diff --git a/dev/.documenter-siteinfo.json b/dev/.documenter-siteinfo.json index e9c8a7f..0cf0539 100644 --- a/dev/.documenter-siteinfo.json +++ b/dev/.documenter-siteinfo.json @@ -1 +1 @@ -{"documenter":{"julia_version":"1.10.4","generation_timestamp":"2024-07-26T08:55:16","documenter_version":"1.5.0"}} \ No newline at end of file +{"documenter":{"julia_version":"1.10.4","generation_timestamp":"2024-08-02T08:56:09","documenter_version":"1.5.0"}} \ No newline at end of file diff --git a/dev/assets/Manifest.toml b/dev/assets/Manifest.toml index f7b195d..4e552b8 100644 --- a/dev/assets/Manifest.toml +++ b/dev/assets/Manifest.toml @@ -26,9 +26,9 @@ version = "0.4.5" [[deps.Accessors]] deps = ["CompositionsBase", "ConstructionBase", "Dates", "InverseFunctions", "LinearAlgebra", "MacroTools", "Markdown", "Test"] -git-tree-sha1 = "c0d491ef0b135fd7d63cbc6404286bc633329425" +git-tree-sha1 = "f61b15be1d76846c0ce31d3fcfac5380ae53db6a" uuid = "7d9f7c33-5ae7-4f3b-8dc6-eff91059b697" -version = "0.1.36" +version = "0.1.37" [deps.Accessors.extensions] AccessorsAxisKeysExt = "AxisKeys" @@ -235,9 +235,9 @@ version = "0.2.3" [[deps.ConstructionBase]] deps = ["LinearAlgebra"] -git-tree-sha1 = "260fd2400ed2dab602a7c15cf10c1933c59930a2" +git-tree-sha1 = "d8a9c0b6ac2d9081bf76324b39c78ca3ce4f0c98" uuid = "187b0558-2788-49d3-abe0-74a17ed4e7c9" -version = "1.5.5" +version = "1.5.6" weakdeps = ["IntervalSets", "StaticArrays"] [deps.ConstructionBase.extensions] @@ -317,6 +317,18 @@ version = "3.6.2" OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed" Sundials = "c3572dad-4567-51f8-b174-8c6c989267f4" +[[deps.DiffEqNoiseProcess]] +deps = ["DiffEqBase", "Distributions", "GPUArraysCore", "LinearAlgebra", "Markdown", "Optim", "PoissonRandom", "QuadGK", "Random", "Random123", "RandomNumbers", "RecipesBase", "RecursiveArrayTools", "Requires", "ResettableStacks", "SciMLBase", "StaticArraysCore", "Statistics"] +git-tree-sha1 = "ed0158e758723b4d429afbbb5d98c5afd3458dc1" +uuid = "77a26b50-5914-5dd7-bc55-306e6241c503" +version = "5.22.0" + + [deps.DiffEqNoiseProcess.extensions] + DiffEqNoiseProcessReverseDiffExt = "ReverseDiff" + + [deps.DiffEqNoiseProcess.weakdeps] + ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" + [[deps.DiffResults]] deps = ["StaticArraysCore"] git-tree-sha1 = "782dd5f4561f5d267313f23853baaaa4c52ea621" @@ -469,6 +481,12 @@ git-tree-sha1 = "27415f162e6028e81c72b82ef756bf321213b6ec" uuid = "e2ba6199-217a-4e67-a87a-7c52f15ade04" version = "0.1.10" +[[deps.Expronicon]] +deps = ["MLStyle", "Pkg", "TOML"] +git-tree-sha1 = "fc3951d4d398b5515f91d7fe5d45fc31dccb3c9b" +uuid = "6b7a57c9-7cc1-4fdf-b7f5-e857abae3636" +version = "0.8.5" + [[deps.EzXML]] deps = ["Printf", "XML2_jll"] git-tree-sha1 = "380053d61bb9064d6aa4a9777413b40429c79901" @@ -477,9 +495,9 @@ version = "1.2.0" [[deps.FastBroadcast]] deps = ["ArrayInterface", "LinearAlgebra", "Polyester", "Static", "StaticArrayInterface", "StrideArraysCore"] -git-tree-sha1 = "bd19de6fe8a3b18888f35e79832f97544684caa7" +git-tree-sha1 = "ab1b34570bcdf272899062e1a56285a53ecaae08" uuid = "7034ab61-46d4-4ed7-9d0f-46aef9175898" -version = "0.3.4" +version = "0.3.5" [[deps.FastClosures]] git-tree-sha1 = "acebe244d53ee1b461970f8910c235b259e772ef" @@ -676,9 +694,9 @@ version = "0.21.4" [[deps.JuliaFormatter]] deps = ["CSTParser", "CommonMark", "DataStructures", "Glob", "Pkg", "PrecompileTools", "Tokenize"] -git-tree-sha1 = "b101a476705594c2a8ba106d731497058874bcf4" +git-tree-sha1 = "0b50446cd3e52a51a7d48b52d49ec1a875aaf6e8" uuid = "98e50ef6-434e-11e9-1051-2b60c6c9e899" -version = "1.0.57" +version = "1.0.58" [[deps.JumpProcesses]] deps = ["ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "FunctionWrappers", "Graphs", "LinearAlgebra", "Markdown", "PoissonRandom", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "SciMLBase", "StaticArrays", "SymbolicIndexingInterface", "UnPack"] @@ -940,10 +958,10 @@ version = "1.2.0" uuid = "a63ad114-7e13-5084-954f-fe012c677804" [[deps.ModelingToolkit]] -deps = ["AbstractTrees", "ArrayInterface", "Combinatorics", "Compat", "ConstructionBase", "DataStructures", "DiffEqBase", "DiffEqCallbacks", "DiffRules", "Distributed", "Distributions", "DocStringExtensions", "DomainSets", "DynamicQuantities", "ExprTools", "FindFirstFunctions", "ForwardDiff", "FunctionWrappersWrappers", "Graphs", "InteractiveUtils", "JuliaFormatter", "JumpProcesses", "LabelledArrays", "Latexify", "Libdl", "LinearAlgebra", "MLStyle", "NaNMath", "NonlinearSolve", "OrderedCollections", "PrecompileTools", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLBase", "SciMLStructures", "Serialization", "Setfield", "SimpleNonlinearSolve", "SparseArrays", "SpecialFunctions", "StaticArrays", "SymbolicIndexingInterface", "SymbolicUtils", "Symbolics", "URIs", "UnPack", "Unitful"] -git-tree-sha1 = "ca53d85a54e5d54e0c7458d784af8fe5078064ce" +deps = ["AbstractTrees", "ArrayInterface", "Combinatorics", "Compat", "ConstructionBase", "DataStructures", "DiffEqBase", "DiffEqCallbacks", "DiffEqNoiseProcess", "DiffRules", "Distributed", "Distributions", "DocStringExtensions", "DomainSets", "DynamicQuantities", "ExprTools", "FindFirstFunctions", "ForwardDiff", "FunctionWrappersWrappers", "Graphs", "InteractiveUtils", "JuliaFormatter", "JumpProcesses", "LabelledArrays", "Latexify", "Libdl", "LinearAlgebra", "MLStyle", "NaNMath", "NonlinearSolve", "OrderedCollections", "PrecompileTools", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLBase", "SciMLStructures", "Serialization", "Setfield", "SimpleNonlinearSolve", "SparseArrays", "SpecialFunctions", "StaticArrays", "SymbolicIndexingInterface", "SymbolicUtils", "Symbolics", "URIs", "UnPack", "Unitful"] +git-tree-sha1 = "568a7c80b2e3ff43c6c6c92212deeeba7ff4e639" uuid = "961ee093-0014-501f-94e3-6117800e7a78" -version = "9.24.0" +version = "9.26.0" [deps.ModelingToolkit.extensions] MTKBifurcationKitExt = "BifurcationKit" @@ -1053,6 +1071,18 @@ git-tree-sha1 = "13652491f6856acfd2db29360e1bbcd4565d04f1" uuid = "efe28fd5-8261-553b-a9e1-b2916fc3738e" version = "0.5.5+0" +[[deps.Optim]] +deps = ["Compat", "FillArrays", "ForwardDiff", "LineSearches", "LinearAlgebra", "NLSolversBase", "NaNMath", "Parameters", "PositiveFactorizations", "Printf", "SparseArrays", "StatsBase"] +git-tree-sha1 = "d9b79c4eed437421ac4285148fcadf42e0700e89" +uuid = "429524aa-4258-5aef-a3af-852621145aeb" +version = "1.9.4" + + [deps.Optim.extensions] + OptimMOIExt = "MathOptInterface" + + [deps.Optim.weakdeps] + MathOptInterface = "b8f27783-ece8-5eb3-8dc8-9495eed66fee" + [[deps.OrderedCollections]] git-tree-sha1 = "dfdf5519f235516220579f949664f1bf44e741c5" uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d" @@ -1110,6 +1140,12 @@ git-tree-sha1 = "645bed98cd47f72f67316fd42fc47dee771aefcd" uuid = "1d0040c9-8b98-4ee7-8388-3f51789ca0ad" version = "0.2.2" +[[deps.PositiveFactorizations]] +deps = ["LinearAlgebra"] +git-tree-sha1 = "17275485f373e6673f7e7f97051f703ed5b15b20" +uuid = "85a6dd25-e78a-55b7-8502-1745935b8125" +version = "0.2.4" + [[deps.PreallocationTools]] deps = ["Adapt", "ArrayInterface", "ForwardDiff"] git-tree-sha1 = "406c29a7f46706d379a3bce45671b4e3a39ddfbc" @@ -1157,6 +1193,12 @@ uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb" deps = ["SHA"] uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" +[[deps.Random123]] +deps = ["Random", "RandomNumbers"] +git-tree-sha1 = "4743b43e5a9c4a2ede372de7061eed81795b12e7" +uuid = "74087812-796a-5b5d-8853-05524746bad3" +version = "1.7.0" + [[deps.RandomNumbers]] deps = ["Random", "Requires"] git-tree-sha1 = "043da614cc7e95c703498a491e2c21f58a2b8111" @@ -1216,6 +1258,12 @@ git-tree-sha1 = "838a3a4188e2ded87a4f9f184b4b0d78a1e91cb7" uuid = "ae029012-a4dd-5104-9daa-d747884805df" version = "1.3.0" +[[deps.ResettableStacks]] +deps = ["StaticArrays"] +git-tree-sha1 = "256eeeec186fa7f26f2801732774ccf277f05db9" +uuid = "ae5879a3-cd67-5da8-be7f-38c6eb64a37b" +version = "1.1.1" + [[deps.Rmath]] deps = ["Random", "Rmath_jll"] git-tree-sha1 = "f65dcb5fa46aee0cf9ed6274ccbd597adc49aa7b" @@ -1250,10 +1298,10 @@ uuid = "476501e8-09a2-5ece-8869-fb82de89a1fa" version = "0.6.43" [[deps.SciMLBase]] -deps = ["ADTypes", "Accessors", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "Printf", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "SciMLStructures", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"] -git-tree-sha1 = "281e82f2ae2b73262fed9e7a518711eb7feb7e59" +deps = ["ADTypes", "Accessors", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "Expronicon", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "Printf", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "SciMLStructures", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"] +git-tree-sha1 = "8501bb749cc6684c86b6f113e17f2e6d60ccf11c" uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462" -version = "2.42.0" +version = "2.45.1" [deps.SciMLBase.extensions] SciMLBaseChainRulesCoreExt = "ChainRulesCore" @@ -1301,9 +1349,9 @@ uuid = "1a1011a3-84de-559e-8e89-a11a2f7dc383" [[deps.SimpleNonlinearSolve]] deps = ["ADTypes", "ArrayInterface", "ConcreteStructs", "DiffEqBase", "DiffResults", "DifferentiationInterface", "FastClosures", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "MaybeInplace", "PrecompileTools", "Reexport", "SciMLBase", "Setfield", "StaticArraysCore"] -git-tree-sha1 = "58b144f34e44252b2de0acb5a9dbbb7ea5cd75d7" +git-tree-sha1 = "03c21a4c373c7c3aa77611430068badaa073d740" uuid = "727e6d20-b764-4bd8-a329-72de5adea6c7" -version = "1.10.1" +version = "1.11.0" [deps.SimpleNonlinearSolve.extensions] SimpleNonlinearSolveChainRulesCoreExt = "ChainRulesCore" @@ -1475,9 +1523,9 @@ version = "2.1.2" [[deps.Symbolics]] deps = ["ADTypes", "ArrayInterface", "Bijections", "CommonWorldInvalidations", "ConstructionBase", "DataStructures", "DiffRules", "Distributions", "DocStringExtensions", "DomainSets", "DynamicPolynomials", "ForwardDiff", "IfElse", "LaTeXStrings", "LambertW", "Latexify", "Libdl", "LinearAlgebra", "LogExpFunctions", "MacroTools", "Markdown", "NaNMath", "PrecompileTools", "RecipesBase", "Reexport", "Requires", "RuntimeGeneratedFunctions", "SciMLBase", "Setfield", "SparseArrays", "SpecialFunctions", "StaticArraysCore", "SymbolicIndexingInterface", "SymbolicLimits", "SymbolicUtils", "TermInterface"] -git-tree-sha1 = "8539a734b448ca27707709c62420b1bf115ed7d9" +git-tree-sha1 = "44356a85991385883acd0f41ef66c6f770d9a2e7" uuid = "0c5d862f-8b57-4792-8d23-62f2024744c7" -version = "5.33.0" +version = "5.34.0" [deps.Symbolics.extensions] SymbolicsGroebnerExt = "Groebner" @@ -1540,9 +1588,9 @@ uuid = "0796e94c-ce3b-5d07-9a54-7f471281c624" version = "0.5.29" [[deps.TranscodingStreams]] -git-tree-sha1 = "60df3f8126263c0d6b357b9a1017bb94f53e3582" +git-tree-sha1 = "96612ac5365777520c3c5396314c8cf7408f436a" uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa" -version = "0.11.0" +version = "0.11.1" weakdeps = ["Random", "Test"] [deps.TranscodingStreams.extensions] @@ -1584,9 +1632,9 @@ uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5" [[deps.Unitful]] deps = ["Dates", "LinearAlgebra", "Random"] -git-tree-sha1 = "dd260903fdabea27d9b6021689b3cd5401a57748" +git-tree-sha1 = "d95fe458f26209c66a187b1114df96fd70839efd" uuid = "1986cc42-f94f-5a68-af5c-568840ba703d" -version = "1.20.0" +version = "1.21.0" weakdeps = ["ConstructionBase", "InverseFunctions"] [deps.Unitful.extensions] diff --git a/dev/index.html b/dev/index.html index 061c052..05b5d8a 100644 --- a/dev/index.html +++ b/dev/index.html @@ -25,7 +25,7 @@ [47edcb42] ADTypes v1.6.1 [a4c015fc] ANSIColoredPrinters v0.0.1 [1520ce14] AbstractTrees v0.4.5 - [7d9f7c33] Accessors v0.1.36 + [7d9f7c33] Accessors v0.1.37 [79e6a3ab] Adapt v4.0.4 [66dad0bd] AliasTables v1.1.3 [ec485272] ArnoldiMethod v0.4.0 @@ -49,7 +49,7 @@ [b152e2b5] CompositeTypes v0.1.4 [a33af91c] CompositionsBase v0.1.2 [2569d6c7] ConcreteStructs v0.2.3 - [187b0558] ConstructionBase v1.5.5 + [187b0558] ConstructionBase v1.5.6 [adafc99b] CpuId v0.3.1 [a8cc5b0e] Crayons v4.1.1 [9a962f9c] DataAPI v1.16.0 @@ -57,6 +57,7 @@ [e2d170a0] DataValueInterfaces v1.0.0 [2b5f629d] DiffEqBase v6.151.5 [459566f4] DiffEqCallbacks v3.6.2 + [77a26b50] DiffEqNoiseProcess v5.22.0 [163ba53b] DiffResults v1.1.0 [b552c78f] DiffRules v1.15.1 [a0c0ee7d] DifferentiationInterface v0.5.9 @@ -70,8 +71,9 @@ [4e289a0a] EnumX v1.0.4 [f151be2c] EnzymeCore v0.7.7 [e2ba6199] ExprTools v0.1.10 +⌅ [6b7a57c9] Expronicon v0.8.5 [8f5d6c58] EzXML v1.2.0 - [7034ab61] FastBroadcast v0.3.4 + [7034ab61] FastBroadcast v0.3.5 [9aa1b823] FastClosures v0.3.2 [29a986be] FastLapackInterface v2.0.4 [1a297f60] FillArrays v1.11.0 @@ -97,7 +99,7 @@ [82899510] IteratorInterfaceExtensions v1.0.0 [692b3bcd] JLLWrappers v1.5.0 [682c06a0] JSON v0.21.4 - [98e50ef6] JuliaFormatter v1.0.57 + [98e50ef6] JuliaFormatter v1.0.58 [ccbc3e58] JumpProcesses v9.11.1 [ef3ab10e] KLU v0.6.0 [ba0b0d4f] Krylov v0.9.6 @@ -120,7 +122,7 @@ [bb5d69b7] MaybeInplace v0.1.3 [c03570c3] Memoize v0.4.4 [e1d29d7a] Missings v1.2.0 - [961ee093] ModelingToolkit v9.24.0 + [961ee093] ModelingToolkit v9.26.0 [46d2c3a1] MuladdMacro v0.2.4 [102ac46a] MultivariatePolynomials v0.5.6 [d8a4904e] MutableArithmetics v1.4.5 @@ -128,6 +130,7 @@ [77ba4419] NaNMath v1.0.2 [8913a72c] NonlinearSolve v3.13.1 [6fe1bfb0] OffsetArrays v1.14.1 + [429524aa] Optim v1.9.4 [bac558e1] OrderedCollections v1.6.3 [90014a1f] PDMats v0.11.31 [65ce6f38] PackageExtensionCompat v1.0.2 @@ -136,11 +139,13 @@ [e409e4f3] PoissonRandom v0.4.4 [f517fe37] Polyester v0.7.15 [1d0040c9] PolyesterWeave v0.2.2 + [85a6dd25] PositiveFactorizations v0.2.4 [d236fae5] PreallocationTools v0.4.22 [aea7be01] PrecompileTools v1.2.1 [21216c6a] Preferences v1.4.3 [43287f4e] PtrArrays v1.2.0 [1fd47b50] QuadGK v2.9.4 + [74087812] Random123 v1.7.0 [e6cf234a] RandomNumbers v1.5.3 [3cdcf5f2] RecipesBase v1.3.4 [731186ca] RecursiveArrayTools v3.26.0 @@ -148,15 +153,16 @@ [189a3867] Reexport v1.2.2 [2792f1a3] RegistryInstances v0.1.0 [ae029012] Requires v1.3.0 + [ae5879a3] ResettableStacks v1.1.1 [79098fc4] Rmath v0.7.1 [7e49a35a] RuntimeGeneratedFunctions v0.5.13 [94e857df] SIMDTypes v0.1.0 [476501e8] SLEEFPirates v0.6.43 - [0bca4576] SciMLBase v2.42.0 + [0bca4576] SciMLBase v2.45.1 [c0aeaf25] SciMLOperators v0.3.8 [53ae85a6] SciMLStructures v1.4.1 [efcf1570] Setfield v1.1.1 - [727e6d20] SimpleNonlinearSolve v1.10.1 + [727e6d20] SimpleNonlinearSolve v1.11.0 [699a6c99] SimpleTraits v0.9.4 [a2af1166] SortingAlgorithms v1.2.1 [47a9eef4] SparseDiffTools v2.19.0 @@ -174,20 +180,20 @@ [2efcf032] SymbolicIndexingInterface v0.3.26 [19f23fe9] SymbolicLimits v0.2.1 [d1185830] SymbolicUtils v2.1.2 - [0c5d862f] Symbolics v5.33.0 + [0c5d862f] Symbolics v5.34.0 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.0 ⌅ [8ea1fca8] TermInterface v0.4.1 [8290d209] ThreadingUtilities v0.5.2 [a759f4b9] TimerOutputs v0.5.24 [0796e94c] Tokenize v0.5.29 - [3bb67fe8] TranscodingStreams v0.11.0 + [3bb67fe8] TranscodingStreams v0.11.1 [d5829a12] TriangularSolve v0.2.1 [410a4b4d] Tricks v0.1.8 [781d530d] TruncatedStacktraces v1.4.0 [5c2747f8] URIs v1.5.1 [3a884ed6] UnPack v1.0.2 - [1986cc42] Unitful v1.20.0 + [1986cc42] Unitful v1.21.0 [a7c27f48] Unityper v0.1.6 [3d5dd08c] VectorizationBase v0.21.70 [19fa3120] VertexSafeGraphs v0.2.0 @@ -249,4 +255,4 @@ [8e850b90] libblastrampoline_jll v5.8.0+1 [8e850ede] nghttp2_jll v1.52.0+1 [3f19e933] p7zip_jll v17.4.0+2 -Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m`

You can also download the manifest file and the project file.

+Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m`

You can also download the manifest file and the project file.

diff --git a/dev/tutorial/index.html b/dev/tutorial/index.html index a9f2802..2b7461f 100644 --- a/dev/tutorial/index.html +++ b/dev/tutorial/index.html @@ -36,4 +36,4 @@ prob = ODEProblem(ml, tspan; p = p) sol = solve(prob, TRBDF2(), dtmax = 1.0) V = map(x -> x[1], sol.u) -plot(sol.t, V)

ODEProblem also accepts a u0 parameter to change the initial conditions (remember u0 = list_initial_conditions(ml)).

+plot(sol.t, V)

ODEProblem also accepts a u0 parameter to change the initial conditions (remember u0 = list_initial_conditions(ml)).