap using IterativeSolvers: cg using ArnoldiMethod: partialschur, partialeigen diff --git a/src/advection_diffusion.jl b/src/advection_diffusion.jl index 8fb52f61..0b9f569b 100644 --- a/src/advection_diffusion.jl +++ b/src/advection_diffusion.jl @@ -4,7 +4,7 @@ # meta function """ - FEM_heatflow(velocity!, ctx, tspan, κ, p=nothing, bdata=BoundaryData(); + FEM_heatflow(velocity!, ctx, tspan, κ, p=SciMLBase.NullParameters(), bdata=BoundaryData(); factor=true, δ=1e-6, solver=default_solver, tolerance=default_tolerance) Compute the heat flow operator for the time-dependent heat equation, which @@ -25,7 +25,7 @@ employing a spatial FEM discretization and temporal implicit-Euler time stepping * `solver`, `tolerance`: are passed to `advect_serialized_quadpoints`. """ # TODO: Restrict tspan to be of Range/linspace type -function FEM_heatflow(odefun!, ctx::GridContext, tspan, κ::Real, p=nothing, bdata=BoundaryData(); +function FEM_heatflow(odefun!, ctx::GridContext, tspan, κ::Real, p=SciMLBase.NullParameters(), bdata=BoundaryData(); factor::Bool=true, δ=1e-6, solver=default_solver, tolerance=default_tolerance) sol = advect_serialized_quadpoints(ctx, tspan, odefun!, p, δ; solver=solver, tolerance=tolerance) @@ -76,24 +76,22 @@ end """ - advect_serialized_quadpoints(ctx, tspan, odefun!, p=nothing, δ=1e-9; + advect_serialized_quadpoints(ctx, tspan, odefun!, p=SciMLBase.NullParameters(), δ=1e-9; solver=default_solver, tolerance=default_tolerance) Advect all quadrature points + finite difference stencils of size `δ`, from `tspan[1]` to `tspan[end]` with ODE rhs given by `odefun!`, whose parameters are contained in `p`. Returns an ODE solution object. """ -function advect_serialized_quadpoints(ctx::GridContext, tspan, odefun!, p=nothing, δ=1e-9; +function advect_serialized_quadpoints(ctx::GridContext, tspan, odefun!, p=SciMLBase.NullParameters(), δ=1e-9; solver=default_solver, tolerance=default_tolerance) u0 = setup_fd_quadpoints_serialized(ctx, δ) - p2 = Dict("ctx" => ctx, "p" => p) - prob = ODEProblem{true}( (du, u, p, t) -> large_rhs(odefun!, du, u, p, t), u0, (tspan[1], tspan[end]), - p2) + (ctx, p)) return solve(prob, solver, abstol=tolerance, reltol=tolerance) end @@ -113,8 +111,8 @@ function stiffnessMatrixTimeT(ctx, sol, t, δ=1e-9; bdata=BoundaryData()) end @inline function large_rhs(odefun!, du, u, p, t) - n_quadpoints = length(p["ctx"].quadrature_points) - @views arraymap!(du, u, p["p"], t, odefun!, 4n_quadpoints, 2) + n_quadpoints = length(p[1].quadrature_points) + @views arraymap!(du, u, p[2], t, odefun!, 4n_quadpoints, 2) end """ diff --git a/src/ellipticLCS.jl b/src/ellipticLCS.jl index 708500d1..a0b6cec8 100644 --- a/src/ellipticLCS.jl +++ b/src/ellipticLCS.jl @@ -689,7 +689,7 @@ function compute_returning_orbit(vf::ODEFunction, seed, save = false, maxiters = return (sol.u, sol.retcode) catch e if e isa BoundsError - return ([typeof(seed)(NaN, NaN)], :BoundsError) + return ([typeof(seed)(NaN, NaN)], ReturnCode.Failure) end rethrow(e) end @@ -705,7 +705,7 @@ function Poincaré_return_distance(vf, seed, save = false; tolerance_ode = 1e-8, max_orbit_length, ) # check if result due to callback - if retcode === :Terminated + if retcode === ReturnCode.Terminated return sol[end][1] - seed[1] else return eltype(seed)(NaN) @@ -826,7 +826,7 @@ function compute_closed_orbits(ps::AbstractVector{<:SVector{2}}, ηfield, cache; p.tolerance_ode, p.max_orbit_length, ) - if retcode === :Terminated + if retcode === ReturnCode.Terminated closed = norm(orbit[1] - orbit[end]) <= p.rdist if cache isa LCScache in_well_defined_squares = @@ -1500,7 +1500,7 @@ function materialbarriersTensors( lcsp; δ = 1e-6, tolerance = 1e-6, - p = nothing, + p = SciMLBase.NullParameters(), kwargs..., ) P0 = AxisArray(SVector{2}.(xspan, yspan'), xspan, yspan) @@ -1520,7 +1520,7 @@ end """ materialbarriers(odefun, xspan, yspan, tspan, lcsp; - on_torus=false, δ=1e-6, tolerance=1e-6, p=nothing, kwargs...) + on_torus=false, δ=1e-6, tolerance=1e-6, p=SciMLBase.NullParameters(), kwargs...) Calculate material barriers to diffusive and stochastic transport on the material domain spanned by `xspan` and `yspan`, where the averaged weighted CG tensor is computed at the @@ -1528,7 +1528,7 @@ time instance contained in `tspan`. The argument `lcsp` must be of type [`LCSParameters`](@ref), and contains parameters used for the elliptic vortex detection. """ function materialbarriers(odefun, xspan, yspan, tspan, lcsp; - δ = 1e-6, tolerance = 1e-6, p = nothing, on_torus = false, kwargs...) + δ = 1e-6, tolerance = 1e-6, p = SciMLBase.NullParameters(), on_torus = false, kwargs...) T0 = materialbarriersTensors( odefun, xspan, diff --git a/src/gridfunctions.jl b/src/gridfunctions.jl index 6a41db3d..17fd0c63 100644 --- a/src/gridfunctions.jl +++ b/src/gridfunctions.jl @@ -153,7 +153,7 @@ function GridContext{1}(::Type{FEM.Line}, loc = Regular1dGridLocator{FEM.Line}(numnodes[1], Vec{1}((LL[1],)), Vec{1}((UR[1],))) dh = FEM.DofHandler(grid) - push!(dh, :T, 1, ip) #The :T is just a generic name for the scalar field + FEM.add!(dh, :T, 1, ip) #The :T is just a generic name for the scalar field FEM.close!(dh) qr = FEM.QuadratureRule{1, FEM.RefCube}(quadrature_order) @@ -186,7 +186,7 @@ function GridContext{1}(::Type{FEM.QuadraticLine}, loc = Regular1dGridLocator{FEM.QuadraticLine}(numnodes[1], Vec{1}((LL[1],)), Vec{1}((UR[1],))) dh = FEM.DofHandler(grid) qr = FEM.QuadratureRule{1, FEM.RefCube}(quadrature_order) - push!(dh, :T, 1) #The :T is just a generic name for the scalar field + FEM.add!(dh, :T, 1) #The :T is just a generic name for the scalar field FEM.close!(dh) result = GridContext{1}(grid, ip, FEM.Lagrange{1,FEM.RefCube,2}(), dh, qr, loc; kwargs...) result.spatialBounds = (LL, UR) @@ -327,7 +327,7 @@ function GridContext{2}( on_torus=on_torus, on_cylinder=on_cylinder, LL=LL, UR=UR) dh = FEM.DofHandler(grid) qr = FEM.QuadratureRule{2, FEM.RefTetrahedron}(quadrature_order) - push!(dh, :T, 1, ip) #The :T is just a generic name for the scalar field + FEM.add!(dh, :T, 1, ip) #The :T is just a generic name for the scalar field FEM.close!(dh) result = GridContext{2}(grid, ip, FEM.Lagrange{2,FEM.RefTetrahedron,1}(), dh, qr, loc; kwargs...) if ip isa FEM.Lagrange @@ -472,7 +472,7 @@ function GridContext{2}( grid, loc = FEM.generate_grid(FEM.QuadraticTriangle, node_list) dh = FEM.DofHandler(grid) qr = FEM.QuadratureRule{2, FEM.RefTetrahedron}(quadrature_order) - push!(dh, :T, 1,ip) #The :T is just a generic name for the scalar field + FEM.add!(dh, :T, 1,ip) #The :T is just a generic name for the scalar field FEM.close!(dh) result = GridContext{2}(grid, ip,FEM.Lagrange{2,FEM.RefTetrahedron,2}(), dh, qr, loc;kwargs...) result.gridType = "irregular P2 Delaunay grid" @@ -519,7 +519,7 @@ function GridContext{2}(::Type{FEM.Triangle}, loc = Regular2DGridLocator{FEM.Triangle}(numnodes[1], numnodes[2], Vec{2}((LL[1], LL[2])), Vec{2}((UR[1], UR[2]))) dh = FEM.DofHandler(grid) qr = FEM.QuadratureRule{2, FEM.RefTetrahedron}(quadrature_order) - push!(dh, :T, 1, ip) #The :T is just a generic name for the scalar field + FEM.add!(dh, :T, 1, ip) #The :T is just a generic name for the scalar field FEM.close!(dh) result = GridContext{2}(grid, ip, FEM.Lagrange{2,FEM.RefTetrahedron,1}(), dh, qr, loc; kwargs...) result.spatialBounds = ((LL[1], LL[2]), (UR[1], UR[2])) @@ -571,7 +571,7 @@ function GridContext{2}(::Type{FEM.QuadraticTriangle}, loc = Regular2DGridLocator{FEM.QuadraticTriangle}(numnodes[1], numnodes[2], Vec{2}((LL[1], LL[2])), Vec{2}((UR[1], UR[2]))) dh = FEM.DofHandler(grid) qr = FEM.QuadratureRule{2, FEM.RefTetrahedron}(quadrature_order) - push!(dh, :T, 1, ip) #The :T is just a generic name for the scalar field + FEM.add!(dh, :T, 1, ip) #The :T is just a generic name for the scalar field FEM.close!(dh) result = GridContext{2}(grid, ip, FEM.Lagrange{2,FEM.RefTetrahedron,2}(), dh, qr, loc; kwargs...) result.spatialBounds = (LL, UR) @@ -612,7 +612,7 @@ function GridContext{2}(::Type{FEM.Quadrilateral}, loc = Regular2DGridLocator{FEM.Quadrilateral}(numnodes[1], numnodes[2], Vec{2}((LL[1], LL[2])), Vec{2}((UR[1], UR[2]))) dh = FEM.DofHandler(grid) qr = FEM.QuadratureRule{2, FEM.RefCube}(quadrature_order) - push!(dh, :T, 1,ip) #The :T is just a generic name for the scalar field + FEM.add!(dh, :T, 1,ip) #The :T is just a generic name for the scalar field FEM.close!(dh) result = GridContext{2}(grid, ip,FEM.Lagrange{2,FEM.RefCube,1}(), dh, qr, loc; kwargs...) result.spatialBounds = (LL, UR) @@ -670,7 +670,7 @@ function GridContext{2}(::Type{FEM.QuadraticQuadrilateral}, loc = Regular2DGridLocator{FEM.QuadraticQuadrilateral}(numnodes[1], numnodes[2], Vec{2}((LL[1], LL[2])), Vec{2}((UR[1], UR[2]))) dh = FEM.DofHandler(grid) qr = FEM.QuadratureRule{2, FEM.RefCube}(quadrature_order) - push!(dh, :T, 1,ip) #The :T is just a generic name for the scalar field + FEM.add!(dh, :T, 1,ip) #The :T is just a generic name for the scalar field FEM.close!(dh) result = GridContext{2}(grid, ip,FEM.Lagrange{2,FEM.RefCube,2}(), dh, qr, loc;kwargs...) result.spatialBounds = (LL, UR) @@ -711,7 +711,7 @@ function GridContext{3}(::Type{FEM.Tetrahedron}, loc = Regular3DGridLocator{FEM.Tetrahedron}(numnodes[1], numnodes[2], numnodes[3], Vec{3}((LL[1], LL[2], LL[3])), Vec{3}((UR[1], UR[2], UR[3]))) dh = FEM.DofHandler(grid) qr = FEM.QuadratureRule{3, FEM.RefTetrahedron}(quadrature_order) - push!(dh, :T, 1,ip) #The :T is just a generic name for the scalar field + FEM.add!(dh, :T, 1,ip) #The :T is just a generic name for the scalar field FEM.close!(dh) result = GridContext{3}(grid, ip,FEM.Lagrange{3,FEM.RefTetrahedron,1}(), dh, qr, loc;kwargs...) result.spatialBounds = (LL, UR) @@ -745,7 +745,7 @@ function GridContext{3}(::Type{FEM.QuadraticTetrahedron}, loc = Regular3DGridLocator{FEM.QuadraticTetrahedron}(numnodes[1], numnodes[2], numnodes[3], Vec{3}((LL[1], LL[2], LL[3])), Vec{3}((UR[1], UR[2], UR[3]))) dh = FEM.DofHandler(grid) qr = FEM.QuadratureRule{3, FEM.RefTetrahedron}(quadrature_order) - push!(dh, :T, 1,ip) #The :T is just a generic name for the scalar field + FEM.add!(dh, :T, 1,ip) #The :T is just a generic name for the scalar field FEM.close!(dh) result = GridContext{3}(grid, ip,FEM.Lagrange{3,FEM.RefTetrahedron,2}(), dh, qr, loc;kwargs...) result.spatialBounds = (LL, UR) diff --git a/src/plotting.jl b/src/plotting.jl index 28f3227e..bc3c5b6f 100644 --- a/src/plotting.jl +++ b/src/plotting.jl @@ -494,7 +494,7 @@ RecipesBase.@userplot Plot_FTLE RecipesBase.@recipe function f( as::Plot_FTLE; tolerance=1e-4, - solver=BS5(), + solver=Tsit5(), # existing_plot=nothing, TODO 1.0 flip_y=false, check_inbounds=always_true, @@ -569,7 +569,7 @@ end """ plot_ftle(odefun, p, tspan, LL, UR, nx, ny; - δ=1e-9, tolerance=1e-4, solver=OrdinaryDiffEq.BS5(), + δ=1e-9, tolerance=1e-4, solver=OrdinaryDiffEq.Tsit5(), existing_plot=nothing, flip_y=false, check_inbounds=always_true, pass_on_errors=false) Make a heatmap of a FTLE field using finite differences. If `existing_plot` is diff --git a/src/pullbacktensors.jl b/src/pullbacktensors.jl index 6f8965df..6cee8d3c 100644 --- a/src/pullbacktensors.jl +++ b/src/pullbacktensors.jl @@ -41,7 +41,7 @@ end odefun::ODEFunction, u0::T, tspan; - p = nothing, + p = SciMLBase.NullParameters(), solver = default_solver, tolerance = default_tolerance, #ctx_for_boundscheck=nothing, @@ -106,7 +106,7 @@ function linearized_flow( δ; tolerance=default_tolerance, solver=default_solver, - p=nothing, + p=SciMLBase.NullParameters(), )::Tuple{Vector{T},Vector{<:Tensor{2,2}}} where {iip,T<:SVector{2}} @inbounds if iip if δ != 0 # use finite differencing @@ -167,7 +167,7 @@ function linearized_flow( δ; tolerance=default_tolerance, solver=default_solver, - p=nothing, + p=SciMLBase.NullParameters(), )::Tuple{Vector{T},Vector{<:Tensor{2,3}}} where {iip,T<:SVector{3}} @inbounds if iip if δ != 0 # use finite differencing diff --git a/src/util.jl b/src/util.jl index f77708c5..51ba9b04 100644 --- a/src/util.jl +++ b/src/util.jl @@ -195,6 +195,29 @@ function cubicinterp(x1, x2, x3, x4) return x2 + p*d32 + eta*n end +struct ShiftAndInvert{TA,TB,TT} + A_fact::TA + B::TB + temp::TT +end + +function (M::ShiftAndInvert)(x) + mul!(M.temp, M.B, x) + # ldiv!(y, M.A_fact, M.temp) # CHOLMOD doesn't have an ldiv! + return M.A_fact \ M.temp +end + +function construct_linear_map(A,B) + a = ShiftAndInvert(factorize(A), B, Vector{eltype(A)}(undef, size(A, 1))) + FunctionMap{eltype(A),false}(a, size(A, 1)) +end + +function get_smallest_eigenpairs(A, B, nev) + decomp, = partialschur(construct_linear_map(A, B), nev=nev) + λs_inv, X = partialeigen(decomp) + return reverse(1 ./ λs_inv), reverse(X, dims=2) +end + """ dof2node(ctx,u) diff --git a/test/test_elliptic.jl b/test/test_elliptic.jl index 86210441..4b5b51a3 100644 --- a/test/test_elliptic.jl +++ b/test/test_elliptic.jl @@ -1,5 +1,5 @@ using Test, CoherentStructures -using StaticArrays, OrdinaryDiffEq, LinearAlgebra, AxisArrays +using StaticArrays, OrdinaryDiffEq, LinearAlgebra, AxisArrays, SciMLBase const CS = CoherentStructures @testset "singularities" begin @@ -88,7 +88,7 @@ end vf(λ) = OrdinaryDiffEq.ODEFunction{false}((u, p, t) -> (Ω - (1.0 - λ) * I) * u) seed = SVector{2}(rand(), 0) ret, info = @inferred CS.compute_returning_orbit(vf(1.0), seed) - @test info === :Terminated + @test info === SciMLBase.ReturnCode.Terminated @test ret[1] ≈ seed d = @inferred CS.Poincaré_return_distance(vf(1.0), seed) @test d ≈ 0 atol = 1e-5 diff --git a/test/test_fem.jl b/test/test_fem.jl index d3da90d3..5811202b 100644 --- a/test/test_fem.jl +++ b/test/test_fem.jl @@ -1,4 +1,5 @@ -using CoherentStructures, Test, Tensors, Arpack, Random, Distances +using CoherentStructures, Test, Tensors, LinearAlgebra, LinearMaps, Random, Distances +using CoherentStructures: get_smallest_eigenpairs @testset "1d grid piecewise_linear" begin ctx, _ = @inferred regular1dP1Grid(3) @@ -81,9 +82,9 @@ end ctx, _ = @inferred grid(200) M = @inferred assemble(Mass(), ctx) K = @inferred assemble(Stiffness(), ctx) - λ, v = eigs(-K, M, which = :SM, nev = 6) + λ, = get_smallest_eigenpairs(-K, M, 6) @test λ[1] ≈ 0 atol = √eps() - @test λ[2:end] ≈ λᵢ[2:end] rtol = 1e-3 + @test λ[2:end] ≈ λᵢ[2:end] rtol = 1e-2 end end @@ -94,7 +95,7 @@ end ctx, _ = @inferred grid(200) M = @inferred assemble(Mass(), ctx; bdata = getHomDBCS(ctx)) K = @inferred assemble(Stiffness(), ctx; bdata = getHomDBCS(ctx)) - λ, v = eigs(-K, M, which = :SM, nev = 6) + λ, = get_smallest_eigenpairs(-K, M, 6) @test λ ≈ λᵢ rtol = 1e-3 end end @@ -152,9 +153,6 @@ end ) D = 0.5 * (S + T) - λ, v = eigs(D, M; which = :SM, nev = 12) - - #Some tests to see nothing changed - @test abs(λ[2] - (-1.3)) < 1e-1 - @test abs(λ[2] - λ[3]) < 1e-1 + λ, = get_smallest_eigenpairs(D, M, 3) + @test all(<(sqrt(eps())), λ) end