diff --git a/docs/Manifest.toml b/docs/Manifest.toml index 927b374..e30a08a 100644 --- a/docs/Manifest.toml +++ b/docs/Manifest.toml @@ -1,8 +1,8 @@ # This file is machine-generated - editing it directly is not advised -julia_version = "1.10.2" +julia_version = "1.10.4" manifest_format = "2.0" -project_hash = "05ea43fa36693c647d8a75059fa294fd7665bcdf" +project_hash = "c2100d26b2cc49b8f6c93a3ad341c80fc172aaaf" [[deps.ANSIColoredPrinters]] git-tree-sha1 = "574baf8110975760d391c710b6341da1afa48d8c" @@ -61,6 +61,12 @@ weakdeps = ["StaticArrays"] [deps.Adapt.extensions] AdaptStaticArraysExt = "StaticArrays" +[[deps.AliasTables]] +deps = ["PtrArrays", "Random"] +git-tree-sha1 = "9876e1e164b144ca45e9e3198d0b689cadfed9ff" +uuid = "66dad0bd-aa9a-41b7-9441-69ab47430ed8" +version = "1.1.3" + [[deps.Animations]] deps = ["Colors"] git-tree-sha1 = "e81c509d2c8e49592413bfb0bb3b08150056c79d" @@ -121,9 +127,9 @@ version = "0.4.7" [[deps.BangBang]] deps = ["Accessors", "Compat", "ConstructionBase", "InitialValues", "LinearAlgebra", "Requires"] -git-tree-sha1 = "490e739172eb18f762e68dc3b928cad2a077983a" +git-tree-sha1 = "08e5fc6620a8d83534bf6149795054f1b1e8370a" uuid = "198e06fe-97b7-11e9-32a5-e1d131e6ad66" -version = "0.4.1" +version = "0.4.2" [deps.BangBang.extensions] BangBangChainRulesCoreExt = "ChainRulesCore" @@ -169,6 +175,12 @@ git-tree-sha1 = "e329286945d0cfc04456972ea732551869af1cfc" uuid = "4e9b3aee-d8a1-5a3d-ad8b-7d824db253f0" version = "1.0.1+0" +[[deps.CSV]] +deps = ["CodecZlib", "Dates", "FilePathsBase", "InlineStrings", "Mmap", "Parsers", "PooledArrays", "PrecompileTools", "SentinelArrays", "Tables", "Unicode", "WeakRefStrings", "WorkerUtilities"] +git-tree-sha1 = "6c834533dc1fabd820c1db03c839bf97e45a3fab" +uuid = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b" +version = "0.10.14" + [[deps.Cairo]] deps = ["Cairo_jll", "Colors", "Glib_jll", "Graphics", "Libdl", "Pango_jll"] git-tree-sha1 = "d0b3f8b4ad16cb0a2988c6788646a5e6a17b6b1b" @@ -183,9 +195,9 @@ version = "0.11.10" [[deps.Cairo_jll]] deps = ["Artifacts", "Bzip2_jll", "CompilerSupportLibraries_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "JLLWrappers", "LZO_jll", "Libdl", "Pixman_jll", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Zlib_jll", "libpng_jll"] -git-tree-sha1 = "a4c43f59baa34011e303e76f5c8c91bf58415aaf" +git-tree-sha1 = "a2f1c8c668c8e3cb4cca4e57a8efdb09067bb3fd" uuid = "83423d85-b0ee-5818-9007-b63ccbeb887a" -version = "1.18.0+1" +version = "1.18.0+2" [[deps.Calculus]] deps = ["LinearAlgebra"] @@ -195,9 +207,9 @@ version = "0.5.1" [[deps.ChainRulesCore]] deps = ["Compat", "LinearAlgebra"] -git-tree-sha1 = "575cd02e080939a33b6df6c5853d14924c08e35b" +git-tree-sha1 = "71acdbf594aab5bbb2cec89b208c41b4c411e49f" uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" -version = "1.23.0" +version = "1.24.0" weakdeps = ["SparseArrays"] [deps.ChainRulesCore.extensions] @@ -217,9 +229,9 @@ version = "0.4.0" [[deps.ColorSchemes]] deps = ["ColorTypes", "ColorVectorSpace", "Colors", "FixedPointNumbers", "PrecompileTools", "Random"] -git-tree-sha1 = "67c1f244b991cad9b0aa4b7540fb758c2488b129" +git-tree-sha1 = "4b270d6465eb21ae89b732182c20dc165f8bf9f2" uuid = "35d6a980-a343-548e-a6ea-1d62b119f2f4" -version = "3.24.0" +version = "3.25.0" [[deps.ColorTypes]] deps = ["FixedPointNumbers", "Random"] @@ -239,9 +251,9 @@ weakdeps = ["SpecialFunctions"] [[deps.Colors]] deps = ["ColorTypes", "FixedPointNumbers", "Reexport"] -git-tree-sha1 = "fc08e5930ee9a4e03f84bfb5211cb54e7769758a" +git-tree-sha1 = "362a287c3aa50601b0bc359053d5c2468f0e7ce0" uuid = "5ae59095-9a9b-59fe-a467-6f913c188581" -version = "0.12.10" +version = "0.12.11" [[deps.Combinatorics]] git-tree-sha1 = "08c8b6831dc00bfea825826be0bc8336fc369860" @@ -256,9 +268,9 @@ version = "0.3.0" [[deps.Compat]] deps = ["TOML", "UUIDs"] -git-tree-sha1 = "c955881e3c981181362ae4088b35995446298b80" +git-tree-sha1 = "b1c55339b7c6c350ee89f2c1604299660525b248" uuid = "34da2185-b29b-5c13-b0c7-acf172513d20" -version = "4.14.0" +version = "4.15.0" weakdeps = ["Dates", "LinearAlgebra"] [deps.Compat.extensions] @@ -267,7 +279,7 @@ weakdeps = ["Dates", "LinearAlgebra"] [[deps.CompilerSupportLibraries_jll]] deps = ["Artifacts", "Libdl"] uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae" -version = "1.1.0+0" +version = "1.1.1+0" [[deps.CompositionsBase]] git-tree-sha1 = "802bb88cd69dfd1509f6670416bd4434015693ad" @@ -301,9 +313,9 @@ version = "1.16.0" [[deps.DataStructures]] deps = ["Compat", "InteractiveUtils", "OrderedCollections"] -git-tree-sha1 = "97d79461925cdb635ee32116978fc735b9463a39" +git-tree-sha1 = "1d0a14036acb104d9e89698bd408f63ab58cdc82" uuid = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8" -version = "0.18.19" +version = "0.18.20" [[deps.DataValueInterfaces]] git-tree-sha1 = "bfc1187b79289637fa0ef6d4436ebdfe6905cbd6" @@ -342,10 +354,10 @@ deps = ["Random", "Serialization", "Sockets"] uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b" [[deps.Distributions]] -deps = ["FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] -git-tree-sha1 = "7c302d7a5fec5214eb8a5a4c466dcf7a51fcf169" +deps = ["AliasTables", "FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] +git-tree-sha1 = "9c405847cc7ecda2dc921ccf18b47ca150d7317e" uuid = "31c24e10-a181-5473-b8eb-7969acd0382f" -version = "0.25.107" +version = "0.25.109" [deps.Distributions.extensions] DistributionsChainRulesCoreExt = "ChainRulesCore" @@ -417,9 +429,9 @@ version = "2.2.8" [[deps.Expat_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "4558ab818dcceaab612d1bb8c19cee87eda2b83c" +git-tree-sha1 = "1c6317308b9dc757616f0b5cb379db10494443a7" uuid = "2e619515-83b5-522b-bb60-26c02a35a201" -version = "2.5.0+0" +version = "2.6.2+0" [[deps.ExprTools]] git-tree-sha1 = "27415f162e6028e81c72b82ef756bf321213b6ec" @@ -427,9 +439,9 @@ uuid = "e2ba6199-217a-4e67-a87a-7c52f15ade04" version = "0.1.10" [[deps.Extents]] -git-tree-sha1 = "2140cd04483da90b2da7f99b2add0750504fc39c" +git-tree-sha1 = "94997910aca72897524d2237c41eb852153b0f65" uuid = "411431e0-e8b7-467b-b5e0-f676ba4f2910" -version = "0.1.2" +version = "0.1.3" [[deps.ExternalDocstrings]] git-tree-sha1 = "1224740fc4d07c989949e1c1b508ebd49a65a5f6" @@ -477,9 +489,9 @@ uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" [[deps.FillArrays]] deps = ["LinearAlgebra"] -git-tree-sha1 = "bfe82a708416cf00b73a3198db0859c82f741558" +git-tree-sha1 = "0653c0a2396a6da5bc4766c43041ef5fd3efbe57" uuid = "1a297f60-69ca-5386-bcde-b61e274b549b" -version = "1.10.0" +version = "1.11.0" weakdeps = ["PDMats", "SparseArrays", "Statistics"] [deps.FillArrays.extensions] @@ -505,9 +517,9 @@ version = "2.23.1" [[deps.FixedPointNumbers]] deps = ["Statistics"] -git-tree-sha1 = "335bfdceacc84c5cdf16aadc768aa5ddfc5383cc" +git-tree-sha1 = "05882d6995ae5c12bb5f36dd2ed3f61c98cbb172" uuid = "53c48c17-4a7d-5ca2-90c5-79b7896eea93" -version = "0.8.4" +version = "0.8.5" [[deps.Folds]] deps = ["Accessors", "BangBang", "Baselet", "DefineSingletons", "Distributed", "ExternalDocstrings", "InitialValues", "MicroCollections", "Referenceables", "Requires", "Test", "ThreadedScans", "Transducers"] @@ -522,10 +534,10 @@ version = "0.2.10" OnlineStatsBase = "925886fa-5bf2-5e8e-b522-a9147a512338" [[deps.Fontconfig_jll]] -deps = ["Artifacts", "Bzip2_jll", "Expat_jll", "FreeType2_jll", "JLLWrappers", "Libdl", "Libuuid_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "21efd19106a55620a188615da6d3d06cd7f6ee03" +deps = ["Artifacts", "Bzip2_jll", "Expat_jll", "FreeType2_jll", "JLLWrappers", "Libdl", "Libuuid_jll", "Zlib_jll"] +git-tree-sha1 = "db16beca600632c95fc8aca29890d83788dd8b23" uuid = "a3f928ae-7b40-5064-980b-68af3947d34b" -version = "2.13.93+0" +version = "2.13.96+0" [[deps.Format]] git-tree-sha1 = "9c68794ef81b08086aeb32eeaf33531668d5f5fc" @@ -550,9 +562,9 @@ version = "4.1.1" [[deps.FreeType2_jll]] deps = ["Artifacts", "Bzip2_jll", "JLLWrappers", "Libdl", "Zlib_jll"] -git-tree-sha1 = "d8db6a5a2fe1381c1ea4ef2cab7c69c2de7f9ea0" +git-tree-sha1 = "5c1d8ae0efc6c2e7b1fc502cbe25def8f661b7bc" uuid = "d7e528f0-a631-5988-bf34-fe36492bcfd7" -version = "2.13.1+0" +version = "2.13.2+0" [[deps.FreeTypeAbstraction]] deps = ["ColorVectorSpace", "Colors", "FreeType", "GeometryBasics"] @@ -561,10 +573,10 @@ uuid = "663a7486-cb36-511b-a19d-713bb74d65c9" version = "0.10.3" [[deps.FriBidi_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "aa31987c2ba8704e23c6c8ba8a4f769d5d7e4f91" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "1ed150b39aebcc805c26b93a8d0122c940f64ce2" uuid = "559328eb-81f9-559d-9380-de523a88c83c" -version = "1.0.10+0" +version = "1.0.14+0" [[deps.Future]] deps = ["Random"] @@ -578,9 +590,9 @@ version = "1.3.4" [[deps.GeometryBasics]] deps = ["EarCut_jll", "Extents", "GeoInterface", "IterTools", "LinearAlgebra", "StaticArrays", "StructArrays", "Tables"] -git-tree-sha1 = "5694b56ccf9d15addedc35e9a4ba9c317721b788" +git-tree-sha1 = "b62f2b2d76cee0d61a2ef2b3118cd2a3215d3134" uuid = "5c1252a2-5f33-56bf-86c9-59e7332b4326" -version = "0.4.10" +version = "0.4.11" [[deps.Gettext_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "XML2_jll"] @@ -602,9 +614,9 @@ version = "2.44.0+2" [[deps.Glib_jll]] deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Zlib_jll"] -git-tree-sha1 = "359a1ba2e320790ddbe4ee8b4d54a305c0ea2aff" +git-tree-sha1 = "7c82e6a6cd34e9d935e9aa4051b66c6ff3af59ba" uuid = "7746bdde-850d-59dc-9ae8-88ece973131d" -version = "2.80.0+0" +version = "2.80.2+0" [[deps.Graphics]] deps = ["Colors", "LinearAlgebra", "NaNMath"] @@ -665,9 +677,9 @@ version = "0.3.23" [[deps.IOCapture]] deps = ["Logging", "Random"] -git-tree-sha1 = "8b72179abc660bfab5e28472e019392b97d0985c" +git-tree-sha1 = "b6d6bfdd7ce25b0f9b2f6b3dd56b2673a66c8770" uuid = "b5f81e59-6552-4d32-b1f0-c071b021bf89" -version = "0.2.4" +version = "0.2.5" [[deps.IfElse]] git-tree-sha1 = "debdd00ffef04665ccbb3e150747a77560e8fad1" @@ -694,9 +706,9 @@ version = "0.10.2" [[deps.ImageIO]] deps = ["FileIO", "IndirectArrays", "JpegTurbo", "LazyModules", "Netpbm", "OpenEXR", "PNGFiles", "QOI", "Sixel", "TiffImages", "UUIDs"] -git-tree-sha1 = "bca20b2f5d00c4fbc192c3212da8fa79f4688009" +git-tree-sha1 = "437abb322a41d527c197fa800455f79d414f0a3c" uuid = "82e4d734-157c-48bb-816b-45c225c6df19" -version = "0.6.7" +version = "0.6.8" [[deps.ImageMetadata]] deps = ["AxisArrays", "ImageAxes", "ImageBase", "ImageCore"] @@ -706,9 +718,9 @@ version = "0.9.9" [[deps.Imath_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "3d09a9f60edf77f8a4d99f9e015e8fbf9989605d" +git-tree-sha1 = "0936ba688c6d201805a83da835b55c61a180db52" uuid = "905a6f67-0a94-5f89-b386-d35d92009cd1" -version = "3.1.7+0" +version = "3.1.11+0" [[deps.IndirectArrays]] git-tree-sha1 = "012e604e1c7458645cb8b436f8fba789a51b257f" @@ -716,15 +728,27 @@ uuid = "9b13fd28-a010-5f03-acff-a1bbcff69959" version = "1.0.0" [[deps.Inflate]] -git-tree-sha1 = "ea8031dea4aff6bd41f1df8f2fdfb25b33626381" +git-tree-sha1 = "d1b1b796e47d94588b3757fe84fbf65a5ec4a80d" uuid = "d25df0c9-e2be-5dd7-82c8-3ad0b3e990b9" -version = "0.1.4" +version = "0.1.5" [[deps.InitialValues]] git-tree-sha1 = "4da0f88e9a39111c2fa3add390ab15f3a44f3ca3" uuid = "22cec73e-a1b8-11e9-2c92-598750a2cf9c" version = "0.3.1" +[[deps.InlineStrings]] +deps = ["Parsers"] +git-tree-sha1 = "86356004f30f8e737eff143d57d41bd580e437aa" +uuid = "842dd82b-1e85-43dc-bf29-5d0ee9dffc48" +version = "1.4.1" + + [deps.InlineStrings.extensions] + ArrowTypesExt = "ArrowTypes" + + [deps.InlineStrings.weakdeps] + ArrowTypes = "31f734f8-188a-4ce0-8406-c8a06bd891cd" + [[deps.IntegerMathUtils]] git-tree-sha1 = "b8ffb903da9f7b8cf695a8bead8e01814aa24b30" uuid = "18e54dd8-cb9d-406c-a71d-865a43cbb235" @@ -732,9 +756,9 @@ version = "0.1.2" [[deps.IntelOpenMP_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "5fdf2fe6724d8caabf43b557b84ce53f3b7e2f6b" +git-tree-sha1 = "be50fe8df3acbffa0274a744f1a99d29c45a57f4" uuid = "1d5cc7b8-4909-519e-a0f8-d0f5ad9712d0" -version = "2024.0.2+0" +version = "2024.1.0+0" [[deps.InteractiveUtils]] deps = ["Markdown"] @@ -754,9 +778,9 @@ version = "0.15.1" [[deps.IntervalArithmetic]] deps = ["CRlibm_jll", "MacroTools", "RoundingEmulator"] -git-tree-sha1 = "23ddd329f4a2a65c7a55b91553b60849bd038575" +git-tree-sha1 = "433b0bb201cd76cb087b017e49244f10394ebe9c" uuid = "d1acc4aa-44c8-5952-acd4-ba5d80a2a253" -version = "0.22.11" +version = "0.22.14" weakdeps = ["DiffRules", "ForwardDiff", "RecipesBase"] [deps.IntervalArithmetic.extensions] @@ -777,9 +801,9 @@ weakdeps = ["Random", "RecipesBase", "Statistics"] [[deps.InverseFunctions]] deps = ["Test"] -git-tree-sha1 = "896385798a8d49a255c398bd49162062e4a4c435" +git-tree-sha1 = "e7cbed5032c4c397a6ac23d1493f3289e01231c4" uuid = "3587e190-3f89-42d0-90ee-14403ec27112" -version = "0.1.13" +version = "0.1.14" weakdeps = ["Dates"] [deps.InverseFunctions.extensions] @@ -838,21 +862,21 @@ version = "0.1.5" [[deps.JpegTurbo_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "3336abae9a713d2210bb57ab484b1e065edd7d23" +git-tree-sha1 = "c84a835e1a09b289ffcd2271bf2a337bbdda6637" uuid = "aacddb02-875f-59d6-b918-886e6ef4fbf8" -version = "3.0.2+0" +version = "3.0.3+0" [[deps.KernelDensity]] deps = ["Distributions", "DocStringExtensions", "FFTW", "Interpolations", "StatsBase"] -git-tree-sha1 = "fee018a29b60733876eb557804b5b109dd3dd8a7" +git-tree-sha1 = "7d703202e65efa1369de1279c162b915e245eed1" uuid = "5ab0869b-81aa-558d-bb23-cbf5423bbe9b" -version = "0.6.8" +version = "0.6.9" [[deps.LAME_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "f6250b16881adf048549549fba48b1161acdac8c" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "170b660facf5df5de098d866564877e119141cbd" uuid = "c1c5ebd0-6772-5130-a774-d5fcae4a789d" -version = "3.100.1+0" +version = "3.100.2+0" [[deps.LLVMOpenMP_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -861,10 +885,10 @@ uuid = "1d63c593-3942-5779-bab2-d838dc0a180e" version = "15.0.7+0" [[deps.LZO_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "e5b909bcf985c5e2605737d2ce278ed791b89be6" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "70c5da094887fd2cae843b8db33920bac4b6f07d" uuid = "dd4b983a-f0e5-5f8d-a1b7-129d4a5fb1ac" -version = "2.10.1+0" +version = "2.10.2+0" [[deps.LaTeXStrings]] git-tree-sha1 = "50901ebc375ed41dbf8058da26f9de442febbbec" @@ -919,16 +943,16 @@ uuid = "e9f186c6-92d2-5b65-8a66-fee21dc1b490" version = "3.2.2+1" [[deps.Libgcrypt_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgpg_error_jll", "Pkg"] -git-tree-sha1 = "64613c82a59c120435c067c2b809fc61cf5166ae" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgpg_error_jll"] +git-tree-sha1 = "9fd170c4bbfd8b935fdc5f8b7aa33532c991a673" uuid = "d4300ac3-e22c-5743-9152-c294e39db1e4" -version = "1.8.7+0" +version = "1.8.11+0" [[deps.Libgpg_error_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "c333716e46366857753e273ce6a69ee0945a6db9" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "fbb1f2bef882392312feb1ede3615ddc1e9b99ed" uuid = "7add5ba3-2f88-524e-9cd5-f83b8a55f7b8" -version = "1.42.0+0" +version = "1.49.0+0" [[deps.Libiconv_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -938,15 +962,15 @@ version = "1.17.0+0" [[deps.Libmount_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "dae976433497a2f841baadea93d27e68f1a12a97" +git-tree-sha1 = "0c4f9c4f1a50d8f35048fa0532dabbadf702f81e" uuid = "4b2f31a3-9ecc-558c-b454-b3730dcb73e9" -version = "2.39.3+0" +version = "2.40.1+0" [[deps.Libuuid_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "0a04a1318df1bf510beb2562cf90fb0c386f58c4" +git-tree-sha1 = "5ee6203157c120d79034c748a2acba45b82b8807" uuid = "38a345b3-de98-5d2b-a5d3-14cd9215e700" -version = "2.39.3+1" +version = "2.40.1+0" [[deps.LightXML]] deps = ["Libdl", "XML2_jll"] @@ -978,9 +1002,9 @@ version = "2.18.0" [[deps.LogExpFunctions]] deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "18144f3e9cbe9b15b070288eef858f71b291ce37" +git-tree-sha1 = "a2d09619db4e765091ee5c6ffe8872849de0feea" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.27" +version = "0.3.28" [deps.LogExpFunctions.extensions] LogExpFunctionsChainRulesCoreExt = "ChainRulesCore" @@ -996,10 +1020,10 @@ version = "0.3.27" uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" [[deps.MKL_jll]] -deps = ["Artifacts", "IntelOpenMP_jll", "JLLWrappers", "LazyArtifacts", "Libdl"] -git-tree-sha1 = "72dc3cf284559eb8f53aa593fe62cb33f83ed0c0" +deps = ["Artifacts", "IntelOpenMP_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "oneTBB_jll"] +git-tree-sha1 = "80b2833b56d466b3858d565adcd16a4a05f2089b" uuid = "856f044c-d86e-5d09-b602-aeab76dc8ba7" -version = "2024.0.0+0" +version = "2024.1.0+0" [[deps.MPI]] deps = ["Distributed", "DocStringExtensions", "Libdl", "MPICH_jll", "MPIPreferences", "MPItrampoline_jll", "MicrosoftMPI_jll", "OpenMPI_jll", "PkgVersion", "PrecompileTools", "Requires", "Serialization", "Sockets"] @@ -1017,21 +1041,21 @@ version = "0.20.19" [[deps.MPICH_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "Hwloc_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "MPIPreferences", "TOML"] -git-tree-sha1 = "656036b9ed6f942d35e536e249600bc31d0f9df8" +git-tree-sha1 = "4099bb6809ac109bfc17d521dad33763bcf026b7" uuid = "7cb0a576-ebde-5e09-9194-50597f1243b4" -version = "4.2.0+0" +version = "4.2.1+1" [[deps.MPIPreferences]] deps = ["Libdl", "Preferences"] -git-tree-sha1 = "8f6af051b9e8ec597fa09d8885ed79fd582f33c9" +git-tree-sha1 = "c105fe467859e7f6e9a852cb15cb4301126fac07" uuid = "3da0fdf6-3ccc-4f1b-acd9-58baa6c99267" -version = "0.1.10" +version = "0.1.11" [[deps.MPItrampoline_jll]] -deps = ["Artifacts", "CompilerSupportLibraries_jll", "Hwloc_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "MPIPreferences", "TOML"] -git-tree-sha1 = "77c3bd69fdb024d75af38713e883d0f249ce19c2" +deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "MPIPreferences", "TOML"] +git-tree-sha1 = "8c35d5420193841b2f367e658540e8d9e0601ed0" uuid = "f1f71cc9-e9ae-5b93-9b94-4fe0e1ad3748" -version = "5.3.2+0" +version = "5.4.0+0" [[deps.MacroTools]] deps = ["Markdown", "Random"] @@ -1179,9 +1203,9 @@ version = "0.3.2" [[deps.OpenEXR_jll]] deps = ["Artifacts", "Imath_jll", "JLLWrappers", "Libdl", "Zlib_jll"] -git-tree-sha1 = "a4ca623df1ae99d09bc9868b008262d0c0ac1e4f" +git-tree-sha1 = "8292dd5c8a38257111ada2174000a33745b06d4e" uuid = "18a262bb-aa17-5467-a713-aee519bc75cb" -version = "3.1.4+0" +version = "3.2.4+0" [[deps.OpenLibm_jll]] deps = ["Artifacts", "Libdl"] @@ -1196,9 +1220,9 @@ version = "4.1.6+0" [[deps.OpenSSL_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "3da7367955dcc5c54c1ba4d402ccdc09a1a3e046" +git-tree-sha1 = "a028ee3cb5641cccc4c24e90c36b0a4f7707bdf5" uuid = "458c3c95-2e84-50aa-8efc-19380b2a3a95" -version = "3.0.13+1" +version = "3.0.14+0" [[deps.OpenSpecFun_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Pkg"] @@ -1266,9 +1290,9 @@ version = "0.5.12" [[deps.Pango_jll]] deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "FriBidi_jll", "Glib_jll", "HarfBuzz_jll", "JLLWrappers", "Libdl"] -git-tree-sha1 = "526f5a03792669e4187e584e8ec9d534248ca765" +git-tree-sha1 = "cb5a2ab6763464ae0f19c86c56c63d4a2b0f5bda" uuid = "36c8627f-9965-5494-a995-c6b170f724f3" -version = "1.52.1+0" +version = "1.52.2+0" [[deps.Parameters]] deps = ["OrderedCollections", "UnPack"] @@ -1296,15 +1320,15 @@ version = "0.15.1" [[deps.Permutations]] deps = ["Combinatorics", "LinearAlgebra", "Random"] -git-tree-sha1 = "eb3f9df2457819bf0a9019bd93cc451697a0751e" +git-tree-sha1 = "4ca430561cf37c75964c8478eddae2d79e96ca9b" uuid = "2ae35dd2-176d-5d53-8349-f30d82d94d4f" -version = "0.4.20" +version = "0.4.21" [[deps.Pixman_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LLVMOpenMP_jll", "Libdl"] -git-tree-sha1 = "64779bc4c9784fee475689a1752ef4d5747c5e87" +git-tree-sha1 = "35621f10a7531bc8fa58f74610b1bfb70a3cfc6b" uuid = "30392449-352a-5448-841d-b1acce4e97dc" -version = "0.42.2+0" +version = "0.43.4+0" [[deps.Pkg]] deps = ["Artifacts", "Dates", "Downloads", "FileWatching", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"] @@ -1329,10 +1353,10 @@ uuid = "647866c9-e3ac-4575-94e7-e3d426903924" version = "0.1.2" [[deps.Polynomials]] -deps = ["LinearAlgebra", "RecipesBase", "Setfield", "SparseArrays"] -git-tree-sha1 = "81a2a9462003a423fdc59e2a3ff84cde93c4637b" +deps = ["LinearAlgebra", "RecipesBase", "Requires", "Setfield", "SparseArrays"] +git-tree-sha1 = "1a9cfb2dc2c2f1bd63f1906d72af39a79b49b736" uuid = "f27b6e38-b328-58d1-80ce-0feddd5e7a45" -version = "4.0.7" +version = "4.0.11" [deps.Polynomials.extensions] PolynomialsChainRulesCoreExt = "ChainRulesCore" @@ -1346,6 +1370,12 @@ version = "4.0.7" MakieCore = "20f20a25-4f0e-4fdf-b5d1-57303727442b" MutableArithmetics = "d8a4904e-b15c-11e9-3269-09a3773c0cb0" +[[deps.PooledArrays]] +deps = ["DataAPI", "Future"] +git-tree-sha1 = "36d8b4b899628fb92c2749eb488d884a926614d3" +uuid = "2dfb63ee-cc39-5dd5-95bd-886bf059d720" +version = "1.4.3" + [[deps.PositiveFactorizations]] deps = ["LinearAlgebra"] git-tree-sha1 = "17275485f373e6673f7e7f97051f703ed5b15b20" @@ -1380,6 +1410,11 @@ git-tree-sha1 = "763a8ceb07833dd51bb9e3bbca372de32c0605ad" uuid = "92933f4c-e287-5a05-a399-4b506db050ca" version = "1.10.0" +[[deps.PtrArrays]] +git-tree-sha1 = "f011fbb92c4d401059b2212c05c0601b70f8b759" +uuid = "43287f4e-b6f4-7ad1-bb20-aadabca52c3d" +version = "1.2.0" + [[deps.QOI]] deps = ["ColorTypes", "FileIO", "FixedPointNumbers"] git-tree-sha1 = "18e8f4d1426e965c7b532ddd260599e1510d26ce" @@ -1463,10 +1498,10 @@ uuid = "79098fc4-a85e-5d69-aa6a-4863f24498fa" version = "0.7.1" [[deps.Rmath_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "6ed52fdd3382cf21947b15e8870ac0ddbff736da" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "d483cd324ce5cf5d61b77930f0bbd6cb61927d21" uuid = "f50d1b31-88e8-58de-be2c-1cc44531875f" -version = "0.4.0+0" +version = "0.4.2+0" [[deps.RoundingEmulator]] git-tree-sha1 = "40b9edad2e5287e05bd413a38f61a8ff55b9557b" @@ -1477,12 +1512,24 @@ version = "0.2.1" uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" version = "0.7.0" +[[deps.SIMD]] +deps = ["PrecompileTools"] +git-tree-sha1 = "2803cab51702db743f3fda07dd1745aadfbf43bd" +uuid = "fdea26ae-647d-5447-a871-4b548cad5224" +version = "3.5.0" + [[deps.Scratch]] deps = ["Dates"] git-tree-sha1 = "3bac05bc7e74a75fd9cba4295cde4045d9fe2386" uuid = "6c6a2e73-6563-6170-7368-637461726353" version = "1.2.1" +[[deps.SentinelArrays]] +deps = ["Dates", "Random"] +git-tree-sha1 = "90b4f68892337554d31cdcdbe19e48989f26c7e6" +uuid = "91c51154-3ec4-41a3-a24f-3f23e20d615c" +version = "1.4.3" + [[deps.Serialization]] uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b" @@ -1566,9 +1613,9 @@ version = "1.10.0" [[deps.SpecialFunctions]] deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "e2cfc4012a19088254b3950b85c3c1d8882d864d" +git-tree-sha1 = "2f5d4697f21388cbe1ff299430dd169ef97d7e14" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "2.3.1" +version = "2.4.0" weakdeps = ["ChainRulesCore"] [deps.SpecialFunctions.extensions] @@ -1605,9 +1652,9 @@ weakdeps = ["OffsetArrays", "StaticArrays"] [[deps.StaticArrays]] deps = ["LinearAlgebra", "PrecompileTools", "Random", "StaticArraysCore"] -git-tree-sha1 = "bf074c045d3d5ffd956fa0a461da38a44685d6b2" +git-tree-sha1 = "6e00379a24597be4ae1ee6b2d882e15392040132" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.9.3" +version = "1.9.5" weakdeps = ["ChainRulesCore", "Statistics"] [deps.StaticArrays.extensions] @@ -1615,9 +1662,9 @@ weakdeps = ["ChainRulesCore", "Statistics"] StaticArraysStatisticsExt = "Statistics" [[deps.StaticArraysCore]] -git-tree-sha1 = "36b3d696ce6366023a0ea192b4cd442268995a0d" +git-tree-sha1 = "192954ef1208c7019899fbf8049e717f92959682" uuid = "1e83bf80-4336-4d27-bf5d-d5a4f845583c" -version = "1.4.2" +version = "1.4.3" [[deps.StaticPermutations]] git-tree-sha1 = "193c3daa18ff3e55c1dae66acb6a762c4a3bdb0b" @@ -1654,15 +1701,15 @@ weakdeps = ["ChainRulesCore", "InverseFunctions"] [[deps.Strided]] deps = ["LinearAlgebra", "StridedViews", "TupleTools"] -git-tree-sha1 = "40c69be0e1b72ee2f42923b7d1ff13e0b04e675c" +git-tree-sha1 = "bd9bd1c70cfc115cc3a30213fc725125a6b43652" uuid = "5e0ebb24-38b0-5f93-81fe-25c709ecae67" -version = "2.0.4" +version = "2.1.0" [[deps.StridedViews]] deps = ["LinearAlgebra", "PackageExtensionCompat"] -git-tree-sha1 = "5b765c4e401693ab08981989f74a36a010aa1d8e" +git-tree-sha1 = "2917996ce0fa6b8a3a85240a5e9ff930e2aeaa43" uuid = "4db3bf67-4bd7-4b4e-b153-31dc3fb37143" -version = "0.2.2" +version = "0.3.1" [deps.StridedViews.extensions] StridedViewsCUDAExt = "CUDA" @@ -1742,21 +1789,21 @@ uuid = "24d252fe-5d94-4a69-83ea-56a14333d47a" version = "0.1.0" [[deps.TiffImages]] -deps = ["ColorTypes", "DataStructures", "DocStringExtensions", "FileIO", "FixedPointNumbers", "IndirectArrays", "Inflate", "Mmap", "OffsetArrays", "PkgVersion", "ProgressMeter", "UUIDs"] -git-tree-sha1 = "34cc045dd0aaa59b8bbe86c644679bc57f1d5bd0" +deps = ["ColorTypes", "DataStructures", "DocStringExtensions", "FileIO", "FixedPointNumbers", "IndirectArrays", "Inflate", "Mmap", "OffsetArrays", "PkgVersion", "ProgressMeter", "SIMD", "UUIDs"] +git-tree-sha1 = "bc7fd5c91041f44636b2c134041f7e5263ce58ae" uuid = "731e570b-9d59-4bfa-96dc-6df516fadf69" -version = "0.6.8" +version = "0.10.0" [[deps.TimerOutputs]] deps = ["ExprTools", "Printf"] -git-tree-sha1 = "f548a9e9c490030e545f72074a41edfd0e5bcdd7" +git-tree-sha1 = "5a13ae8a41237cff5ecf34f73eb1b8f42fff6531" uuid = "a759f4b9-e2f1-59dc-863e-4aeb61b1ea8f" -version = "0.5.23" +version = "0.5.24" [[deps.TranscodingStreams]] -git-tree-sha1 = "71509f04d045ec714c4748c785a59045c3736349" +git-tree-sha1 = "d73336d81cafdc277ff45558bb7eaa2b04a8e472" uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa" -version = "0.10.7" +version = "0.10.10" weakdeps = ["Random", "Test"] [deps.TranscodingStreams.extensions] @@ -1764,9 +1811,9 @@ weakdeps = ["Random", "Test"] [[deps.Transducers]] deps = ["Accessors", "Adapt", "ArgCheck", "BangBang", "Baselet", "CompositionsBase", "ConstructionBase", "DefineSingletons", "Distributed", "InitialValues", "Logging", "Markdown", "MicroCollections", "Requires", "SplittablesBase", "Tables"] -git-tree-sha1 = "47e516e2eabd0cf1304cd67839d9a85d52dd659d" +git-tree-sha1 = "5215a069867476fc8e3469602006b9670e68da23" uuid = "28d57a85-8fef-5791-bfe6-a80928e7c999" -version = "0.4.81" +version = "0.4.82" [deps.Transducers.extensions] TransducersBlockArraysExt = "BlockArrays" @@ -1821,17 +1868,28 @@ git-tree-sha1 = "58d6e80b4ee071f5efd07fda82cb9fbe17200868" uuid = "81def892-9a0e-5fdd-b105-ffc91e053289" version = "1.3.0" +[[deps.WeakRefStrings]] +deps = ["DataAPI", "InlineStrings", "Parsers"] +git-tree-sha1 = "b1be2855ed9ed8eac54e5caff2afcdb442d52c23" +uuid = "ea10d353-3f73-51f8-a26c-33c1cb351aa5" +version = "1.4.2" + [[deps.WoodburyMatrices]] deps = ["LinearAlgebra", "SparseArrays"] git-tree-sha1 = "c1a7aa6219628fcd757dede0ca95e245c5cd9511" uuid = "efce3f68-66dc-5838-9240-27a6d6f5f9b6" version = "1.0.0" +[[deps.WorkerUtilities]] +git-tree-sha1 = "cd1659ba0d57b71a464a29e64dbc67cfe83d54e7" +uuid = "76eceee3-57b5-4d4a-8e66-0e911cebbf60" +version = "1.6.1" + [[deps.XML2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Zlib_jll"] -git-tree-sha1 = "532e22cf7be8462035d092ff21fada7527e2c488" +git-tree-sha1 = "52ff2af32e591541550bd753c0da8b9bc92bb9d9" uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a" -version = "2.12.6+0" +version = "2.12.7+0" [[deps.XSLT_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgcrypt_jll", "Libgpg_error_jll", "Libiconv_jll", "Pkg", "XML2_jll", "Zlib_jll"] @@ -1858,16 +1916,16 @@ uuid = "a3789734-cfe1-5b06-b2d0-1dd0d9d62d05" version = "1.1.4+0" [[deps.Xorg_libXext_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll"] -git-tree-sha1 = "b7c0aa8c376b31e4852b360222848637f481f8c3" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libX11_jll"] +git-tree-sha1 = "d2d1a5c49fae4ba39983f63de6afcbea47194e85" uuid = "1082639a-0dae-5f34-9b06-72781eeb8cb3" -version = "1.3.4+4" +version = "1.3.6+0" [[deps.Xorg_libXrender_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll"] -git-tree-sha1 = "19560f30fd49f4d4efbe7002a1037f8c43d43b96" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libX11_jll"] +git-tree-sha1 = "47e45cd78224c53109495b3e324df0c37bb61fbe" uuid = "ea2f1a96-1ddc-540d-b46f-429655e07cfa" -version = "0.9.10+4" +version = "0.9.11+0" [[deps.Xorg_libpthread_stubs_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -1911,10 +1969,10 @@ uuid = "477f73a3-ac25-53e9-8cc3-50b2fa2566f0" version = "1.1.2+0" [[deps.libaom_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "3a2ea60308f0996d26f1e5354e10c24e9ef905d4" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "1827acba325fdcdf1d2647fc8d5301dd9ba43a9d" uuid = "a4ae2306-e953-59d6-aa16-d00cac43593b" -version = "3.4.0+0" +version = "3.9.0+0" [[deps.libass_jll]] deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "HarfBuzz_jll", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] @@ -1956,6 +2014,12 @@ deps = ["Artifacts", "Libdl"] uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d" version = "1.52.0+1" +[[deps.oneTBB_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "7d0ea0f4895ef2f5cb83645fa689e52cb55cf493" +uuid = "1317d2d5-d96f-522e-a858-c73665f53c3e" +version = "2021.12.0+0" + [[deps.p7zip_jll]] deps = ["Artifacts", "Libdl"] uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0" diff --git a/docs/Project.toml b/docs/Project.toml index 9af26b0..976ed14 100644 --- a/docs/Project.toml +++ b/docs/Project.toml @@ -1,4 +1,5 @@ [deps] +CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b" CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0" Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4" DocumenterInterLinks = "d12716ef-a0f6-4df4-a9f1-a5a34e75c656" @@ -6,6 +7,7 @@ LaTeXStrings = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f" Literate = "98b081ad-f1c9-55d3-8b20-4c87d4299306" MPI = "da04e1cc-30fd-572f-bb4f-1f8673147195" NPZ = "15e1cf62-19b3-5cfa-8e77-841668bca605" +PencilFFTs = "4a48f351-57a6-4416-9ec4-c37015456aae" UltraDark = "1c8d022d-dfc0-4b41-80ab-3fc7e88cdfea" [compat] diff --git a/docs/make.jl b/docs/make.jl index 960a785..0f54945 100644 --- a/docs/make.jl +++ b/docs/make.jl @@ -52,7 +52,8 @@ makedocs(; "Simulation Configuration"=>"man/config.md", "Summary Statistics"=>"man/summary.md", ], - "Examples" => Any["PencilGrids"=>"examples/soliton_velocity.md",], + "Examples" => + Any["PencilGrids"=>"examples/soliton_velocity.md", "2D"=>"examples/2d.md"], "API" => "api.md", ], repo = Remotes.GitHub("musoke", "UltraDark.jl"), diff --git a/examples/2d.ipynb b/examples/2d.ipynb deleted file mode 100644 index 58919d5..0000000 --- a/examples/2d.ipynb +++ /dev/null @@ -1,314 +0,0 @@ -{ - "cells": [ - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "# Example: 2D Simulation" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "## Set up Julia environment" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "metadata": { - "scrolled": true - }, - "outputs": [], - "source": [ - "import Pkg\n", - "Pkg.activate(mktempdir())\n", - "\n", - "Pkg.add(\"CairoMakie\")\n", - "Pkg.add(\"CSV\")\n", - "Pkg.add(\"NPZ\")\n", - "Pkg.add(\"PencilFFTs\")\n", - "Pkg.develop(path=joinpath(@__DIR__, \"..\")) # Load version of UltraDark in this repo" - ] - }, - { - "cell_type": "code", - "execution_count": 3, - "metadata": {}, - "outputs": [], - "source": [ - "using UltraDark\n", - "using Test\n", - "using NPZ\n", - "using CairoMakie\n", - "using CSV" - ] - }, - { - "cell_type": "code", - "execution_count": 4, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "8" - ] - }, - "execution_count": 4, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "Threads.nthreads()" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "## Define initial conditions" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "Load a function that initialises solitons." - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "Define a 2D grid." - ] - }, - { - "cell_type": "code", - "execution_count": 6, - "metadata": {}, - "outputs": [], - "source": [ - "resol = 128\n", - "len = 10.0\n", - "\n", - "grids = Grids((len, len, len/resol), (resol, resol, 1));" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "Add some solitons to the grid. Strictly speaking, these aren't solitons in 2D, but they'll do for demonstration purposes." - ] - }, - { - "cell_type": "code", - "execution_count": 7, - "metadata": {}, - "outputs": [], - "source": [ - "mass = 10\n", - "position_1 = [-len/5, -len/5, 0]\n", - "position_2 = [-len/5, +len/5, 0]\n", - "velocity = [1, 0, 0]\n", - "phase_1 = 0\n", - "phase_2 = π\n", - "t0 = 0\n", - "\n", - "UltraDark.Initialise.add_fdm_soliton!(grids, mass, position_1, velocity, phase_1, t0)\n", - "UltraDark.Initialise.add_fdm_soliton!(grids, mass, position_2, velocity, phase_2, t0)" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "## Set options" - ] - }, - { - "cell_type": "code", - "execution_count": 8, - "metadata": {}, - "outputs": [], - "source": [ - "output_dir = joinpath(mktempdir(), \"output\", \"2D\")\n", - "\n", - "output_times = 0:0.1:5\n", - "output_config = OutputConfig(output_dir, output_times);" - ] - }, - { - "cell_type": "code", - "execution_count": 9, - "metadata": {}, - "outputs": [], - "source": [ - "options = Config.SimulationConfig();" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "## Run simulation" - ] - }, - { - "cell_type": "code", - "execution_count": 10, - "metadata": { - "scrolled": true - }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - " 7.058545 seconds (9.16 M allocations: 914.631 MiB, 4.09% gc time, 88.05% compilation time: 7% of which was recompilation)\n" - ] - } - ], - "source": [ - "@time simulate!(grids, options, output_config)" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "## Plot output" - ] - }, - { - "cell_type": "code", - "execution_count": 11, - "metadata": {}, - "outputs": [], - "source": [ - "summary = CSV.File(joinpath(output_config.directory, \"summary.csv\"));" - ] - }, - { - "cell_type": "code", - "execution_count": 12, - "metadata": {}, - "outputs": [], - "source": [ - "rho_init = npzread(\"$(output_config.directory)/rho_1.npy\");\n", - "rho_last = npzread(\"$(output_config.directory)/rho_$(length(output_times)).npy\");" - ] - }, - { - "cell_type": "code", - "execution_count": 13, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "(0, 132.3429061865363)" - ] - }, - "execution_count": 13, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "# lims = extrema(rho_last)\n", - "rho_lims = (0, maximum(rho_last))" - ] - }, - { - "cell_type": "code", - "execution_count": 14, - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "" - ], - "text/plain": [ - "VideoStream(Base.PipeEndpoint(RawFD(53) open, 0 bytes waiting), Process(`\u001b[4mffmpeg\u001b[24m \u001b[4m-y\u001b[24m \u001b[4m-loglevel\u001b[24m \u001b[4mquiet\u001b[24m \u001b[4m-threads\u001b[24m \u001b[4m16\u001b[24m \u001b[4m-framerate\u001b[24m \u001b[4m5\u001b[24m \u001b[4m-pixel_format\u001b[24m \u001b[4mrgb24\u001b[24m \u001b[4m-f\u001b[24m \u001b[4mrawvideo\u001b[24m \u001b[4m-s:v\u001b[24m \u001b[4m800x600\u001b[24m \u001b[4m-r\u001b[24m \u001b[4m5\u001b[24m \u001b[4m-i\u001b[24m \u001b[4mpipe:0\u001b[24m \u001b[4m-vf\u001b[24m \u001b[4mvflip\u001b[24m \u001b[4m-profile:v\u001b[24m \u001b[4mhigh422\u001b[24m \u001b[4m-crf\u001b[24m \u001b[4m20\u001b[24m \u001b[4m-preset\u001b[24m \u001b[4mslow\u001b[24m \u001b[4m-c:v\u001b[24m \u001b[4mlibx264\u001b[24m \u001b[4m-pix_fmt\u001b[24m \u001b[4myuv420p\u001b[24m \u001b[4m-an\u001b[24m \u001b[4m'/tmp/jl_MgLwwY/##video#227.mp4'\u001b[24m`, ProcessRunning), CairoMakie.Screen{CairoMakie.IMAGE}(Scene (800px, 600px):\n", - " 0 Plots\n", - " 2 Child Scenes:\n", - " ├ Scene (800px, 600px)\n", - " └ Scene (800px, 600px), Cairo.CairoSurfaceImage{ColorTypes.ARGB32}(Ptr{Nothing} @0x000000000484ad70, 800.0, 600.0, ColorTypes.ARGB32[ARGB32(1.0N0f8,1.0N0f8,1.0N0f8,1.0N0f8) ARGB32(1.0N0f8,1.0N0f8,1.0N0f8,1.0N0f8) … ARGB32(1.0N0f8,1.0N0f8,1.0N0f8,1.0N0f8) ARGB32(1.0N0f8,1.0N0f8,1.0N0f8,1.0N0f8); 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ARGB32(1.0N0f8,1.0N0f8,1.0N0f8,1.0N0f8) ARGB32(1.0N0f8,1.0N0f8,1.0N0f8,1.0N0f8) … ARGB32(1.0N0f8,1.0N0f8,1.0N0f8,1.0N0f8) ARGB32(1.0N0f8,1.0N0f8,1.0N0f8,1.0N0f8)]), Ptr{Nothing} @0x000000000973a010), 1.0, 6, false, CairoMakie.ScreenConfig(1.0, 0.75, :best, false, false)), ColorTypes.RGB{FixedPointNumbers.N0f8}[RGB{N0f8}(1.0,1.0,1.0) RGB{N0f8}(1.0,1.0,1.0) … RGB{N0f8}(1.0,1.0,1.0) RGB{N0f8}(1.0,1.0,1.0); RGB{N0f8}(1.0,1.0,1.0) RGB{N0f8}(1.0,1.0,1.0) … RGB{N0f8}(1.0,1.0,1.0) RGB{N0f8}(1.0,1.0,1.0); … ; RGB{N0f8}(1.0,1.0,1.0) RGB{N0f8}(1.0,1.0,1.0) … RGB{N0f8}(1.0,1.0,1.0) RGB{N0f8}(1.0,1.0,1.0); RGB{N0f8}(1.0,1.0,1.0) RGB{N0f8}(1.0,1.0,1.0) … RGB{N0f8}(1.0,1.0,1.0) RGB{N0f8}(1.0,1.0,1.0)], \"/tmp/jl_MgLwwY/##video#227.mp4\", Makie.VideoStreamOptions(\"mp4\", 5, 20, \"high422\", \"yuv420p\", nothing, \"quiet\", \"pipe:0\", true))" - ] - }, - "execution_count": 14, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "fig_anim = Figure()\n", - "ax_anim = Axis(\n", - " fig_anim[1, 1],\n", - " aspect=DataAspect(),\n", - ")\n", - "\n", - "hidedecorations!(ax_anim)\n", - "\n", - "δ_lims = extrema(rho_last.-1)\n", - "\n", - "cb_density = Colorbar(\n", - " fig_anim[1, 2],\n", - " limits=δ_lims,\n", - " label = L\"$\\rho/\\rho_{\\text{crit}}$\",\n", - ")\n", - "\n", - "frame = Observable(1)\n", - "\n", - "rho = lift(i -> npzread(joinpath(output_config.directory, \"rho_$(i).npy\"))[:, :, 1], frame)\n", - "δ = @lift($rho .- 1)\n", - "\n", - "contourf!(\n", - " ax_anim,\n", - " grids.x[:, 1, 1], grids.y[1, :, 1],\n", - " δ,\n", - " colorrange = rho_lims,\n", - ")\n", - "\n", - "Record(fig_anim, 1:length(output_times); framerate = 5) do f\n", - " frame[] = f\n", - "end" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [] - } - ], - "metadata": { - "kernelspec": { - "display_name": "Julia (8 threads) 1.10.0-beta2", - "language": "julia", - "name": "julia-_8-threads_-1.10" - }, - "language_info": { - "file_extension": ".jl", - "mimetype": "application/julia", - "name": "julia", - "version": "1.10.0" - } - }, - "nbformat": 4, - "nbformat_minor": 4 -} diff --git a/examples/2d.jl b/examples/2d.jl new file mode 100644 index 0000000..df4a862 --- /dev/null +++ b/examples/2d.jl @@ -0,0 +1,69 @@ +# # Example: 2D Simulation + +using UltraDark +using Test +using NPZ +using CairoMakie +using CSV + +Threads.nthreads() + +# ## Define initial conditions +# +# Define a 2D grid. + +resol = 128 +len = 10.0 + +grids = Grids((len, len, len / resol), (resol, resol, 1)); + +# Add some solitons to the grid. Strictly speaking, these aren't solitons in 2D, but they'll do for demonstration purposes. + +mass = 10 +position_1 = [-len / 5, -len / 5, 0] +position_2 = [-len / 5, +len / 5, 0] +velocity = [1, 0, 0] +phase_1 = 0 +phase_2 = π +t0 = 0 + +UltraDark.Initialise.add_fdm_soliton!(grids, mass, position_1, velocity, phase_1, t0) +UltraDark.Initialise.add_fdm_soliton!(grids, mass, position_2, velocity, phase_2, t0) + +# ## Set options + +output_dir = joinpath(mktempdir(), "output", "2D") + +output_times = 0:0.1:5 +output_config = OutputConfig(output_dir, output_times); + +options = Config.SimulationConfig(); + +# ## Run simulation + +@time simulate!(grids, options, output_config) + +# ## Plot output + +summary = CSV.File(joinpath(output_config.directory, "summary.csv")); + +rho_last = npzread("$(output_config.directory)/rho_$(length(output_times)).npy"); +δ_lims = extrema(rho_last .- 1) + +fig_anim = Figure() +ax_anim = Axis(fig_anim[1, 1], aspect = DataAspect()) + +hidedecorations!(ax_anim) + +cb_density = Colorbar(fig_anim[1, 2], limits = δ_lims, label = L"$\rho/\rho_{\text{crit}}$") + +frame = Observable(1) + +rho = lift(i -> npzread(joinpath(output_config.directory, "rho_$(i).npy"))[:, :, 1], frame) +δ = @lift($rho .- 1) + +contourf!(ax_anim, grids.x[:, 1, 1], grids.y[1, :, 1], δ, levels = range(-1, δ_lims[2], 10)) + +record(fig_anim, "2d.mkv", 1:length(output_times); framerate = 5) do f + frame[] = f +end diff --git a/test/runtests.jl b/test/runtests.jl index 4748a44..6654ddf 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -56,9 +56,8 @@ using NBInclude @nbinclude("../examples/growth.ipynb") end -module TwoDNotebook -using NBInclude -@nbinclude("../examples/2d.ipynb") +@safetestset "2d example" begin + include("../examples/2d.jl") end @testset "Aqua.jl" begin