diff --git a/Manifest.toml b/Manifest.toml index 9e37312..ce734d0 100644 --- a/Manifest.toml +++ b/Manifest.toml @@ -1,1555 +1,1836 @@ # This file is machine-generated - editing it directly is not advised -[[ACE1]] +julia_version = "1.10.2" +manifest_format = "2.0" +project_hash = "bbd11741a2aaffb22c888d7a681b3f16938826ca" + +[[deps.ACE1]] deps = ["BenchmarkTools", "Combinatorics", "ForwardDiff", "InteractiveUtils", "JuLIP", "LinearAlgebra", "NeighbourLists", "Parameters", "Pkg", "Printf", "QuadGK", "Random", "Reexport", "SparseArrays", "StaticArrays", "Test"] git-tree-sha1 = "8a552a375f0d8eb9c0c930f950b8f8995b777d9f" uuid = "e3f9bc04-086e-409a-ba78-e9769fe067bb" version = "0.10.5" -[[ADTypes]] +[[deps.ADTypes]] git-tree-sha1 = "016833eb52ba2d6bea9fcb50ca295980e728ee24" uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b" version = "0.2.7" -[[AbstractFFTs]] -deps = ["ChainRulesCore", "LinearAlgebra", "Test"] +[[deps.AbstractFFTs]] +deps = ["LinearAlgebra"] git-tree-sha1 = "d92ad398961a3ed262d8bf04a1a2b8340f915fef" uuid = "621f4979-c628-5d54-868e-fcf4e3e8185c" version = "1.5.0" +weakdeps = ["ChainRulesCore", "Test"] -[[AbstractMCMC]] + [deps.AbstractFFTs.extensions] + AbstractFFTsChainRulesCoreExt = "ChainRulesCore" + AbstractFFTsTestExt = "Test" + +[[deps.AbstractMCMC]] deps = ["BangBang", "ConsoleProgressMonitor", "Distributed", "FillArrays", "LogDensityProblems", "Logging", "LoggingExtras", "ProgressLogging", "Random", "StatsBase", "TerminalLoggers", "Transducers"] git-tree-sha1 = "b0489adc45a7c8cf0d8e2ddf764f89c1c3decebd" uuid = "80f14c24-f653-4e6a-9b94-39d6b0f70001" version = "5.2.0" -[[AbstractTrees]] +[[deps.AbstractTrees]] git-tree-sha1 = "2d9c9a55f9c93e8887ad391fbae72f8ef55e1177" uuid = "1520ce14-60c1-5f80-bbc7-55ef81b5835c" version = "0.4.5" -[[Adapt]] +[[deps.Accessors]] +deps = ["CompositionsBase", "ConstructionBase", "Dates", "InverseFunctions", "LinearAlgebra", "MacroTools", "Markdown", "Test"] +git-tree-sha1 = "c0d491ef0b135fd7d63cbc6404286bc633329425" +uuid = "7d9f7c33-5ae7-4f3b-8dc6-eff91059b697" +version = "0.1.36" + + [deps.Accessors.extensions] + AccessorsAxisKeysExt = "AxisKeys" + AccessorsIntervalSetsExt = "IntervalSets" + AccessorsStaticArraysExt = "StaticArrays" + AccessorsStructArraysExt = "StructArrays" + AccessorsUnitfulExt = "Unitful" + + [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" + Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d" + +[[deps.Adapt]] deps = ["LinearAlgebra", "Requires"] -git-tree-sha1 = "cde29ddf7e5726c9fb511f340244ea3481267608" +git-tree-sha1 = "6a55b747d1812e699320963ffde36f1ebdda4099" uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e" -version = "3.7.2" +version = "4.0.4" +weakdeps = ["StaticArrays"] + + [deps.Adapt.extensions] + AdaptStaticArraysExt = "StaticArrays" -[[AdvancedHMC]] +[[deps.AdvancedHMC]] deps = ["AbstractMCMC", "ArgCheck", "DocStringExtensions", "InplaceOps", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "ProgressMeter", "Random", "Requires", "Setfield", "SimpleUnPack", "Statistics", "StatsBase", "StatsFuns"] git-tree-sha1 = "dfa0e3508fc3df81d28624b328f3b937c1df8bc2" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" version = "0.6.1" -[[AlgebraicMultigrid]] + [deps.AdvancedHMC.extensions] + AdvancedHMCCUDAExt = "CUDA" + AdvancedHMCMCMCChainsExt = "MCMCChains" + AdvancedHMCOrdinaryDiffEqExt = "OrdinaryDiffEq" + + [deps.AdvancedHMC.weakdeps] + CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" + MCMCChains = "c7f686f2-ff18-58e9-bc7b-31028e88f75d" + OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed" + +[[deps.AlgebraicMultigrid]] deps = ["CommonSolve", "LinearAlgebra", "LinearSolve", "Printf", "Reexport", "SparseArrays"] git-tree-sha1 = 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+ ArrayInterfaceGPUArraysCoreExt = "GPUArraysCore" + ArrayInterfaceReverseDiffExt = "ReverseDiff" + 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" + ChainRules = "082447d4-558c-5d27-93f4-14fc19e9eca2" + GPUArraysCore = "46192b85-c4d5-4398-a991-12ede77f4527" + ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" + StaticArraysCore = "1e83bf80-4336-4d27-bf5d-d5a4f845583c" + Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" + +[[deps.ArrayLayouts]] +deps = ["FillArrays", "LinearAlgebra"] +git-tree-sha1 = "33207a8be6267bc389d0701e97a9bce6a4de68eb" +uuid = "4c555306-a7a7-4459-81d9-ec55ddd5c99a" +version = "1.9.2" +weakdeps = ["SparseArrays"] + + [deps.ArrayLayouts.extensions] + ArrayLayoutsSparseArraysExt = "SparseArrays" + +[[deps.Artifacts]] uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" -[[Atomix]] +[[deps.Atomix]] deps = ["UnsafeAtomics"] git-tree-sha1 = "c06a868224ecba914baa6942988e2f2aade419be" uuid = "a9b6321e-bd34-4604-b9c9-b65b8de01458" version = "0.1.0" -[[AtomsBase]] +[[deps.AtomsBase]] deps = ["LinearAlgebra", "PeriodicTable", "Printf", "Requires", "StaticArrays", "Unitful", "UnitfulAtomic"] git-tree-sha1 = "995c2b6b17840cd87b722ce9c6cdd72f47bab545" uuid = "a963bdd2-2df7-4f54-a1ee-49d51e6be12a" version = "0.3.5" -[[BFloat16s]] -deps = ["LinearAlgebra", "Printf", "Random", "Test"] -git-tree-sha1 = "dbf84058d0a8cbbadee18d25cf606934b22d7c66" -uuid = "ab4f0b2a-ad5b-11e8-123f-65d77653426b" -version = "0.4.2" - -[[BangBang]] +[[deps.BangBang]] deps = ["Compat", "ConstructionBase", "InitialValues", "LinearAlgebra", "Requires", "Setfield", "Tables"] git-tree-sha1 = "7aa7ad1682f3d5754e3491bb59b8103cae28e3a3" uuid = "198e06fe-97b7-11e9-32a5-e1d131e6ad66" version = "0.3.40" -[[Base64]] + [deps.BangBang.extensions] + BangBangChainRulesCoreExt = "ChainRulesCore" + BangBangDataFramesExt = "DataFrames" + BangBangStaticArraysExt = "StaticArrays" + BangBangStructArraysExt = "StructArrays" + BangBangTypedTablesExt = "TypedTables" + + [deps.BangBang.weakdeps] + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" + DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" + StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" + StructArrays = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" + TypedTables = "9d95f2ec-7b3d-5a63-8d20-e2491e220bb9" + +[[deps.Base64]] uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f" -[[Baselet]] +[[deps.Baselet]] git-tree-sha1 = "aebf55e6d7795e02ca500a689d326ac979aaf89e" uuid = "9718e550-a3fa-408a-8086-8db961cd8217" version = "0.1.1" -[[BenchmarkTools]] +[[deps.BenchmarkTools]] deps = ["JSON", "Logging", "Printf", "Profile", "Statistics", "UUIDs"] git-tree-sha1 = "f1dff6729bc61f4d49e140da1af55dcd1ac97b2f" uuid = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf" version = "1.5.0" -[[BitFlags]] +[[deps.BitFlags]] git-tree-sha1 = "2dc09997850d68179b69dafb58ae806167a32b1b" uuid = "d1d4a3ce-64b1-5f1a-9ba4-7e7e69966f35" version = "0.1.8" -[[BitTwiddlingConvenienceFunctions]] +[[deps.BitTwiddlingConvenienceFunctions]] deps = ["Static"] git-tree-sha1 = "0c5f81f47bbbcf4aea7b2959135713459170798b" uuid = "62783981-4cbd-42fc-bca8-16325de8dc4b" version = "0.1.5" -[[Bzip2_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "9e2a6b69137e6969bab0152632dcb3bc108c8bdd" -uuid = "6e34b625-4abd-537c-b88f-471c36dfa7a0" -version = "1.0.8+1" - -[[CEnum]] +[[deps.CEnum]] git-tree-sha1 = "eb4cb44a499229b3b8426dcfb5dd85333951ff90" uuid = "fa961155-64e5-5f13-b03f-caf6b980ea82" version = "0.4.2" -[[CPUSummary]] +[[deps.CPUSummary]] deps = ["CpuId", "IfElse", "PrecompileTools", "Static"] git-tree-sha1 = "601f7e7b3d36f18790e2caf83a882d88e9b71ff1" uuid = "2a0fbf3d-bb9c-48f3-b0a9-814d99fd7ab9" version = "0.2.4" -[[CUDA]] -deps = ["AbstractFFTs", "Adapt", "BFloat16s", "CEnum", 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"LayoutPointers", "LinearAlgebra", "LoopVectorization", "Polyester", "Static", "VectorizationBase"] -git-tree-sha1 = "fadebab77bf3ae041f77346dd1c290173da5a443" +git-tree-sha1 = "66c68a20907800c0b7c04ff8a6164115e8747de2" uuid = "d5829a12-d9aa-46ab-831f-fb7c9ab06edf" -version = "0.1.20" - -[[Tricks]] -git-tree-sha1 = "eae1bb484cd63b36999ee58be2de6c178105112f" -uuid = "410a4b4d-49e4-4fbc-ab6d-cb71b17b3775" -version = "0.1.8" - -[[TruncatedStacktraces]] -deps = ["InteractiveUtils", "MacroTools", "Preferences"] -git-tree-sha1 = "ea3e54c2bdde39062abf5a9758a23735558705e1" -uuid = "781d530d-4396-4725-bb49-402e4bee1e77" -version = "1.4.0" +version = "0.2.0" -[[URIs]] +[[deps.URIs]] git-tree-sha1 = "67db6cc7b3821e19ebe75791a9dd19c9b1188f2b" uuid = "5c2747f8-b7ea-4ff2-ba2e-563bfd36b1d4" version = "1.5.1" -[[UUIDs]] +[[deps.UUIDs]] deps = ["Random", "SHA"] uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4" -[[UnPack]] +[[deps.UnPack]] git-tree-sha1 = "387c1f73762231e86e0c9c5443ce3b4a0a9a0c2b" uuid = 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+[[deps.UnsafeAtomicsLLVM]] deps = ["LLVM", "UnsafeAtomics"] git-tree-sha1 = "323e3d0acf5e78a56dfae7bd8928c989b4f3083e" uuid = "d80eeb9a-aca5-4d75-85e5-170c8b632249" version = "0.1.3" -[[VectorizationBase]] +[[deps.VectorizationBase]] deps = ["ArrayInterface", "CPUSummary", "HostCPUFeatures", "IfElse", "LayoutPointers", "Libdl", "LinearAlgebra", "SIMDTypes", "Static", "StaticArrayInterface"] -git-tree-sha1 = "7209df901e6ed7489fe9b7aa3e46fb788e15db85" +git-tree-sha1 = "ac377f0a248753a1b1d58bbc92a64f5a726dfb71" uuid = "3d5dd08c-fd9d-11e8-17fa-ed2836048c2f" -version = "0.21.65" +version = "0.21.66" -[[YAML]] +[[deps.YAML]] deps = ["Base64", "Dates", "Printf", "StringEncodings"] git-tree-sha1 = "e6330e4b731a6af7959673621e91645eb1356884" uuid = "ddb6d928-2868-570f-bddf-ab3f9cf99eb6" version = "0.4.9" -[[ZipFile]] +[[deps.ZipFile]] deps = ["Libdl", "Printf", "Zlib_jll"] git-tree-sha1 = "f492b7fe1698e623024e873244f10d89c95c340a" uuid = "a5390f91-8eb1-5f08-bee0-b1d1ffed6cea" version = "0.10.1" -[[Zlib_jll]] +[[deps.Zlib_jll]] deps = ["Libdl"] uuid = "83775a58-1f1d-513f-b197-d71354ab007a" -version = "1.2.12+3" +version = "1.2.13+1" -[[Zygote]] +[[deps.Zygote]] deps = ["AbstractFFTs", "ChainRules", "ChainRulesCore", "DiffRules", "Distributed", "FillArrays", "ForwardDiff", "GPUArrays", "GPUArraysCore", "IRTools", "InteractiveUtils", "LinearAlgebra", "LogExpFunctions", "MacroTools", "NaNMath", "PrecompileTools", "Random", "Requires", "SparseArrays", "SpecialFunctions", "Statistics", "ZygoteRules"] git-tree-sha1 = "4ddb4470e47b0094c93055a3bcae799165cc68f1" uuid = "e88e6eb3-aa80-5325-afca-941959d7151f" version = "0.6.69" -[[ZygoteRules]] + [deps.Zygote.extensions] + ZygoteColorsExt = "Colors" + ZygoteDistancesExt = "Distances" + ZygoteTrackerExt = "Tracker" + + [deps.Zygote.weakdeps] + Colors = "5ae59095-9a9b-59fe-a467-6f913c188581" + Distances = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7" + Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" + +[[deps.ZygoteRules]] deps = ["ChainRulesCore", "MacroTools"] git-tree-sha1 = "27798139afc0a2afa7b1824c206d5e87ea587a00" uuid = "700de1a5-db45-46bc-99cf-38207098b444" version = "0.2.5" -[[cuDNN]] -deps = ["CEnum", "CUDA", "CUDNN_jll"] -git-tree-sha1 = "5a1ba43303c62f4a09b0d6751422de03424ab0cd" -uuid = "02a925ec-e4fe-4b08-9a7e-0d78e3d38ccd" -version = "1.1.1" - -[[extxyz_jll]] +[[deps.extxyz_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "PCRE2_jll", "libcleri_jll"] git-tree-sha1 = "873d06b969d13a1bd315ed847824b8cfded76542" uuid = "6ecdc6fc-93a8-5528-aee3-ac7ae1c60be7" version = "0.1.3+0" -[[libblastrampoline_jll]] -deps = ["Artifacts", "Libdl", "OpenBLAS_jll"] +[[deps.libblastrampoline_jll]] +deps = ["Artifacts", "Libdl"] uuid = "8e850b90-86db-534c-a0d3-1478176c7d93" -version = "5.1.1+0" +version = "5.8.0+1" -[[libcleri_jll]] +[[deps.libcleri_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "PCRE2_jll", "Pkg"] git-tree-sha1 = "9cf7bea1bc957a2133fe6ea57c95b36b5addc364" uuid = "cdc7adba-bef8-5cba-a7ee-c792dee3081e" version = "0.12.1+3" -[[libevent_jll]] +[[deps.libevent_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "OpenSSL_jll"] git-tree-sha1 = "f04ec6d9a186115fb38f858f05c0c4e1b7fc9dcb" uuid = "1080aeaf-3a6a-583e-a51c-c537b09f60ec" version = "2.1.13+1" -[[nghttp2_jll]] +[[deps.nghttp2_jll]] deps = ["Artifacts", "Libdl"] uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d" -version = "1.48.0+0" +version = "1.52.0+1" -[[p7zip_jll]] +[[deps.p7zip_jll]] deps = ["Artifacts", "Libdl"] uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0" -version = "17.4.0+0" +version = "17.4.0+2" -[[prrte_jll]] +[[deps.prrte_jll]] deps = ["Artifacts", "Hwloc_jll", "JLLWrappers", "Libdl", "PMIx_jll", "libevent_jll"] git-tree-sha1 = "5adb2d7a18a30280feb66cad6f1a1dfdca2dc7b0" uuid = "eb928a42-fffd-568d-ab9c-3f5d54fc65b9" diff --git a/src/Integrators/quadrature.jl b/src/Integrators/quadrature.jl index be27f03..fe8a0be 100644 --- a/src/Integrators/quadrature.jl +++ b/src/Integrators/quadrature.jl @@ -12,8 +12,8 @@ Contains parameters for 1D or 2D Gauss quadrature integration. - `d :: Real` : dimension """ struct GaussQuadrature <: QuadIntegrator - ξ :: Union{Vector{<:Real}, Vector{<:Vector}, Vector} - w :: Vector{<:Real} + ξ :: Union{Vector{<:Real}, Vector{<:Vector}} + w :: Union{Vector{<:Real}, Vector{<:Vector}} end # simple grid integration @@ -36,7 +36,7 @@ Computes 1D Gauss quadrature points with a change of domain to limits=[ll, ul]. - `ξ :: Vector{<:Real}` : quadrature points ranging [ll, ul] - `w :: Vector{<:Real}` : quadrature weights """ -function gaussquad(nquad::Integer, gaussbasis::Function, args...; limits=[-1,1]) +function gaussquad(nquad::Integer, gaussbasis::Function, args...; limits::Vector{<:Real}=[-1,1]) ξ, w = gaussbasis(nquad, args...) ξ, w = rescale(ξ, w, limits) return ξ, w @@ -62,7 +62,7 @@ function gaussquad_2D(nquad::Integer, gaussbasis::Function, args...; limits=[[-1 ξ, w = gaussbasis(nquad, args...) if typeof(limits) <: Vector{<:Real} ξ1, w1 = rescale(ξ, w, limits) - ξ2 = ξ1; w1 = w2 + ξ2 = ξ1; w2 = w1 else ξ1, w1 = rescale(ξ, w, limits[1]) ξ2, w2 = rescale(ξ, w, limits[2]) diff --git a/test/qoi_integration_tests.jl b/test/qoi_integration_tests.jl index 1d1bf6a..6dd793d 100644 --- a/test/qoi_integration_tests.jl +++ b/test/qoi_integration_tests.jl @@ -104,14 +104,6 @@ end πg = Gibbs(πgibbs, θ=θtest) Z = normconst(πg, GQint) - - # check this section - nsamp = 10000 - nuts = NUTS() - g = Gibbs(V=V, ∇xV=∇xV, ∇θV=∇θV, β=1.0, θ=[3,3]) - MCint = MCMC(nsamp, nuts, ρx0) - Qmc = expectation(θtest, q, MCint) - @time ∇Qmc = grad_expectation(θtest, q, MCint) end