diff --git a/extra/Manifest.toml b/extra/Manifest.toml index 2568c0a..e19d92c 100644 --- a/extra/Manifest.toml +++ b/extra/Manifest.toml @@ -2,7 +2,12 @@ julia_version = "1.9.0" manifest_format = "2.0" -project_hash = "c2d6b8d509c28c0a45b4666f22950ffd19be6dda" +project_hash = "6e0892593020fbee926aa667f72677d6c75e8979" + +[[deps.ADTypes]] +git-tree-sha1 = "332e5d7baeff8497b923b730b994fa480601efc7" +uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b" +version = "0.2.5" [[deps.AbstractFFTs]] deps = ["LinearAlgebra"] @@ -24,6 +29,25 @@ git-tree-sha1 = "793501dcd3fa7ce8d375a2c878dca2296232686e" uuid = "6e696c72-6542-2067-7265-42206c756150" version = "1.2.2" +[[deps.Accessors]] +deps = ["CompositionsBase", "ConstructionBase", "Dates", "InverseFunctions", "LinearAlgebra", "MacroTools", "Test"] +git-tree-sha1 = "a7055b939deae2455aa8a67491e034f735dd08d3" +uuid = "7d9f7c33-5ae7-4f3b-8dc6-eff91059b697" +version = "0.1.33" + + [deps.Accessors.extensions] + AccessorsAxisKeysExt = "AxisKeys" + AccessorsIntervalSetsExt = "IntervalSets" + AccessorsStaticArraysExt = "StaticArrays" + AccessorsStructArraysExt = "StructArrays" + + [deps.Accessors.weakdeps] + AxisKeys = "94b1ba4f-4ee9-5380-92f1-94cde586c3c5" + IntervalSets = "8197267c-284f-5f27-9208-e0e47529a953" + Requires = "ae029012-a4dd-5104-9daa-d747884805df" + StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" + StructArrays = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" + [[deps.Adapt]] deps = ["LinearAlgebra", "Requires"] git-tree-sha1 = "02f731463748db57cc2ebfbd9fbc9ce8280d3433" @@ -38,6 +62,12 @@ weakdeps = ["StaticArrays"] uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f" version = "1.1.1" +[[deps.ArnoldiMethod]] +deps = ["LinearAlgebra", "Random", "StaticArrays"] +git-tree-sha1 = "62e51b39331de8911e4a7ff6f5aaf38a5f4cc0ae" +uuid = "ec485272-7323-5ecc-a04f-4719b315124d" +version = "0.2.0" + [[deps.Arpack]] deps = ["Arpack_jll", "Libdl", "LinearAlgebra", "Logging"] git-tree-sha1 = "9b9b347613394885fd1c8c7729bfc60528faa436" @@ -50,6 +80,28 @@ git-tree-sha1 = "5ba6c757e8feccf03a1554dfaf3e26b3cfc7fd5e" uuid = "68821587-b530-5797-8361-c406ea357684" version = "3.5.1+1" +[[deps.ArrayInterface]] +deps = ["Adapt", "LinearAlgebra", "Requires", "SparseArrays", "SuiteSparse"] +git-tree-sha1 = "247efbccf92448be332d154d6ca56b9fcdd93c31" +uuid = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9" +version = "7.6.1" + + [deps.ArrayInterface.extensions] + ArrayInterfaceBandedMatricesExt = "BandedMatrices" + ArrayInterfaceBlockBandedMatricesExt = "BlockBandedMatrices" + ArrayInterfaceCUDAExt = "CUDA" + ArrayInterfaceGPUArraysCoreExt = "GPUArraysCore" + 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" + GPUArraysCore = "46192b85-c4d5-4398-a991-12ede77f4527" + StaticArraysCore = "1e83bf80-4336-4d27-bf5d-d5a4f845583c" + Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" + [[deps.Artifacts]] uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" @@ -61,12 +113,24 @@ git-tree-sha1 = "2dc09997850d68179b69dafb58ae806167a32b1b" uuid = "d1d4a3ce-64b1-5f1a-9ba4-7e7e69966f35" version = "0.1.8" +[[deps.BitTwiddlingConvenienceFunctions]] +deps = ["Static"] +git-tree-sha1 = "0c5f81f47bbbcf4aea7b2959135713459170798b" +uuid = "62783981-4cbd-42fc-bca8-16325de8dc4b" +version = "0.1.5" + [[deps.Bzip2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] git-tree-sha1 = "19a35467a82e236ff51bc17a3a44b69ef35185a2" uuid = "6e34b625-4abd-537c-b88f-471c36dfa7a0" version = "1.0.8+0" +[[deps.CPUSummary]] +deps = ["CpuId", "IfElse", "PrecompileTools", "Static"] +git-tree-sha1 = "601f7e7b3d36f18790e2caf83a882d88e9b71ff1" +uuid = "2a0fbf3d-bb9c-48f3-b0a9-814d99fd7ab9" +version = "0.2.4" + [[deps.Cairo_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" @@ -85,6 +149,12 @@ git-tree-sha1 = "a0d0d0372dbc00735bce1976928094acedfdbf8e" uuid = "ae650224-84b6-46f8-82ea-d812ca08434e" version = "2.0.3" +[[deps.CloseOpenIntervals]] +deps = ["Static", "StaticArrayInterface"] +git-tree-sha1 = "70232f82ffaab9dc52585e0dd043b5e0c6b714f1" +uuid = "fb6a15b2-703c-40df-9091-08a04967cfa9" +version = "0.1.12" + [[deps.CodeTracking]] deps = ["InteractiveUtils", "UUIDs"] git-tree-sha1 = "c0216e792f518b39b22212127d4a84dc31e4e386" @@ -125,6 +195,17 @@ git-tree-sha1 = "fc08e5930ee9a4e03f84bfb5211cb54e7769758a" uuid = "5ae59095-9a9b-59fe-a467-6f913c188581" version = "0.12.10" +[[deps.CommonSolve]] +git-tree-sha1 = "0eee5eb66b1cf62cd6ad1b460238e60e4b09400c" +uuid = "38540f10-b2f7-11e9-35d8-d573e4eb0ff2" +version = "0.2.4" + +[[deps.CommonSubexpressions]] +deps = ["MacroTools", "Test"] +git-tree-sha1 = "7b8a93dba8af7e3b42fecabf646260105ac373f7" +uuid = "bbf7d656-a473-5ed7-a52c-81e309532950" +version = "0.3.0" + [[deps.Compat]] deps = ["UUIDs"] git-tree-sha1 = "886826d76ea9e72b35fcd000e535588f7b60f21d" @@ -140,6 +221,20 @@ deps = ["Artifacts", "Libdl"] uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae" version = "1.0.2+0" +[[deps.CompositionsBase]] +git-tree-sha1 = "802bb88cd69dfd1509f6670416bd4434015693ad" +uuid = "a33af91c-f02d-484b-be07-31d278c5ca2b" +version = "0.1.2" +weakdeps = ["InverseFunctions"] + + [deps.CompositionsBase.extensions] + CompositionsBaseInverseFunctionsExt = "InverseFunctions" + +[[deps.ConcreteStructs]] +git-tree-sha1 = "f749037478283d372048690eb3b5f92a79432b34" +uuid = "2569d6c7-a4a2-43d3-a901-331e8e4be471" +version = "0.2.3" + [[deps.ConcurrentUtilities]] deps = ["Serialization", "Sockets"] git-tree-sha1 = "8cfa272e8bdedfa88b6aefbbca7c19f1befac519" @@ -171,6 +266,12 @@ git-tree-sha1 = "d05d9e7b7aedff4e5b51a029dced05cfb6125781" uuid = "d38c429a-6771-53c6-b99e-75d170b6e991" version = "0.6.2" +[[deps.CpuId]] +deps = ["Markdown"] +git-tree-sha1 = "fcbb72b032692610bfbdb15018ac16a36cf2e406" +uuid = "adafc99b-e345-5852-983c-f28acb93d879" +version = "0.3.1" + [[deps.DataAPI]] git-tree-sha1 = "8da84edb865b0b5b0100c0666a9bc9a0b71c553c" uuid = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a" @@ -197,6 +298,62 @@ git-tree-sha1 = "9e2f36d3c96a820c678f2f1f1782582fcf685bae" uuid = "8bb1440f-4735-579b-a4ab-409b98df4dab" version = "1.9.1" +[[deps.DiffEqBase]] +deps = ["ArrayInterface", "DataStructures", "DocStringExtensions", "EnumX", "EnzymeCore", "FastBroadcast", "ForwardDiff", "FunctionWrappers", "FunctionWrappersWrappers", "LinearAlgebra", "Logging", "Markdown", "MuladdMacro", "Parameters", "PreallocationTools", "PrecompileTools", "Printf", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "Setfield", "SparseArrays", "Static", "StaticArraysCore", "Statistics", "Tricks", "TruncatedStacktraces"] +git-tree-sha1 = "309efb205c30d43b595466283bbecf2769283e22" +uuid = "2b5f629d-d688-5b77-993f-72d75c75574e" +version = "6.141.0" + + [deps.DiffEqBase.extensions] + DiffEqBaseChainRulesCoreExt = "ChainRulesCore" + DiffEqBaseDistributionsExt = "Distributions" + DiffEqBaseEnzymeExt = ["ChainRulesCore", "Enzyme"] + DiffEqBaseGeneralizedGeneratedExt = "GeneralizedGenerated" + DiffEqBaseMPIExt = "MPI" + DiffEqBaseMeasurementsExt = "Measurements" + DiffEqBaseMonteCarloMeasurementsExt = "MonteCarloMeasurements" + DiffEqBaseReverseDiffExt = "ReverseDiff" + DiffEqBaseTrackerExt = "Tracker" + DiffEqBaseUnitfulExt = "Unitful" + + [deps.DiffEqBase.weakdeps] + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" + Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f" + Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" + GeneralizedGenerated = "6b9d7cbe-bcb9-11e9-073f-15a7a543e2eb" + MPI = "da04e1cc-30fd-572f-bb4f-1f8673147195" + Measurements = "eff96d63-e80a-5855-80a2-b1b0885c5ab7" + MonteCarloMeasurements = "0987c9cc-fe09-11e8-30f0-b96dd679fdca" + ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" + Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" + Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d" + +[[deps.DiffResults]] +deps = ["StaticArraysCore"] +git-tree-sha1 = "782dd5f4561f5d267313f23853baaaa4c52ea621" +uuid = "163ba53b-c6d8-5494-b064-1a9d43ac40c5" +version = "1.1.0" + +[[deps.DiffRules]] +deps = ["IrrationalConstants", "LogExpFunctions", "NaNMath", "Random", "SpecialFunctions"] +git-tree-sha1 = "23163d55f885173722d1e4cf0f6110cdbaf7e272" +uuid = "b552c78f-8df3-52c6-915a-8e097449b14b" +version = "1.15.1" + +[[deps.Distances]] +deps = ["LinearAlgebra", "Statistics", "StatsAPI"] +git-tree-sha1 = "66c4c81f259586e8f002eacebc177e1fb06363b0" +uuid = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7" +version = "0.10.11" + + [deps.Distances.extensions] + DistancesChainRulesCoreExt = "ChainRulesCore" + DistancesSparseArraysExt = "SparseArrays" + + [deps.Distances.weakdeps] + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" + SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" + [[deps.Distributed]] deps = ["Random", "Serialization", "Sockets"] uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b" @@ -234,6 +391,17 @@ git-tree-sha1 = "5837a837389fccf076445fce071c8ddaea35a566" uuid = "fa6b7ba4-c1ee-5f82-b5fc-ecf0adba8f74" version = "0.6.8" +[[deps.EnumX]] +git-tree-sha1 = "bdb1942cd4c45e3c678fd11569d5cccd80976237" +uuid = "4e289a0a-7415-4d19-859d-a7e5c4648b56" +version = "1.0.4" + +[[deps.EnzymeCore]] +deps = ["Adapt"] +git-tree-sha1 = "2efe862de93cd87f620ad6ac9c9e3f83f1b2841b" +uuid = "f151be2c-9106-41f4-ab19-57ee4f262869" +version = "0.6.4" + [[deps.EpollShim_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] git-tree-sha1 = "8e9441ee83492030ace98f9789a654a6d0b1f643" @@ -252,6 +420,12 @@ git-tree-sha1 = "4558ab818dcceaab612d1bb8c19cee87eda2b83c" uuid = "2e619515-83b5-522b-bb60-26c02a35a201" version = "2.5.0+0" +[[deps.ExponentialUtilities]] +deps = ["Adapt", "ArrayInterface", "GPUArraysCore", "GenericSchur", "LinearAlgebra", "PrecompileTools", "Printf", "SparseArrays", "libblastrampoline_jll"] +git-tree-sha1 = "602e4585bcbd5a25bc06f514724593d13ff9e862" +uuid = "d4d017d3-3776-5f7e-afef-a10c40355c18" +version = "1.25.0" + [[deps.ExprTools]] git-tree-sha1 = "27415f162e6028e81c72b82ef756bf321213b6ec" uuid = "e2ba6199-217a-4e67-a87a-7c52f15ade04" @@ -286,12 +460,29 @@ git-tree-sha1 = "c6033cc3892d0ef5bb9cd29b7f2f0331ea5184ea" uuid = "f5851436-0d7a-5f13-b9de-f02708fd171a" version = "3.3.10+0" +[[deps.FastBroadcast]] +deps = ["ArrayInterface", "LinearAlgebra", "Polyester", "Static", "StaticArrayInterface", "StrideArraysCore"] +git-tree-sha1 = "a6e756a880fc419c8b41592010aebe6a5ce09136" +uuid = "7034ab61-46d4-4ed7-9d0f-46aef9175898" +version = "0.2.8" + +[[deps.FastClosures]] +git-tree-sha1 = "acebe244d53ee1b461970f8910c235b259e772ef" +uuid = "9aa1b823-49e4-5ca5-8b0f-3971ec8bab6a" +version = "0.3.2" + [[deps.FastGaussQuadrature]] deps = ["LinearAlgebra", "SpecialFunctions", "StaticArrays"] git-tree-sha1 = "0f478d8bad6f52573fb7658a263af61f3d96e43a" uuid = "442a2c76-b920-505d-bb47-c5924d526838" version = "0.5.1" +[[deps.FastLapackInterface]] +deps = ["LinearAlgebra"] +git-tree-sha1 = "b12f05108e405dadcc2aff0008db7f831374e051" +uuid = "29a986be-02c6-4525-aec4-84b980013641" +version = "2.0.0" + [[deps.FileWatching]] uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" @@ -307,6 +498,22 @@ weakdeps = ["PDMats", "SparseArrays", "Statistics"] FillArraysSparseArraysExt = "SparseArrays" FillArraysStatisticsExt = "Statistics" +[[deps.FiniteDiff]] +deps = ["ArrayInterface", "LinearAlgebra", "Requires", "Setfield", "SparseArrays"] +git-tree-sha1 = "c6e4a1fbe73b31a3dea94b1da449503b8830c306" +uuid = "6a86dc24-6348-571c-b903-95158fe2bd41" +version = "2.21.1" + + [deps.FiniteDiff.extensions] + FiniteDiffBandedMatricesExt = "BandedMatrices" + FiniteDiffBlockBandedMatricesExt = "BlockBandedMatrices" + FiniteDiffStaticArraysExt = "StaticArrays" + + [deps.FiniteDiff.weakdeps] + BandedMatrices = "aae01518-5342-5314-be14-df237901396f" + BlockBandedMatrices = "ffab5731-97b5-5995-9138-79e8c1846df0" + StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" + [[deps.FixedPointNumbers]] deps = ["Statistics"] git-tree-sha1 = "335bfdceacc84c5cdf16aadc768aa5ddfc5383cc" @@ -325,6 +532,16 @@ git-tree-sha1 = "8339d61043228fdd3eb658d86c926cb282ae72a8" uuid = "59287772-0a20-5a39-b81b-1366585eb4c0" version = "0.4.2" +[[deps.ForwardDiff]] +deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "LinearAlgebra", "LogExpFunctions", "NaNMath", "Preferences", "Printf", "Random", "SpecialFunctions"] +git-tree-sha1 = "cf0fe81336da9fb90944683b8c41984b08793dad" +uuid = "f6369f11-7733-5829-9624-2563aa707210" +version = "0.10.36" +weakdeps = ["StaticArrays"] + + [deps.ForwardDiff.extensions] + ForwardDiffStaticArraysExt = "StaticArrays" + [[deps.FreeType2_jll]] deps = ["Artifacts", "Bzip2_jll", "JLLWrappers", "Libdl", "Zlib_jll"] git-tree-sha1 = "d8db6a5a2fe1381c1ea4ef2cab7c69c2de7f9ea0" @@ -337,6 +554,21 @@ git-tree-sha1 = "aa31987c2ba8704e23c6c8ba8a4f769d5d7e4f91" uuid = "559328eb-81f9-559d-9380-de523a88c83c" version = "1.0.10+0" +[[deps.FunctionWrappers]] +git-tree-sha1 = "d62485945ce5ae9c0c48f124a84998d755bae00e" +uuid = "069b7b12-0de2-55c6-9aab-29f3d0a68a2e" +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"] +uuid = "9fa8497b-333b-5362-9e8d-4d0656e87820" + [[deps.FuzzyCompletions]] deps = ["REPL"] git-tree-sha1 = "c8d37d615586bea181063613dccc555499feb298" @@ -373,6 +605,12 @@ git-tree-sha1 = "055849d7a602c31eda477a0b0b86c9473a3e4fb9" uuid = "e4b2fa32-6e09-5554-b718-106ed5adafe9" version = "2.2.4" +[[deps.GenericSchur]] +deps = ["LinearAlgebra", "Printf"] +git-tree-sha1 = "fb69b2a645fa69ba5f474af09221b9308b160ce6" +uuid = "c145ed77-6b09-5dd9-b285-bf645a82121e" +version = "0.5.3" + [[deps.Gettext_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "XML2_jll"] git-tree-sha1 = "9b02998aba7bf074d14de89f9d37ca24a1a0b046" @@ -391,6 +629,12 @@ git-tree-sha1 = "344bf40dcab1073aca04aa0df4fb092f920e4011" uuid = "3b182d85-2403-5c21-9c21-1e1f0cc25472" version = "1.3.14+0" +[[deps.Graphs]] +deps = ["ArnoldiMethod", "Compat", "DataStructures", "Distributed", "Inflate", "LinearAlgebra", "Random", "SharedArrays", "SimpleTraits", "SparseArrays", "Statistics"] +git-tree-sha1 = "899050ace26649433ef1af25bc17a815b3db52b7" +uuid = "86223c79-3864-5bf0-83f7-82e725a168b6" +version = "1.9.0" + [[deps.Grisu]] git-tree-sha1 = "53bb909d1151e57e2484c3d1b53e19552b887fb2" uuid = "42e2da0e-8278-4e71-bc24-59509adca0fe" @@ -420,6 +664,12 @@ git-tree-sha1 = "129acf094d168394e80ee1dc4bc06ec835e510a3" uuid = "2e76f6c2-a576-52d4-95c1-20adfe4de566" version = "2.8.1+1" +[[deps.HostCPUFeatures]] +deps = ["BitTwiddlingConvenienceFunctions", "IfElse", "Libdl", "Static"] +git-tree-sha1 = "eb8fed28f4994600e29beef49744639d985a04b2" +uuid = "3e5b6fbb-0976-4d2c-9146-d79de83f2fb0" +version = "0.1.16" + [[deps.Hwloc_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] git-tree-sha1 = "8ecb0b34472a3c98f945e3c75fc7d5428d165511" @@ -450,6 +700,21 @@ git-tree-sha1 = "d75853a0bdbfb1ac815478bacd89cd27b550ace6" uuid = "b5f81e59-6552-4d32-b1f0-c071b021bf89" version = "0.2.3" +[[deps.IfElse]] +git-tree-sha1 = "debdd00ffef04665ccbb3e150747a77560e8fad1" +uuid = "615f187c-cbe4-4ef1-ba3b-2fcf58d6d173" +version = "0.1.1" + +[[deps.Inflate]] +git-tree-sha1 = "ea8031dea4aff6bd41f1df8f2fdfb25b33626381" +uuid = "d25df0c9-e2be-5dd7-82c8-3ad0b3e990b9" +version = "0.1.4" + +[[deps.IntegerMathUtils]] +git-tree-sha1 = "b8ffb903da9f7b8cf695a8bead8e01814aa24b30" +uuid = "18e54dd8-cb9d-406c-a71d-865a43cbb235" +version = "0.1.2" + [[deps.IntelOpenMP_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] git-tree-sha1 = "ad37c091f7d7daf900963171600d7c1c5c3ede32" @@ -460,6 +725,12 @@ version = "2023.2.0+0" deps = ["Markdown"] uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240" +[[deps.InverseFunctions]] +deps = ["Test"] +git-tree-sha1 = "68772f49f54b479fa88ace904f6127f0a3bb2e46" +uuid = "3587e190-3f89-42d0-90ee-14403ec27112" +version = "0.1.12" + [[deps.IrrationalConstants]] git-tree-sha1 = "630b497eafcc20001bba38a4651b327dcfc491d2" uuid = "92d709cd-6900-40b7-9082-c6be49f344b6" @@ -500,6 +771,18 @@ git-tree-sha1 = "e49bce680c109bc86e3e75ebcb15040d6ad9e1d3" uuid = "aa1ae85d-cabe-5617-a682-6adf51b2e16a" version = "0.9.27" +[[deps.KLU]] +deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse_jll"] +git-tree-sha1 = "884c2968c2e8e7e6bf5956af88cb46aa745c854b" +uuid = "ef3ab10e-7fda-4108-b977-705223b18434" +version = "0.4.1" + +[[deps.Krylov]] +deps = ["LinearAlgebra", "Printf", "SparseArrays"] +git-tree-sha1 = "17e462054b42dcdda73e9a9ba0c67754170c88ae" +uuid = "ba0b0d4f-ebba-5204-a429-3ac8c609bfb7" +version = "0.9.4" + [[deps.LAME_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] git-tree-sha1 = "f6250b16881adf048549549fba48b1161acdac8c" @@ -543,11 +826,29 @@ version = "0.16.1" DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" SymEngine = "123dc426-2d89-5057-bbad-38513e3affd8" +[[deps.LatticeRules]] +deps = ["Random"] +git-tree-sha1 = "7f5b02258a3ca0221a6a9710b0a0a2e8fb4957fe" +uuid = "73f95e8e-ec14-4e6a-8b18-0d2e271c4e55" +version = "0.0.1" + +[[deps.LayoutPointers]] +deps = ["ArrayInterface", "LinearAlgebra", "ManualMemory", "SIMDTypes", "Static", "StaticArrayInterface"] +git-tree-sha1 = "62edfee3211981241b57ff1cedf4d74d79519277" +uuid = "10f19ff3-798f-405d-979b-55457f8fc047" +version = "0.1.15" + [[deps.LazilyInitializedFields]] git-tree-sha1 = "8f7f3cabab0fd1800699663533b6d5cb3fc0e612" uuid = "0e77f7df-68c5-4e49-93ce-4cd80f5598bf" version = "1.2.2" +[[deps.Lazy]] +deps = ["MacroTools"] +git-tree-sha1 = "1370f8202dac30758f3c345f9909b97f53d87d3f" +uuid = "50d2b5c4-7a5e-59d5-8109-a42b560f39c0" +version = "0.15.1" + [[deps.LazyArtifacts]] deps = ["Artifacts", "Pkg"] uuid = "4af54fe1-eca0-43a8-85a7-787d91b784e3" @@ -622,10 +923,50 @@ git-tree-sha1 = "7f3efec06033682db852f8b3bc3c1d2b0a0ab066" uuid = "38a345b3-de98-5d2b-a5d3-14cd9215e700" version = "2.36.0+0" +[[deps.LineSearches]] +deps = ["LinearAlgebra", "NLSolversBase", "NaNMath", "Parameters", "Printf"] +git-tree-sha1 = "7bbea35cec17305fc70a0e5b4641477dc0789d9d" +uuid = "d3d80556-e9d4-5f37-9878-2ab0fcc64255" +version = "7.2.0" + [[deps.LinearAlgebra]] deps = ["Libdl", "OpenBLAS_jll", "libblastrampoline_jll"] uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" +[[deps.LinearSolve]] +deps = ["ArrayInterface", "ConcreteStructs", "DocStringExtensions", "EnumX", "EnzymeCore", "FastLapackInterface", "GPUArraysCore", "InteractiveUtils", "KLU", "Krylov", "Libdl", "LinearAlgebra", "MKL_jll", "PrecompileTools", "Preferences", "RecursiveFactorization", "Reexport", "Requires", "SciMLBase", "SciMLOperators", "Setfield", "SparseArrays", "Sparspak", "UnPack"] +git-tree-sha1 = "051943b8b8e81c548e9d099d6eb3d3ed23093c35" +uuid = "7ed4a6bd-45f5-4d41-b270-4a48e9bafcae" +version = "2.20.0" + + [deps.LinearSolve.extensions] + LinearSolveBandedMatricesExt = "BandedMatrices" + LinearSolveBlockDiagonalsExt = "BlockDiagonals" + LinearSolveCUDAExt = "CUDA" + LinearSolveEnzymeExt = "Enzyme" + LinearSolveFastAlmostBandedMatricesExt = ["FastAlmostBandedMatrices"] + LinearSolveHYPREExt = "HYPRE" + LinearSolveIterativeSolversExt = "IterativeSolvers" + LinearSolveKernelAbstractionsExt = "KernelAbstractions" + LinearSolveKrylovKitExt = "KrylovKit" + LinearSolveMetalExt = "Metal" + LinearSolvePardisoExt = "Pardiso" + LinearSolveRecursiveArrayToolsExt = "RecursiveArrayTools" + + [deps.LinearSolve.weakdeps] + BandedMatrices = "aae01518-5342-5314-be14-df237901396f" + BlockDiagonals = "0a1fb500-61f7-11e9-3c65-f5ef3456f9f0" + CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" + Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" + FastAlmostBandedMatrices = "9d29842c-ecb8-4973-b1e9-a27b1157504e" + HYPRE = "b5ffcf37-a2bd-41ab-a3da-4bd9bc8ad771" + IterativeSolvers = "42fd0dbc-a981-5370-80f2-aaf504508153" + KernelAbstractions = "63c18a36-062a-441e-b654-da1e3ab1ce7c" + KrylovKit = "0b1a1467-8014-51b9-945f-bf0ae24f4b77" + Metal = "dde4c033-4e86-420c-a63e-0dd931031962" + Pardiso = "46dd5b70-b6fb-5a00-ae2d-e8fea33afaf2" + RecursiveArrayTools = "731186ca-8d62-57ce-b412-fbd966d074cd" + [[deps.LogExpFunctions]] deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] git-tree-sha1 = "7d6dd4e9212aebaeed356de34ccf262a3cd415aa" @@ -651,6 +992,21 @@ git-tree-sha1 = "c1dd6d7978c12545b4179fb6153b9250c96b0075" uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" version = "1.0.3" +[[deps.LoopVectorization]] +deps = ["ArrayInterface", "CPUSummary", "CloseOpenIntervals", "DocStringExtensions", "HostCPUFeatures", "IfElse", "LayoutPointers", "LinearAlgebra", "OffsetArrays", "PolyesterWeave", "PrecompileTools", "SIMDTypes", "SLEEFPirates", "Static", "StaticArrayInterface", "ThreadingUtilities", "UnPack", "VectorizationBase"] +git-tree-sha1 = "0f5648fbae0d015e3abe5867bca2b362f67a5894" +uuid = "bdcacae8-1622-11e9-2a5c-532679323890" +version = "0.12.166" + + [deps.LoopVectorization.extensions] + ForwardDiffExt = ["ChainRulesCore", "ForwardDiff"] + SpecialFunctionsExt = "SpecialFunctions" + + [deps.LoopVectorization.weakdeps] + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" + ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210" + SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b" + [[deps.LoweredCodeUtils]] deps = ["JuliaInterpreter"] git-tree-sha1 = "c165f205e030208760ebd75b5e1f7706761d9218" @@ -712,6 +1068,11 @@ git-tree-sha1 = "18cf4151e390fce29ca846b92b06baf9bc6e002e" uuid = "36869731-bdee-424d-aa32-cab38c994e3b" version = "1.1.1" +[[deps.ManualMemory]] +git-tree-sha1 = "bcaef4fc7a0cfe2cba636d84cda54b5e4e4ca3cd" +uuid = "d125e4d3-2237-4719-b19c-fa641b8a4667" +version = "0.1.8" + [[deps.Markdown]] deps = ["Base64"] uuid = "d6f4376e-aef5-505a-96c1-9c027394607a" @@ -757,6 +1118,23 @@ git-tree-sha1 = "fc8c15ca848b902015bd4a745d350f02cf791c2a" uuid = "99f44e22-a591-53d1-9472-aa23ef4bd671" version = "1.2.0" +[[deps.MuladdMacro]] +git-tree-sha1 = "cac9cc5499c25554cba55cd3c30543cff5ca4fab" +uuid = "46d2c3a1-f734-5fdb-9937-b9b9aeba4221" +version = "0.2.4" + +[[deps.NLSolversBase]] +deps = ["DiffResults", "Distributed", "FiniteDiff", "ForwardDiff"] +git-tree-sha1 = "a0b464d183da839699f4c79e7606d9d186ec172c" +uuid = "d41bc354-129a-5804-8e4c-c37616107c6c" +version = "7.8.3" + +[[deps.NLsolve]] +deps = ["Distances", "LineSearches", "LinearAlgebra", "NLSolversBase", "Printf", "Reexport"] +git-tree-sha1 = "019f12e9a1a7880459d0173c182e6a99365d7ac1" +uuid = "2774e3e8-f4cf-5e23-947b-6d7e65073b56" +version = "4.5.1" + [[deps.NaNMath]] deps = ["OpenLibm_jll"] git-tree-sha1 = "0877504529a3e5c3343c6f8b4c0381e57e4387e4" @@ -767,6 +1145,28 @@ version = "1.0.2" uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908" version = "1.2.0" +[[deps.NonlinearSolve]] +deps = ["ADTypes", "ArrayInterface", "ConcreteStructs", "DiffEqBase", "EnumX", "FastBroadcast", "FiniteDiff", "ForwardDiff", "LineSearches", "LinearAlgebra", "LinearSolve", "PrecompileTools", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SimpleNonlinearSolve", "SparseArrays", "SparseDiffTools", "StaticArraysCore", "UnPack"] +git-tree-sha1 = "6166ccd8f79c93c636ca61ab4cd18f555932563d" +uuid = "8913a72c-1f9b-4ce2-8d82-65094dcecaec" +version = "2.8.2" + + [deps.NonlinearSolve.extensions] + NonlinearSolveBandedMatricesExt = "BandedMatrices" + NonlinearSolveFastLevenbergMarquardtExt = "FastLevenbergMarquardt" + NonlinearSolveLeastSquaresOptimExt = "LeastSquaresOptim" + + [deps.NonlinearSolve.weakdeps] + BandedMatrices = "aae01518-5342-5314-be14-df237901396f" + FastLevenbergMarquardt = "7a0df574-e128-4d35-8cbd-3d84502bf7ce" + LeastSquaresOptim = "0fc2ff8b-aaa3-5acd-a817-1944a5e08891" + +[[deps.OffsetArrays]] +deps = ["Adapt"] +git-tree-sha1 = "2ac17d29c523ce1cd38e27785a7d23024853a4bb" +uuid = "6fe1bfb0-de20-5000-8ca7-80f57d26f881" +version = "1.12.10" + [[deps.Ogg_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] git-tree-sha1 = "887579a3eb005446d514ab7aeac5d1d027658b8f" @@ -818,6 +1218,12 @@ git-tree-sha1 = "dfdf5519f235516220579f949664f1bf44e741c5" uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d" version = "1.6.3" +[[deps.OrdinaryDiffEq]] +deps = ["ADTypes", "Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "ExponentialUtilities", "FastBroadcast", "FastClosures", "FiniteDiff", "ForwardDiff", "FunctionWrappersWrappers", "IfElse", "InteractiveUtils", "LineSearches", "LinearAlgebra", "LinearSolve", "Logging", "LoopVectorization", "MacroTools", "MuladdMacro", "NLsolve", "NonlinearSolve", "Polyester", "PreallocationTools", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLNLSolve", "SciMLOperators", "SimpleNonlinearSolve", "SimpleUnPack", "SparseArrays", "SparseDiffTools", "StaticArrayInterface", "StaticArrays", "TruncatedStacktraces"] +git-tree-sha1 = "5f9e7ce227d0e447c3803cc05ef5d8f75f84b9ea" +uuid = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed" +version = "6.59.3" + [[deps.PCRE2_jll]] deps = ["Artifacts", "Libdl"] uuid = "efcefdf7-47ab-520b-bdef-62a2eaa19f15" @@ -835,6 +1241,18 @@ git-tree-sha1 = "8b3b19351fa24791f94d7ae85faf845ca1362541" uuid = "32165bc3-0280-59bc-8c0b-c33b6203efab" version = "4.2.7+0" +[[deps.PackageExtensionCompat]] +git-tree-sha1 = "fb28e33b8a95c4cee25ce296c817d89cc2e53518" +uuid = "65ce6f38-6b18-4e1d-a461-8949797d7930" +version = "1.0.2" +weakdeps = ["Requires", "TOML"] + +[[deps.Parameters]] +deps = ["OrderedCollections", "UnPack"] +git-tree-sha1 = "34c0e9ad262e5f7fc75b10a9952ca7692cfc5fbe" +uuid = "d96e819e-fc66-5662-9728-84c9c7592b0a" +version = "0.12.3" + [[deps.Parsers]] deps = ["Dates", "PrecompileTools", "UUIDs"] git-tree-sha1 = "a935806434c9d4c506ba941871b327b96d41f2bf" @@ -925,6 +1343,30 @@ git-tree-sha1 = "bd7c69c7f7173097e7b5e1be07cee2b8b7447f51" uuid = "7f904dfe-b85e-4ff6-b463-dae2292396a8" version = "0.7.54" +[[deps.Polyester]] +deps = ["ArrayInterface", "BitTwiddlingConvenienceFunctions", "CPUSummary", "IfElse", "ManualMemory", "PolyesterWeave", "Requires", "Static", "StaticArrayInterface", "StrideArraysCore", "ThreadingUtilities"] +git-tree-sha1 = "fca25670784a1ae44546bcb17288218310af2778" +uuid = "f517fe37-dbe3-4b94-8317-1923a5111588" +version = "0.7.9" + +[[deps.PolyesterWeave]] +deps = ["BitTwiddlingConvenienceFunctions", "CPUSummary", "IfElse", "Static", "ThreadingUtilities"] +git-tree-sha1 = "240d7170f5ffdb285f9427b92333c3463bf65bf6" +uuid = "1d0040c9-8b98-4ee7-8388-3f51789ca0ad" +version = "0.2.1" + +[[deps.PreallocationTools]] +deps = ["Adapt", "ArrayInterface", "ForwardDiff", "Requires"] +git-tree-sha1 = "f739b1b3cc7b9949af3b35089931f2b58c289163" +uuid = "d236fae5-4411-538c-8e31-a6e3d9e00b46" +version = "0.4.12" + + [deps.PreallocationTools.extensions] + PreallocationToolsReverseDiffExt = "ReverseDiff" + + [deps.PreallocationTools.weakdeps] + ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" + [[deps.PrecompileSignatures]] git-tree-sha1 = "18ef344185f25ee9d51d80e179f8dad33dc48eb1" uuid = "91cefc8d-f054-46dc-8f8c-26e11d7c5411" @@ -942,6 +1384,12 @@ git-tree-sha1 = "00805cd429dcb4870060ff49ef443486c262e38e" uuid = "21216c6a-2e73-6563-6e65-726566657250" version = "1.4.1" +[[deps.Primes]] +deps = ["IntegerMathUtils"] +git-tree-sha1 = "1d05623b5952aed1307bf8b43bec8b8d1ef94b6e" +uuid = "27ebfcd6-29c5-5fa9-bf4b-fb8fc14df3ae" +version = "0.5.5" + [[deps.Printf]] deps = ["Unicode"] uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7" @@ -958,6 +1406,16 @@ git-tree-sha1 = "9ebcd48c498668c7fa0e97a9cae873fbee7bfee1" uuid = "1fd47b50-473d-5c70-9696-f719f8f3bcdc" version = "2.9.1" +[[deps.QuasiMonteCarlo]] +deps = ["Accessors", "ConcreteStructs", "LatticeRules", "LinearAlgebra", "Primes", "Random", "Requires", "Sobol", "StatsBase"] +git-tree-sha1 = "cc086f8485bce77b6187141e1413c3b55f9a4341" +uuid = "8a4e6c94-4038-4cdc-81c3-7e6ffdb2a71b" +version = "0.3.3" +weakdeps = ["Distributions"] + + [deps.QuasiMonteCarlo.extensions] + QuasiMonteCarloDistributionsExt = "Distributions" + [[deps.REPL]] deps = ["InteractiveUtils", "Markdown", "Sockets", "Unicode"] uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb" @@ -978,6 +1436,30 @@ git-tree-sha1 = "45cf9fd0ca5839d06ef333c8201714e888486342" uuid = "01d81517-befc-4cb6-b9ec-a95719d0359c" version = "0.6.12" +[[deps.RecursiveArrayTools]] +deps = ["Adapt", "ArrayInterface", "DocStringExtensions", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "Requires", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"] +git-tree-sha1 = "d7087c013e8a496ff396bae843b1e16d9a30ede8" +uuid = "731186ca-8d62-57ce-b412-fbd966d074cd" +version = "2.38.10" + + [deps.RecursiveArrayTools.extensions] + RecursiveArrayToolsMeasurementsExt = "Measurements" + RecursiveArrayToolsMonteCarloMeasurementsExt = "MonteCarloMeasurements" + RecursiveArrayToolsTrackerExt = "Tracker" + RecursiveArrayToolsZygoteExt = "Zygote" + + [deps.RecursiveArrayTools.weakdeps] + Measurements = "eff96d63-e80a-5855-80a2-b1b0885c5ab7" + MonteCarloMeasurements = "0987c9cc-fe09-11e8-30f0-b96dd679fdca" + Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" + Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" + +[[deps.RecursiveFactorization]] +deps = ["LinearAlgebra", "LoopVectorization", "Polyester", "PrecompileTools", "StrideArraysCore", "TriangularSolve"] +git-tree-sha1 = "8bc86c78c7d8e2a5fe559e3721c0f9c9e303b2ed" +uuid = "f2c3362d-daeb-58d1-803e-2bc74f2840b4" +version = "0.2.21" + [[deps.Reexport]] git-tree-sha1 = "45e428421666073eab6f2da5c9d310d99bb12f9b" uuid = "189a3867-3050-52da-a836-e630ba90ab69" @@ -1019,10 +1501,62 @@ git-tree-sha1 = "6ed52fdd3382cf21947b15e8870ac0ddbff736da" uuid = "f50d1b31-88e8-58de-be2c-1cc44531875f" version = "0.4.0+0" +[[deps.RuntimeGeneratedFunctions]] +deps = ["ExprTools", "SHA", "Serialization"] +git-tree-sha1 = "6aacc5eefe8415f47b3e34214c1d79d2674a0ba2" +uuid = "7e49a35a-f44a-4d26-94aa-eba1b4ca6b47" +version = "0.5.12" + [[deps.SHA]] uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" version = "0.7.0" +[[deps.SIMDTypes]] +git-tree-sha1 = "330289636fb8107c5f32088d2741e9fd7a061a5c" +uuid = "94e857df-77ce-4151-89e5-788b33177be4" +version = "0.1.0" + +[[deps.SLEEFPirates]] +deps = ["IfElse", "Static", "VectorizationBase"] +git-tree-sha1 = "3aac6d68c5e57449f5b9b865c9ba50ac2970c4cf" +uuid = "476501e8-09a2-5ece-8869-fb82de89a1fa" +version = "0.6.42" + +[[deps.SciMLBase]] +deps = ["ADTypes", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FillArrays", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "Printf", "QuasiMonteCarlo", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "TruncatedStacktraces"] +git-tree-sha1 = "d432b4c4cc922fb7b21b555c138aa87f9fb7beb8" +uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462" +version = "2.9.1" + + [deps.SciMLBase.extensions] + SciMLBaseChainRulesCoreExt = "ChainRulesCore" + SciMLBasePartialFunctionsExt = "PartialFunctions" + SciMLBasePyCallExt = "PyCall" + SciMLBasePythonCallExt = "PythonCall" + SciMLBaseRCallExt = "RCall" + SciMLBaseZygoteExt = "Zygote" + + [deps.SciMLBase.weakdeps] + ChainRules = "082447d4-558c-5d27-93f4-14fc19e9eca2" + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" + PartialFunctions = "570af359-4316-4cb7-8c74-252c00c2016b" + PyCall = "438e738f-606a-5dbb-bf0a-cddfbfd45ab0" + PythonCall = "6099a3de-0909-46bc-b1f4-468b9a2dfc0d" + RCall = "6f49c342-dc21-5d91-9882-a32aef131414" + Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" + +[[deps.SciMLNLSolve]] +deps = ["DiffEqBase", "LineSearches", "NLsolve", "Reexport", "SciMLBase"] +git-tree-sha1 = "765b788339abd7d983618c09cfc0192e2b6b15fd" +uuid = "e9a6253c-8580-4d32-9898-8661bb511710" +version = "0.1.9" + +[[deps.SciMLOperators]] +deps = ["ArrayInterface", "DocStringExtensions", "Lazy", "LinearAlgebra", "Setfield", "SparseArrays", "StaticArraysCore", "Tricks"] +git-tree-sha1 = "51ae235ff058a64815e0a2c34b1db7578a06813d" +uuid = "c0aeaf25-5076-4817-a8d5-81caf7dfa961" +version = "0.3.7" + [[deps.Scratch]] deps = ["Dates"] git-tree-sha1 = "3bac05bc7e74a75fd9cba4295cde4045d9fe2386" @@ -1032,6 +1566,16 @@ version = "1.2.1" [[deps.Serialization]] uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b" +[[deps.Setfield]] +deps = ["ConstructionBase", "Future", "MacroTools", "StaticArraysCore"] +git-tree-sha1 = "e2cc6d8c88613c05e1defb55170bf5ff211fbeac" +uuid = "efcf1570-3423-57d1-acb7-fd33fddbac46" +version = "1.1.1" + +[[deps.SharedArrays]] +deps = ["Distributed", "Mmap", "Random", "Serialization"] +uuid = "1a1011a3-84de-559e-8e89-a11a2f7dc383" + [[deps.Showoff]] deps = ["Dates", "Grisu"] git-tree-sha1 = "91eddf657aca81df9ae6ceb20b959ae5653ad1de" @@ -1043,6 +1587,35 @@ git-tree-sha1 = "874e8867b33a00e784c8a7e4b60afe9e037b74e1" uuid = "777ac1f9-54b0-4bf8-805c-2214025038e7" version = "1.1.0" +[[deps.SimpleNonlinearSolve]] +deps = ["ArrayInterface", "DiffEqBase", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "PrecompileTools", "Reexport", "SciMLBase", "StaticArraysCore"] +git-tree-sha1 = "69b1a53374dd14d7c165d98cb646aeb5f36f8d07" +uuid = "727e6d20-b764-4bd8-a329-72de5adea6c7" +version = "0.1.25" + + [deps.SimpleNonlinearSolve.extensions] + SimpleNonlinearSolveNNlibExt = "NNlib" + + [deps.SimpleNonlinearSolve.weakdeps] + NNlib = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" + +[[deps.SimpleTraits]] +deps = ["InteractiveUtils", "MacroTools"] +git-tree-sha1 = "5d7e3f4e11935503d3ecaf7186eac40602e7d231" +uuid = "699a6c99-e7fa-54fc-8d76-47d257e15c1d" +version = "0.9.4" + +[[deps.SimpleUnPack]] +git-tree-sha1 = "58e6353e72cde29b90a69527e56df1b5c3d8c437" +uuid = "ce78b400-467f-4804-87d8-8f486da07d0a" +version = "1.1.0" + +[[deps.Sobol]] +deps = ["DelimitedFiles", "Random"] +git-tree-sha1 = "5a74ac22a9daef23705f010f72c81d6925b19df8" +uuid = "ed01d8cd-4d21-5b2a-85b4-cc3bdc58bad4" +version = "1.5.0" + [[deps.Sockets]] uuid = "6462fe0b-24de-5631-8697-dd941f90decc" @@ -1056,6 +1629,28 @@ version = "1.2.0" deps = ["Libdl", "LinearAlgebra", "Random", "Serialization", "SuiteSparse_jll"] uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" +[[deps.SparseDiffTools]] +deps = ["ADTypes", "Adapt", "ArrayInterface", "Compat", "DataStructures", "FiniteDiff", "ForwardDiff", "Graphs", "LinearAlgebra", "PackageExtensionCompat", "Random", "Reexport", "SciMLOperators", "Setfield", "SparseArrays", "StaticArrayInterface", "StaticArrays", "Tricks", "UnPack", "VertexSafeGraphs"] +git-tree-sha1 = "07272c80c278947baca092df0a01da4a10622ad5" +uuid = "47a9eef4-7e08-11e9-0b38-333d64bd3804" +version = "2.13.0" + + [deps.SparseDiffTools.extensions] + SparseDiffToolsEnzymeExt = "Enzyme" + SparseDiffToolsSymbolicsExt = "Symbolics" + SparseDiffToolsZygoteExt = "Zygote" + + [deps.SparseDiffTools.weakdeps] + Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" + Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7" + Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" + +[[deps.Sparspak]] +deps = ["Libdl", "LinearAlgebra", "Logging", "OffsetArrays", "Printf", "SparseArrays", "Test"] +git-tree-sha1 = "342cf4b449c299d8d1ceaf00b7a49f4fbc7940e7" +uuid = "e56a9233-b9d6-4f03-8d0f-1825330902ac" +version = "0.3.9" + [[deps.SpecialFunctions]] deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] git-tree-sha1 = "e2cfc4012a19088254b3950b85c3c1d8882d864d" @@ -1068,6 +1663,23 @@ version = "2.3.1" [deps.SpecialFunctions.weakdeps] ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" +[[deps.Static]] +deps = ["IfElse"] +git-tree-sha1 = "f295e0a1da4ca425659c57441bcb59abb035a4bc" +uuid = "aedffcd0-7271-4cad-89d0-dc628f76c6d3" +version = "0.8.8" + +[[deps.StaticArrayInterface]] +deps = ["ArrayInterface", "Compat", "IfElse", "LinearAlgebra", "PrecompileTools", "Requires", "SparseArrays", "Static", "SuiteSparse"] +git-tree-sha1 = "03fec6800a986d191f64f5c0996b59ed526eda25" +uuid = "0d7ed370-da01-4f52-bd93-41d350b8b718" +version = "1.4.1" +weakdeps = ["OffsetArrays", "StaticArrays"] + + [deps.StaticArrayInterface.extensions] + StaticArrayInterfaceOffsetArraysExt = "OffsetArrays" + StaticArrayInterfaceStaticArraysExt = "StaticArrays" + [[deps.StaticArrays]] deps = ["LinearAlgebra", "PrecompileTools", "Random", "StaticArraysCore"] git-tree-sha1 = "5ef59aea6f18c25168842bded46b16662141ab87" @@ -1114,6 +1726,12 @@ version = "1.3.0" ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" InverseFunctions = "3587e190-3f89-42d0-90ee-14403ec27112" +[[deps.StrideArraysCore]] +deps = ["ArrayInterface", "CloseOpenIntervals", "IfElse", "LayoutPointers", "ManualMemory", "SIMDTypes", "Static", "StaticArrayInterface", "ThreadingUtilities"] +git-tree-sha1 = "d6415f66f3d89c615929af907fdc6a3e17af0d8c" +uuid = "7792a7ef-975c-4747-a70f-980b88e8d1da" +version = "0.5.2" + [[deps.StringEncodings]] deps = ["Libiconv_jll"] git-tree-sha1 = "b765e46ba27ecf6b44faf70df40c57aa3a547dcb" @@ -1135,6 +1753,12 @@ deps = ["Artifacts", "Libdl", "Pkg", "libblastrampoline_jll"] uuid = "bea87d4a-7f5b-5778-9afe-8cc45184846c" version = "5.10.1+6" +[[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" @@ -1172,6 +1796,12 @@ git-tree-sha1 = "8621ba2637b49748e2dc43ba3d84340be2938022" uuid = "1c621080-faea-4a02-84b6-bbd5e436b8fe" version = "0.1.1" +[[deps.ThreadingUtilities]] +deps = ["ManualMemory"] +git-tree-sha1 = "eda08f7e9818eb53661b3deb74e3159460dfbc27" +uuid = "8290d209-cae3-49c0-8002-c8c24d57dab5" +version = "0.5.2" + [[deps.TimerOutputs]] deps = ["ExprTools", "Printf"] git-tree-sha1 = "f548a9e9c490030e545f72074a41edfd0e5bcdd7" @@ -1187,11 +1817,23 @@ weakdeps = ["Random", "Test"] [deps.TranscodingStreams.extensions] TestExt = ["Test", "Random"] +[[deps.TriangularSolve]] +deps = ["CloseOpenIntervals", "IfElse", "LayoutPointers", "LinearAlgebra", "LoopVectorization", "Polyester", "Static", "VectorizationBase"] +git-tree-sha1 = "fadebab77bf3ae041f77346dd1c290173da5a443" +uuid = "d5829a12-d9aa-46ab-831f-fb7c9ab06edf" +version = "0.1.20" + [[deps.Tricks]] git-tree-sha1 = "eae1bb484cd63b36999ee58be2de6c178105112f" uuid = "410a4b4d-49e4-4fbc-ab6d-cb71b17b3775" version = "0.1.8" +[[deps.TruncatedStacktraces]] +deps = ["InteractiveUtils", "MacroTools", "Preferences"] +git-tree-sha1 = "ea3e54c2bdde39062abf5a9758a23735558705e1" +uuid = "781d530d-4396-4725-bb49-402e4bee1e77" +version = "1.4.0" + [[deps.URIs]] git-tree-sha1 = "67db6cc7b3821e19ebe75791a9dd19c9b1188f2b" uuid = "5c2747f8-b7ea-4ff2-ba2e-563bfd36b1d4" @@ -1201,6 +1843,11 @@ version = "1.5.1" deps = ["Random", "SHA"] uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4" +[[deps.UnPack]] +git-tree-sha1 = "387c1f73762231e86e0c9c5443ce3b4a0a9a0c2b" +uuid = "3a884ed6-31ef-47d7-9d2a-63182c4928ed" +version = "1.0.2" + [[deps.Unicode]] uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5" @@ -1215,15 +1862,12 @@ deps = ["Dates", "LinearAlgebra", "Random"] git-tree-sha1 = "3c793be6df9dd77a0cf49d80984ef9ff996948fa" uuid = "1986cc42-f94f-5a68-af5c-568840ba703d" version = "1.19.0" +weakdeps = ["ConstructionBase", "InverseFunctions"] [deps.Unitful.extensions] ConstructionBaseUnitfulExt = "ConstructionBase" InverseFunctionsUnitfulExt = "InverseFunctions" - [deps.Unitful.weakdeps] - ConstructionBase = "187b0558-2788-49d3-abe0-74a17ed4e7c9" - InverseFunctions = "3587e190-3f89-42d0-90ee-14403ec27112" - [[deps.UnitfulLatexify]] deps = ["LaTeXStrings", "Latexify", "Unitful"] git-tree-sha1 = "e2d817cc500e960fdbafcf988ac8436ba3208bfd" @@ -1235,6 +1879,18 @@ git-tree-sha1 = "ca0969166a028236229f63514992fc073799bb78" uuid = "41fe7b60-77ed-43a1-b4f0-825fd5a5650d" version = "0.2.0" +[[deps.VectorizationBase]] +deps = ["ArrayInterface", "CPUSummary", "HostCPUFeatures", "IfElse", "LayoutPointers", "Libdl", "LinearAlgebra", "SIMDTypes", "Static", "StaticArrayInterface"] +git-tree-sha1 = "7209df901e6ed7489fe9b7aa3e46fb788e15db85" +uuid = "3d5dd08c-fd9d-11e8-17fa-ed2836048c2f" +version = "0.21.65" + +[[deps.VertexSafeGraphs]] +deps = ["Graphs"] +git-tree-sha1 = "8351f8d73d7e880bfc042a8b6922684ebeafb35c" +uuid = "19fa3120-7c27-5ec5-8db8-b0b0aa330d6f" +version = "0.2.0" + [[deps.Vulkan_Loader_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Wayland_jll", "Xorg_libX11_jll", "Xorg_libXrandr_jll", "xkbcommon_jll"] git-tree-sha1 = "2f0486047a07670caad3a81a075d2e518acc5c59" diff --git a/extra/Project.toml b/extra/Project.toml index c24d46b..f4dabb0 100644 --- a/extra/Project.toml +++ b/extra/Project.toml @@ -3,10 +3,12 @@ DelimitedFiles = "8bb1440f-4735-579b-a4ab-409b98df4dab" Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f" GaussianRandomFields = "e4b2fa32-6e09-5554-b718-106ed5adafe9" HDF5 = "f67ccb44-e63f-5c2f-98bd-6dc0ccc4ba2f" +OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed" PDMats = "90014a1f-27ba-587c-ab20-58faa44d9150" ParticleDA = "61cd1fb4-f4c4-4bc8-80c6-ea5639a6ca2e" Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" Pluto = "c3e4b0f8-55cb-11ea-2926-15256bba5781" PlutoLinks = "0ff47ea0-7a50-410d-8455-4348d5de0420" PlutoUI = "7f904dfe-b85e-4ff6-b463-dae2292396a8" +SciMLBase = "0bca4576-84f4-4d90-8ffe-ffa030f20462" YAML = "ddb6d928-2868-570f-bddf-ab3f9cf99eb6" diff --git a/extra/lorenz63_example.jl b/extra/lorenz63_example.jl new file mode 100644 index 0000000..8b24349 --- /dev/null +++ b/extra/lorenz63_example.jl @@ -0,0 +1,254 @@ +### A Pluto.jl notebook ### +# v0.19.32 + +using Markdown +using InteractiveUtils + +# This Pluto notebook uses @bind for interactivity. When running this notebook outside of Pluto, the following 'mock version' of @bind gives bound variables a default value (instead of an error). +macro bind(def, element) + quote + local iv = try Base.loaded_modules[Base.PkgId(Base.UUID("6e696c72-6542-2067-7265-42206c756150"), "AbstractPlutoDingetjes")].Bonds.initial_value catch; b -> missing; end + local el = $(esc(element)) + global $(esc(def)) = Core.applicable(Base.get, el) ? Base.get(el) : iv(el) + el + end +end + +# ╔═╡ 86be08c2-5337-4b00-bdcc-26a2f04ff162 +begin + using Pkg + Pkg.activate(".") + using ParticleDA + using PlutoLinks: @ingredients + using PlutoUI + using Plots + using HDF5 + using Random + using Statistics + using YAML +end + +# ╔═╡ 7709ac00-728f-11ed-1f00-1f458e5ad3e2 +Lorenz63 = @ingredients("../test/models/lorenz63.jl").Lorenz63 + +# ╔═╡ 16a443e1-7b7f-4ba5-8999-2dd59eed50d3 +function load_simulation_outputs(output_filename) + h5open(output_filename, "r") do file + n_time_step = length(file["observations"]) + observation_dim = length(first(file["observations"])) + observation_eltype = eltype(first(file["observations"])) + state_dim = length(first(file["state"])) + state_eltype = eltype(first(file["state"])) + observation_sequence = Matrix{observation_eltype}( + undef, observation_dim, n_time_step + ) + state_true_sequence = Matrix{state_eltype}( + undef, state_dim, n_time_step + ) + for t in 1:n_time_step + key = ParticleDA.time_index_to_hdf5_key(t) + observation_sequence[:, t] = read(file["observations"][key]) + state_true_sequence[:, t] = read(file["state"][key]) + end + return observation_sequence, state_true_sequence + end +end + +# ╔═╡ cfb7be2d-772f-454f-b822-80899ed6ff55 +function load_filtering_outputs(output_filename) + h5open(output_filename, "r") do file + n_time_step = length(file["weights"]) - 1 + state_dim = length(first(file["state_avg"])) + state_eltype = eltype(first(file["state_avg"])) + n_particle = length(first(file["weights"])) + state_mean_sequence = Matrix{Float64}(undef, state_dim, n_time_step) + state_std_sequence = Matrix{Float64}(undef, state_dim, n_time_step) + weights_sequence = Matrix{Float64}(undef, n_particle, n_time_step) + for t in 1:n_time_step + key = ParticleDA.time_index_to_hdf5_key(t) + state_mean_sequence[:, t] = read(file["state_avg"][key]) + state_std_sequence[:, t] = read(file["state_var"][key]) + weights_sequence[:, t] = read(file["weights"][key]) + end + return state_mean_sequence, state_std_sequence, weights_sequence + end +end + +# ╔═╡ b10b319f-964a-43d0-a5fb-9847af748ae9 +function plot_effective_sample_sizes(weights_sequence) + n_time_step = size(weights_sequence, 2) + ess_sequence = 1 ./ sum(x -> x.^2, weights_sequence; dims=1)[1, :] + plot( + 1:n_time_step, + ess_sequence, + xlabel="Time index", + ylabel="Estimated ESS", + size=(800, 200), + legend=:none, + margin=20Plots.px, + ) +end + +# ╔═╡ 9243268a-daf7-450b-b275-ebebb3150c86 +function plot_rmses(state_true_sequence, state_mean_sequence) + n_time_step = size(state_mean_sequence, 2) + rmse_sequence = sqrt.( + mean(x -> x.^2, state_mean_sequence .- state_true_sequence; dims=1) + )[1, :] + plot( + 1:n_time_step, + rmse_sequence, + xlabel="Time index", + ylabel="RMSE(mean, truth)", + size=(800, 200), + legend=:none, + margin=20Plots.px, + ) +end + +# ╔═╡ 01da3a88-aa3c-4f32-b5c8-cd447665a3be +function plot_3d_comparison( + observed_indices, + observation_sequence, + state_true_sequence, + state_mean_sequence, +) + n_time_step = size(state_mean_sequence, 2) + p = plot(size=(800, 800), xlabel="x₁", ylabel="x₂", zlabel="x₃") + plot!(p, eachrow(state_true_sequence)..., label="True", ) + plot!(p, eachrow(state_mean_sequence)..., label="Filtering estimate (mean)") +end + +# ╔═╡ f9c5199a-3cd3-44c8-9bfc-8b90a8d8c9b9 +function plot_per_dimension_comparison( + observed_indices, + observation_sequence, + state_true_sequence, + state_mean_sequence, + state_std_sequence, +) + n_time_step = size(state_mean_sequence, 2) + plots = Array{Plots.Plot}(undef, 3) + for (i, (mean, std, state, label)) in enumerate(zip( + eachrow(state_mean_sequence), + eachrow(state_std_sequence), + eachrow(state_true_sequence), + ["x₁", "x₂", "x₃"] + )) + plots[i] = plot( + 1:n_time_step, + mean, + xlabel="Time index", + ylabel=label, + label="Filtering estimate", + ribbon=3 * std, + fillalpha=0.5, + legend=:outerright, + ) + if i in observed_indices + j = findfirst(isequal(i), observed_indices) + plot!( + plots[i], + 1:n_time_step, + observation_sequence[j, :], + seriestype=[:scatter], + label="Observations", + markersize=2, + markerstrokewidth=0, + ) + end + plot!(plots[i], 1:n_time_step, state, label="Truth") + end + plot( + plots..., + layout=(3, 1), + size=(800, 800), + margin=20Plots.px, + ) +end + +# ╔═╡ 4715bcaa-b726-4439-aa38-22708a918df4 +md""" +Number of particles $(@bind n_particle NumberField(1:1000, default=100))\ +Number of timesteps $(@bind n_time_step NumberField(1:1000, default=500))\ +Filter type $(@bind filter_type Select([OptimalFilter => "locally optimal", BootstrapFilter => "bootstrap"]))\ +Initial state std. $(@bind initial_state_std NumberField(0:0.1:10, default=0.5))\ +State noise std. $(@bind state_noise_std NumberField(0:0.1:10, default=0.5))\ +Observation noise std. $(@bind observation_noise_std NumberField(0:0.1:10, default=1.))\ +Observed state indices $(@bind observed_indices MultiCheckBox([1, 2, 3], default=[1,2,3])) +Show 3D plot $(@bind show_3d_plot CheckBox(default=true)) +""" + +# ╔═╡ 4d57d231-78fb-4383-a559-da84444ff7c1 +let + simulation_filename = tempname() + filtering_filename = tempname() + rng = Random.TaskLocalRNG() + Random.seed!(rng, 1234) + model_dict = Dict( + "observation_noise_std" => observation_noise_std, + "initial_state_std" => initial_state_std, + "state_noise_std" => state_noise_std, + "observed_indices" => observed_indices, + ) + model = Lorenz63.init(model_dict) + h5open(simulation_filename, "w") do file + ParticleDA.simulate_observations_from_model( + model, n_time_step; output_file=file, rng=rng + ) + end + observation_sequence, state_true_sequence = load_simulation_outputs( + simulation_filename + ) + filter_parameters = ParticleDA.FilterParameters( + nprt=n_particle, verbose=true, output_filename=filtering_filename + ) + ParticleDA.run_particle_filter( + Lorenz63.init, + filter_parameters, + model_dict, + observation_sequence, + filter_type, + ParticleDA.MeanAndVarSummaryStat; + rng=rng + ) + state_mean_sequence, state_std_sequence, weights_sequence = load_filtering_outputs( + filtering_filename + ) + ess_plot = plot_effective_sample_sizes(weights_sequence) + rmse_plot = plot_rmses(state_true_sequence, state_mean_sequence) + if show_3d_plot + state_plot = plot_3d_comparison( + observed_indices, + observation_sequence, + state_true_sequence, + state_mean_sequence, + ) + else + state_plot = plot_per_dimension_comparison( + observed_indices, + observation_sequence, + state_true_sequence, + state_mean_sequence, + state_std_sequence + ) + end + plot( + ess_plot, rmse_plot, state_plot, + layout=grid(3, 1, heights=[0.15 ,0.15, 0.7]), + size=(800, 1200) + ) + +end + +# ╔═╡ Cell order: +# ╠═86be08c2-5337-4b00-bdcc-26a2f04ff162 +# ╠═7709ac00-728f-11ed-1f00-1f458e5ad3e2 +# ╠═16a443e1-7b7f-4ba5-8999-2dd59eed50d3 +# ╠═cfb7be2d-772f-454f-b822-80899ed6ff55 +# ╠═b10b319f-964a-43d0-a5fb-9847af748ae9 +# ╠═9243268a-daf7-450b-b275-ebebb3150c86 +# ╠═01da3a88-aa3c-4f32-b5c8-cd447665a3be +# ╠═f9c5199a-3cd3-44c8-9bfc-8b90a8d8c9b9 +# ╟─4715bcaa-b726-4439-aa38-22708a918df4 +# ╠═4d57d231-78fb-4383-a559-da84444ff7c1