diff --git a/Manifest.toml b/Manifest.toml index 4849931..38789ed 100644 --- a/Manifest.toml +++ b/Manifest.toml @@ -2,7 +2,7 @@ julia_version = "1.9.2" manifest_format = "2.0" -project_hash = "3cb3efc1daa833e06773d949d12011bd0cc455e9" +project_hash = "547bf31d5dc2e6452ad979d2c526bfa03b483ccd" [[deps.AbstractFFTs]] deps = ["LinearAlgebra"] @@ -25,9 +25,9 @@ version = "0.4.4" [[deps.Adapt]] deps = ["LinearAlgebra", "Requires"] -git-tree-sha1 = "76289dc51920fdc6e0013c872ba9551d54961c24" +git-tree-sha1 = "f8c724a2066b2d37d0234fe4022ec67987022d00" uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e" -version = "3.6.2" +version = "4.0.0" weakdeps = ["StaticArrays"] [deps.Adapt.extensions] @@ -50,9 +50,9 @@ version = "1.1.1" [[deps.ArrayInterface]] deps = ["Adapt", "LinearAlgebra", "Requires", "SparseArrays", "SuiteSparse"] -git-tree-sha1 = "f83ec24f76d4c8f525099b2ac475fc098138ec31" +git-tree-sha1 = "bbec08a37f8722786d87bedf84eae19c020c4efa" uuid = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9" -version = "7.4.11" +version = "7.7.0" [deps.ArrayInterface.extensions] ArrayInterfaceBandedMatricesExt = "BandedMatrices" @@ -72,9 +72,9 @@ version = "7.4.11" [[deps.ArrayLayouts]] deps = ["FillArrays", "LinearAlgebra"] -git-tree-sha1 = "9a731850434825d183af39c6e6cd0a1c32dd7e20" +git-tree-sha1 = "b08a4043e1c14096ef8efe4dd97e07de5cacf240" uuid = "4c555306-a7a7-4459-81d9-ec55ddd5c99a" -version = "1.4.2" +version = "1.4.5" weakdeps = ["SparseArrays"] [deps.ArrayLayouts.extensions] @@ -85,9 +85,9 @@ uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" [[deps.AutoHashEquals]] deps = ["Pkg"] -git-tree-sha1 = "16d2cc66d4de2b4cac1b0942671e07edbfb922c5" +git-tree-sha1 = "daaeb6f7f77b88c072a83a2451801818acb5c63b" uuid = "15f4f7f2-30c1-5605-9d31-71845cf9641f" -version = "2.0.0" +version = "2.1.0" [[deps.BSON]] git-tree-sha1 = "2208958832d6e1b59e49f53697483a84ca8d664e" @@ -99,9 +99,9 @@ uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f" [[deps.BlockArrays]] deps = ["ArrayLayouts", "FillArrays", "LinearAlgebra"] -git-tree-sha1 = "54cd829dd26330c42e1cf9df68470dd4df602c61" +git-tree-sha1 = "fc69cbdb4277042f72c6e59cbc7024fbe3034b89" uuid = "8e7c35d0-a365-5155-bbbb-fb81a777f24e" -version = "0.16.38" +version = "0.16.39" [[deps.Bzip2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -122,9 +122,9 @@ version = "1.16.1+1" [[deps.CircularArrays]] deps = ["OffsetArrays"] -git-tree-sha1 = "61bc114e595167090b4cbcb7305ddeacd4274f16" +git-tree-sha1 = "3f7b8a37359ae592cfa7aca7f811da045deff222" uuid = "7a955b69-7140-5f4e-a0ed-f168c5e2e749" -version = "1.3.2" +version = "1.3.3" [[deps.CodecZlib]] deps = ["TranscodingStreams", "Zlib_jll"] @@ -157,9 +157,9 @@ version = "0.3.0" [[deps.Compat]] deps = ["UUIDs"] -git-tree-sha1 = "8a62af3e248a8c4bad6b32cbbe663ae02275e32c" +git-tree-sha1 = "886826d76ea9e72b35fcd000e535588f7b60f21d" uuid = "34da2185-b29b-5c13-b0c7-acf172513d20" -version = "4.10.0" +version = "4.10.1" weakdeps = ["Dates", "LinearAlgebra"] [deps.Compat.extensions] @@ -208,9 +208,9 @@ version = "1.15.1" [[deps.Distances]] deps = ["LinearAlgebra", "Statistics", "StatsAPI"] -git-tree-sha1 = "5225c965635d8c21168e32a12954675e7bea1151" +git-tree-sha1 = "66c4c81f259586e8f002eacebc177e1fb06363b0" uuid = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7" -version = "0.10.10" +version = "0.10.11" [deps.Distances.extensions] DistancesChainRulesCoreExt = "ChainRulesCore" @@ -249,9 +249,9 @@ version = "2.5.0+0" [[deps.FFTW]] deps = ["AbstractFFTs", "FFTW_jll", "LinearAlgebra", "MKL_jll", "Preferences", "Reexport"] -git-tree-sha1 = "b4fbdd20c889804969571cc589900803edda16b7" +git-tree-sha1 = "ec22cbbcd01cba8f41eecd7d44aac1f23ee985e3" uuid = "7a1cc6ca-52ef-59f5-83cd-3a7055c09341" -version = "1.7.1" +version = "1.7.2" [[deps.FFTW_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -282,15 +282,20 @@ uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" [[deps.FillArrays]] deps = ["LinearAlgebra", "Random"] -git-tree-sha1 = "a20eaa3ad64254c61eeb5f230d9306e937405434" +git-tree-sha1 = "5b93957f6dcd33fc343044af3d48c215be2562f1" uuid = "1a297f60-69ca-5386-bcde-b61e274b549b" -version = "1.6.1" -weakdeps = ["SparseArrays", "Statistics"] +version = "1.9.3" [deps.FillArrays.extensions] + FillArraysPDMatsExt = "PDMats" FillArraysSparseArraysExt = "SparseArrays" FillArraysStatisticsExt = "Statistics" + [deps.FillArrays.weakdeps] + PDMats = "90014a1f-27ba-587c-ab20-58faa44d9150" + SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" + Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" + [[deps.FiniteDiff]] deps = ["ArrayInterface", "LinearAlgebra", "Requires", "Setfield", "SparseArrays"] git-tree-sha1 = "c6e4a1fbe73b31a3dea94b1da449503b8830c306" @@ -375,19 +380,19 @@ version = "1.3.1" [[deps.Gridap]] deps = ["AbstractTrees", "BSON", "BlockArrays", "Combinatorics", "DataStructures", "DocStringExtensions", "FastGaussQuadrature", "FileIO", "FillArrays", "ForwardDiff", "JLD2", "JSON", "LineSearches", "LinearAlgebra", "NLsolve", "NearestNeighbors", "PolynomialBases", "QuadGK", "Random", "SparseArrays", "SparseMatricesCSR", "StaticArrays", "Test", "WriteVTK"] -git-tree-sha1 = "666d4d66201e7cc9142fe940f8e42ac6fb616291" +git-tree-sha1 = "0ff991a6beee6cbe9e0804ef3cb368cbe4ed83ab" repo-rev = "master" repo-url = "https://github.com/gridap/Gridap.jl.git" uuid = "56d4f2e9-7ea1-5844-9cf6-b9c51ca7ce8e" -version = "0.17.20" +version = "0.17.21" [[deps.GridapDistributed]] deps = ["BlockArrays", "FillArrays", "Gridap", "LinearAlgebra", "MPI", "PartitionedArrays", "SparseArrays", "SparseMatricesCSR", "WriteVTK"] -git-tree-sha1 = "a61a30f052a9a9d2a1548c80d1a130e78c62cb3c" +git-tree-sha1 = "acad4231797aa33b8ad3f636ad8e8d075eee024a" repo-rev = "master" repo-url = "https://github.com/gridap/GridapDistributed.jl.git" uuid = "f9701e48-63b3-45aa-9a63-9bc6c271f355" -version = "0.3.1" +version = "0.3.5" [[deps.GridapGmsh]] deps = ["Gridap", "GridapDistributed", "Libdl", "Metis", "PartitionedArrays", "gmsh_jll"] @@ -397,22 +402,24 @@ version = "0.7.0" [[deps.GridapP4est]] deps = ["ArgParse", "FillArrays", "Gridap", "GridapDistributed", "Libdl", "MPI", "P4est_wrapper", "PartitionedArrays", "Test"] -git-tree-sha1 = "8188694b39e7afafd19539d9864db96ad67159b9" -repo-rev = "uniform-3d" +git-tree-sha1 = "db6555cabb76b1362f0044f5a7b90ef145c86389" +repo-rev = "main" repo-url = "https://github.com/gridap/GridapP4est.jl.git" uuid = "c2c8e14b-f5fd-423d-9666-1dd9ad120af9" -version = "0.3.1" +version = "0.3.4" [[deps.GridapPETSc]] deps = ["Gridap", "GridapDistributed", "Libdl", "LinearAlgebra", "MPI", "PETSc_jll", "PartitionedArrays", "Random", "SparseArrays", "SparseMatricesCSR"] -git-tree-sha1 = "fc15fcc0833736ce264b0454edad40e8f3176b7f" +git-tree-sha1 = "fdef4c7834299334044da32dae4003d3020ebf5f" +repo-rev = "add_missing_api" +repo-url = "https://github.com/gridap/GridapPETSc.jl.git" uuid = "bcdc36c2-0c3e-11ea-095a-c9dadae499f1" version = "0.5.0" [[deps.GridapSolvers]] -deps = ["AbstractTrees", "ArgParse", "BlockArrays", "FillArrays", "Gridap", "GridapDistributed", "GridapP4est", "GridapPETSc", "IterativeSolvers", "LinearAlgebra", "MPI", "PartitionedArrays", "Printf", "SparseArrays", "SparseMatricesCSR"] -git-tree-sha1 = "f2176c38ef5bf05e5e10603770c36416b01a2bae" -repo-rev = "develop" +deps = ["AbstractTrees", "ArgParse", "BlockArrays", "FillArrays", "Gridap", "GridapDistributed", "GridapP4est", "GridapPETSc", "IterativeSolvers", "LinearAlgebra", "MPI", "P4est_wrapper", "PartitionedArrays", "Printf", "SparseArrays", "SparseMatricesCSR"] +git-tree-sha1 = "e4808b9bfa48625c23c9f7a2494a108fb464e99c" +repo-rev = "block-solvers" repo-url = "https://github.com/gridap/GridapSolvers.jl.git" uuid = "6d3209ee-5e3c-4db7-a716-942eb12ed534" version = "0.2.0" @@ -429,10 +436,10 @@ uuid = "9b13fd28-a010-5f03-acff-a1bbcff69959" version = "1.0.0" [[deps.IntelOpenMP_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "ad37c091f7d7daf900963171600d7c1c5c3ede32" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "5fdf2fe6724d8caabf43b557b84ce53f3b7e2f6b" uuid = "1d5cc7b8-4909-519e-a0f8-d0f5ad9712d0" -version = "2023.2.0+0" +version = "2024.0.2+0" [[deps.InteractiveUtils]] deps = ["Markdown"] @@ -445,15 +452,15 @@ version = "0.2.2" [[deps.IterativeSolvers]] deps = ["LinearAlgebra", "Printf", "Random", "RecipesBase", "SparseArrays"] -git-tree-sha1 = "1169632f425f79429f245113b775a0e3d121457c" +git-tree-sha1 = "b435d190ef8369cf4d79cc9dd5fba88ba0165307" uuid = "42fd0dbc-a981-5370-80f2-aaf504508153" -version = "0.9.2" +version = "0.9.3" [[deps.JLD2]] -deps = ["FileIO", "MacroTools", "Mmap", "OrderedCollections", "Pkg", "Printf", "Reexport", "Requires", "TranscodingStreams", "UUIDs"] -git-tree-sha1 = "c11d691a0dc8e90acfa4740d293ade57f68bfdbb" +deps = ["FileIO", "MacroTools", "Mmap", "OrderedCollections", "Pkg", "PrecompileTools", "Printf", "Reexport", "Requires", "TranscodingStreams", "UUIDs"] +git-tree-sha1 = "c2d0f45afcb5f6209155670bffd100c3b4937ea3" uuid = "033835bb-8acc-5ee8-8aae-3f567f8a3819" -version = "0.4.35" +version = "0.4.40" [[deps.JLLWrappers]] deps = ["Artifacts", "Preferences"] @@ -469,15 +476,15 @@ version = "0.21.4" [[deps.JpegTurbo_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "6f2675ef130a300a112286de91973805fcc5ffbc" +git-tree-sha1 = "60b1194df0a3298f460063de985eae7b01bc011a" uuid = "aacddb02-875f-59d6-b918-886e6ef4fbf8" -version = "2.1.91+0" +version = "3.0.1+0" [[deps.LLVMOpenMP_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "f689897ccbe049adb19a065c495e75f372ecd42b" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "d986ce2d884d49126836ea94ed5bfb0f12679713" uuid = "1d63c593-3942-5779-bab2-d838dc0a180e" -version = "15.0.4+0" +version = "15.0.7+0" [[deps.LZO_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -561,9 +568,9 @@ version = "2.36.0+0" [[deps.LightXML]] deps = ["Libdl", "XML2_jll"] -git-tree-sha1 = "e129d9391168c677cd4800f5c0abb1ed8cb3794f" +git-tree-sha1 = "3a994404d3f6709610701c7dabfc03fed87a81f8" uuid = "9c8b4983-aa76-5018-a973-4c85ecc9e179" -version = "0.9.0" +version = "0.9.1" [[deps.LineSearches]] deps = ["LinearAlgebra", "NLSolversBase", "NaNMath", "Parameters", "Printf"] @@ -607,10 +614,10 @@ uuid = "d00139f3-1899-568f-a2f0-47f597d42d70" version = "5.1.2+0" [[deps.MKL_jll]] -deps = ["Artifacts", "IntelOpenMP_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "Pkg"] -git-tree-sha1 = "eb006abbd7041c28e0d16260e50a24f8f9104913" +deps = ["Artifacts", "IntelOpenMP_jll", "JLLWrappers", "LazyArtifacts", "Libdl"] +git-tree-sha1 = "72dc3cf284559eb8f53aa593fe62cb33f83ed0c0" uuid = "856f044c-d86e-5d09-b602-aeab76dc8ba7" -version = "2023.2.0+0" +version = "2024.0.0+0" [[deps.MMG_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "LinearElasticity_jll", "Pkg", "SCOTCH_jll"] @@ -620,9 +627,9 @@ version = "5.6.0+0" [[deps.MPI]] deps = ["Distributed", "DocStringExtensions", "Libdl", "MPICH_jll", "MPIPreferences", "MPItrampoline_jll", "MicrosoftMPI_jll", "OpenMPI_jll", "PkgVersion", "PrecompileTools", "Requires", "Serialization", "Sockets"] -git-tree-sha1 = "b4d8707e42b693720b54f0b3434abee6dd4d947a" +git-tree-sha1 = "4e3136db3735924f96632a5b40a5979f1f53fa07" uuid = "da04e1cc-30fd-572f-bb4f-1f8673147195" -version = "0.20.16" +version = "0.20.19" [deps.MPI.extensions] AMDGPUExt = "AMDGPU" @@ -634,27 +641,27 @@ version = "0.20.16" [[deps.MPICH_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "MPIPreferences", "TOML"] -git-tree-sha1 = "8a5b4d2220377d1ece13f49438d71ad20cf1ba83" +git-tree-sha1 = "2ee75365ca243c1a39d467e35ffd3d4d32eef11e" uuid = "7cb0a576-ebde-5e09-9194-50597f1243b4" -version = "4.1.2+0" +version = "4.1.2+1" [[deps.MPIPreferences]] deps = ["Libdl", "Preferences"] -git-tree-sha1 = "781916a2ebf2841467cda03b6f1af43e23839d85" +git-tree-sha1 = "8f6af051b9e8ec597fa09d8885ed79fd582f33c9" uuid = "3da0fdf6-3ccc-4f1b-acd9-58baa6c99267" -version = "0.1.9" +version = "0.1.10" [[deps.MPItrampoline_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "MPIPreferences", "TOML"] -git-tree-sha1 = "6979eccb6a9edbbb62681e158443e79ecc0d056a" +git-tree-sha1 = "8eeb3c73bbc0ca203d0dc8dad4008350bbe5797b" uuid = "f1f71cc9-e9ae-5b93-9b94-4fe0e1ad3748" -version = "5.3.1+0" +version = "5.3.1+1" [[deps.MacroTools]] deps = ["Markdown", "Random"] -git-tree-sha1 = "9ee1618cbf5240e6d4e0371d6f24065083f60c48" +git-tree-sha1 = "b211c553c199c111d998ecdaf7623d1b89b69f93" uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09" -version = "0.5.11" +version = "0.5.12" [[deps.Markdown]] deps = ["Base64"] @@ -683,9 +690,9 @@ version = "1.4.0" [[deps.MicrosoftMPI_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "a7023883872e52bc29bcaac74f19adf39347d2d5" +git-tree-sha1 = "b01beb91d20b0d1312a9471a36017b5b339d26de" uuid = "9237b28f-5490-5468-be7b-bb81f5f5e6cf" -version = "10.1.4+0" +version = "10.1.4+1" [[deps.Mmap]] uuid = "a63ad114-7e13-5084-954f-fe012c677804" @@ -714,9 +721,9 @@ version = "1.0.2" [[deps.NearestNeighbors]] deps = ["Distances", "StaticArrays"] -git-tree-sha1 = "2c3726ceb3388917602169bed973dbc97f1b51a8" +git-tree-sha1 = "ded64ff6d4fdd1cb68dfcbb818c69e144a5b2e4c" uuid = "b8a86587-4115-5ab1-83bc-aa920d37bbce" -version = "0.4.13" +version = "0.4.16" [[deps.NetworkOptions]] uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908" @@ -729,10 +736,13 @@ uuid = "baad4e97-8daa-5946-aac2-2edac59d34e1" version = "7.6.2+2" [[deps.OffsetArrays]] -deps = ["Adapt"] -git-tree-sha1 = "2ac17d29c523ce1cd38e27785a7d23024853a4bb" +git-tree-sha1 = "6a731f2b5c03157418a20c12195eb4b74c8f8621" uuid = "6fe1bfb0-de20-5000-8ca7-80f57d26f881" -version = "1.12.10" +version = "1.13.0" +weakdeps = ["Adapt"] + + [deps.OffsetArrays.extensions] + OffsetArraysAdaptExt = "Adapt" [[deps.OpenBLAS32_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Pkg"] @@ -769,9 +779,9 @@ uuid = "efe28fd5-8261-553b-a9e1-b2916fc3738e" version = "0.5.5+0" [[deps.OrderedCollections]] -git-tree-sha1 = "2e73fe17cac3c62ad1aebe70d44c963c3cfdc3e3" +git-tree-sha1 = "dfdf5519f235516220579f949664f1bf44e741c5" uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d" -version = "1.6.2" +version = "1.6.3" [[deps.P4est_jll]] deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "MPICH_jll", "MPIPreferences", "MPItrampoline_jll", "MicrosoftMPI_jll", "OpenMPI_jll", "Pkg", "TOML", "Zlib_jll"] @@ -781,7 +791,9 @@ version = "2.8.1+2" [[deps.P4est_wrapper]] deps = ["CEnum", "Libdl", "MPI", "P4est_jll"] -git-tree-sha1 = "c182e067e6bac213c6e75e4139d01ebfb7ea0a58" +git-tree-sha1 = "d1dc7da59aefe29ff874970dc141fab07378e791" +repo-rev = "p4est-2.3+" +repo-url = "https://github.com/gridap/P4est_wrapper.jl.git" uuid = "3743d7c0-8adf-11ea-380b-7d33b0ecc1da" version = "0.2.0" @@ -797,10 +809,10 @@ uuid = "8fa3689e-f0b9-5420-9873-adf6ccf46f2d" version = "3.15.2+0" [[deps.PackageCompiler]] -deps = ["Artifacts", "Glob", "LazyArtifacts", "Libdl", "Pkg", "Printf", "RelocatableFolders", "TOML", "UUIDs"] -git-tree-sha1 = "d24f0920777c64c0265e9725eb4a3ec450bc36dd" +deps = ["Artifacts", "Glob", "LazyArtifacts", "Libdl", "Pkg", "Printf", "RelocatableFolders", "TOML", "UUIDs", "p7zip_jll"] +git-tree-sha1 = "8b880733c61c4a99a069302390de2d057ee166ce" uuid = "9b87118b-4619-50d2-8e1e-99f35a4d4d9d" -version = "2.1.10" +version = "2.1.16" [[deps.Parameters]] deps = ["OrderedCollections", "UnPack"] @@ -810,9 +822,9 @@ version = "0.12.3" [[deps.Parsers]] deps = ["Dates", "PrecompileTools", "UUIDs"] -git-tree-sha1 = "716e24b21538abc91f6205fd1d8363f39b442851" +git-tree-sha1 = "8489905bcdbcfac64d1daa51ca07c0d8f0283821" uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0" -version = "2.7.2" +version = "2.8.1" [[deps.PartitionedArrays]] deps = ["CircularArrays", "Distances", "FillArrays", "IterativeSolvers", "LinearAlgebra", "MPI", "Printf", "Random", "SparseArrays", "SparseMatricesCSR"] @@ -912,9 +924,9 @@ version = "0.7.0" [[deps.Scratch]] deps = ["Dates"] -git-tree-sha1 = "30449ee12237627992a99d5e30ae63e4d78cd24a" +git-tree-sha1 = "3bac05bc7e74a75fd9cba4295cde4045d9fe2386" uuid = "6c6a2e73-6563-6170-7368-637461726353" -version = "1.2.0" +version = "1.2.1" [[deps.Serialization]] uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b" @@ -956,15 +968,19 @@ version = "2.3.1" ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" [[deps.StaticArrays]] -deps = ["LinearAlgebra", "Random", "StaticArraysCore"] -git-tree-sha1 = "0adf069a2a490c47273727e029371b31d44b72b2" +deps = ["LinearAlgebra", "PrecompileTools", "Random", "StaticArraysCore"] +git-tree-sha1 = "fba11dbe2562eecdfcac49a05246af09ee64d055" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.6.5" -weakdeps = ["Statistics"] +version = "1.8.1" [deps.StaticArrays.extensions] + StaticArraysChainRulesCoreExt = "ChainRulesCore" StaticArraysStatisticsExt = "Statistics" + [deps.StaticArrays.weakdeps] + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" + Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" + [[deps.StaticArraysCore]] git-tree-sha1 = "36b3d696ce6366023a0ea192b4cd442268995a0d" uuid = "1e83bf80-4336-4d27-bf5d-d5a4f845583c" @@ -1034,15 +1050,15 @@ version = "1.0.1" [[deps.WriteVTK]] deps = ["Base64", "CodecZlib", "FillArrays", "LightXML", "TranscodingStreams", "VTKBase"] -git-tree-sha1 = "7b46936613e41cfe1c6a5897d243ddcab8feabec" +git-tree-sha1 = "41f0dc2a8f6fd860c266b91fd5cdf4fead65ae69" uuid = "64499a7a-5c06-52f2-abe2-ccb03c286192" -version = "1.18.0" +version = "1.18.1" [[deps.XML2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Zlib_jll"] -git-tree-sha1 = "24b81b59bd35b3c42ab84fa589086e19be919916" +git-tree-sha1 = "801cbe47eae69adc50f36c3caec4758d2650741b" uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a" -version = "2.11.5+0" +version = "2.12.2+0" [[deps.XSLT_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgcrypt_jll", "Libgpg_error_jll", "Libiconv_jll", "Pkg", "XML2_jll", "Zlib_jll"] @@ -1133,10 +1149,10 @@ uuid = "8e850b90-86db-534c-a0d3-1478176c7d93" version = "5.8.0+0" [[deps.libpng_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] -git-tree-sha1 = "94d180a6d2b5e55e447e2d27a29ed04fe79eb30c" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Zlib_jll"] +git-tree-sha1 = "93284c28274d9e75218a416c65ec49d0e0fcdf3d" uuid = "b53b4c65-9356-5827-b1ea-8c7a1a84506f" -version = "1.6.38+0" +version = "1.6.40+0" [[deps.nghttp2_jll]] deps = ["Artifacts", "Libdl"] diff --git a/Project.toml b/Project.toml index 8a47ff6..1db192c 100644 --- a/Project.toml +++ b/Project.toml @@ -17,6 +17,7 @@ GridapPETSc = "bcdc36c2-0c3e-11ea-095a-c9dadae499f1" GridapSolvers = "6d3209ee-5e3c-4db7-a716-942eb12ed534" LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" MPI = "da04e1cc-30fd-572f-bb4f-1f8673147195" +P4est_wrapper = "3743d7c0-8adf-11ea-380b-7d33b0ecc1da" PackageCompiler = "9b87118b-4619-50d2-8e1e-99f35a4d4d9d" PartitionedArrays = "5a9dfac6-5c52-46f7-8278-5e2210713be9" Profile = "9abbd945-dff8-562f-b5e8-e1ebf5ef1b79" diff --git a/src/FEOperators.jl b/src/FEOperators.jl deleted file mode 100644 index 085bf2e..0000000 --- a/src/FEOperators.jl +++ /dev/null @@ -1,52 +0,0 @@ -""" - -""" -struct FEOperatorMHD <: Gridap.FESpaces.FEOperator - op_global :: FEOperator # global operator - op_u :: FEOperator # operator for u -end - -Gridap.FESpaces.get_test(op::FEOperatorMHD) = get_test(op.op_global) -Gridap.FESpaces.get_trial(op::FEOperatorMHD) = get_trial(op.op_global) - -# Delegate most of the methods to the global operator -Gridap.FESpaces.allocate_residual(op::FEOperatorMHD,uh) = allocate_residual(op.op_global,uh) -Gridap.FESpaces.residual!(b::AbstractVector,op::FEOperatorMHD,uh) = residual!(b,op.op_global,uh) -Gridap.FESpaces.residual_and_jacobian(op::FEOperatorMHD,uh) = residual_and_jacobian(op.op_global,uh) -Gridap.FESpaces.residual_and_jacobian!(b::AbstractVector,A::AbstractMatrix,op::FEOperatorMHD,uh) = residual_and_jacobian!(b,A,op.op_global,uh) - -# When updating the matrix, only update the u-u block -Gridap.FESpaces.allocate_jacobian(op::FEOperatorMHD,uh) = allocate_jacobian(op.op_global,uh) -Gridap.FESpaces.jacobian(op::FEOperatorMHD,uh) = jacobian(op.op_global,uh) -function Gridap.FESpaces.jacobian!(A::AbstractBlockMatrix,op::FEOperatorMHD,xh) - uh, ph, jh, φh = xh - jacobian!(A[Block(1,1)],op.op_u,uh) - return A -end - -function weakform_uu(params,k) - fluid = params[:fluid] - Ωf = _interior(params[:model],fluid[:domain]) - dΩf = Measure(Ωf,2*k) - - α = fluid[:α] - β = fluid[:β] - f = fluid[:f] - ζ = params[:ζ] - - #function a(u,dv) - # r = ∫(β*(∇(u)⊙∇(dv))) * dΩf - # if ζ !== nothing - # r += ∫(ζ*(∇⋅u)*(∇⋅dv)) * dΩf - # end - # return r - #end - a(u,dv) = ∫(β*(∇(u)⊙∇(dv))) * dΩf - l(dv) = ∫( dv⋅f ) * dΩf - c(u,dv) = ∫( α*dv⋅(conv∘(u,∇(u))) ) * dΩf - dc(u,du,dv) = ∫( α*dv⋅( (conv∘(u,∇(du))) + (conv∘(du,∇(u))) ) ) * dΩf - - res(u,dv) = c(u,dv) + a(u,dv) - l(dv) - jac(u,du,dv) = dc(u,du,dv) + a(du,dv) - return res, jac -end diff --git a/src/GridapMHD.jl b/src/GridapMHD.jl index cd98305..d54e551 100644 --- a/src/GridapMHD.jl +++ b/src/GridapMHD.jl @@ -31,7 +31,7 @@ using GridapPETSc.PETSC using GridapSolvers using GridapSolvers.LinearSolvers -using GridapSolvers.LinearSolvers: allocate_col_vector, allocate_row_vector +using GridapSolvers.LinearSolvers: allocate_in_domain, allocate_in_range using PartitionedArrays using PartitionedArrays: getany @@ -45,7 +45,6 @@ include("Li2019/Li2019.jl") # Main driver include("Fixes.jl") include("ExtraFunctions.jl") -include("FEOperators.jl") include("parameters.jl") include("Main.jl") diff --git a/src/Li2019/Li2019.jl b/src/Li2019/Li2019.jl index 18fd7a6..43775ab 100644 --- a/src/Li2019/Li2019.jl +++ b/src/Li2019/Li2019.jl @@ -25,10 +25,9 @@ using GridapPETSc using GridapSolvers using GridapSolvers.LinearSolvers -using GridapSolvers.LinearSolvers: allocate_col_vector, allocate_row_vector +using GridapSolvers.LinearSolvers: allocate_in_domain, allocate_in_range include("NLSolvers.jl") -include("PETScLinearSolvers.jl") include("blocks.jl") include("preconditioner.jl") diff --git a/src/Li2019/NLSolvers.jl b/src/Li2019/NLSolvers.jl index 75c6788..4c8e5c1 100644 --- a/src/Li2019/NLSolvers.jl +++ b/src/Li2019/NLSolvers.jl @@ -2,7 +2,7 @@ function Gridap.Algebra.solve!(x::AbstractVector,nls::NewtonRaphsonSolver,op::NonlinearOperator,cache::Nothing) b = residual(op, x) A = jacobian(op, x) - dx = allocate_col_vector(A) + dx = allocate_in_domain(A) ns = numerical_setup(symbolic_setup(nls.ls, A), A) Gridap.Algebra._solve_nr!(x,A,b,dx,ns,nls,op) diff --git a/src/Li2019/PETScLinearSolvers.jl b/src/Li2019/PETScLinearSolvers.jl deleted file mode 100644 index 8302afd..0000000 --- a/src/Li2019/PETScLinearSolvers.jl +++ /dev/null @@ -1,67 +0,0 @@ - -using GridapPETSc: PETScMatrix, PETScVector, PETScLinearSolverSS -using GridapPETSc.PETSC -using MPI - -mutable struct CachedPETScLinearSolverNS <: NumericalSetup - B::PETScMatrix - ksp::Ref{KSP} - initialized::Bool - caches - function CachedPETScLinearSolverNS(B::PETScMatrix,caches) - new(B,Ref{KSP}(),false,caches) - end -end - -function Init(a::CachedPETScLinearSolverNS) - @assert Threads.threadid() == 1 - GridapPETSc._NREFS[] += 1 - a.initialized = true - finalizer(Finalize,a) -end - -function Finalize(ns::CachedPETScLinearSolverNS) - if ns.initialized && GridapPETSc.Initialized() - if ns.B.comm == MPI.COMM_SELF - @check_error_code PETSC.KSPDestroy(ns.ksp) - else - @check_error_code PETSC.PetscObjectRegisterDestroy(ns.ksp[].ptr) - end - ns.initialized = false - @assert Threads.threadid() == 1 - GridapPETSc._NREFS[] -= 1 - end - nothing -end - -function get_petsc_caches(A::AbstractMatrix) - X = convert(PETScVector,allocate_col_vector(A)) - B = convert(PETScVector,allocate_col_vector(A)) - return X,B -end - -function Algebra.numerical_setup(ss::PETScLinearSolverSS,A::AbstractMatrix) - B = convert(PETScMatrix,A) - caches = get_petsc_caches(A) - ns = CachedPETScLinearSolverNS(B,caches) - @check_error_code PETSC.KSPCreate(B.comm,ns.ksp) - @check_error_code PETSC.KSPSetOperators(ns.ksp[],ns.B.mat[],ns.B.mat[]) - ss.solver.setup(ns.ksp) - @check_error_code PETSC.KSPSetUp(ns.ksp[]) - Init(ns) -end - -function Algebra.solve!(x::AbstractVector{PetscScalar},ns::CachedPETScLinearSolverNS,b::AbstractVector{PetscScalar}) - X, B = ns.caches - copy!(B,b) - @check_error_code PETSC.KSPSolve(ns.ksp[],B.vec[],X.vec[]) - copy!(x,X) - return x -end - -function Algebra.numerical_setup!(ns::CachedPETScLinearSolverNS,A::AbstractMatrix) - copy!(ns.B,A) - @check_error_code PETSC.KSPSetOperators(ns.ksp[],ns.B.mat[],ns.B.mat[]) - @check_error_code PETSC.KSPSetUp(ns.ksp[]) - return ns -end diff --git a/src/Li2019/preconditioner.jl b/src/Li2019/preconditioner.jl index 474b177..4ef416f 100644 --- a/src/Li2019/preconditioner.jl +++ b/src/Li2019/preconditioner.jl @@ -25,10 +25,10 @@ mutable struct LI2019_NS <: Gridap.Algebra.NumericalSetup end function allocate_caches(solver::Li2019_Preconditioner,A::AbstractBlockMatrix) - du = allocate_col_vector(A[Block(1,1)]) - dp = allocate_col_vector(A[Block(2,2)]) - dj = allocate_col_vector(A[Block(3,3)]) - dφ = allocate_col_vector(A[Block(4,4)]) + du = allocate_in_domain(A[Block(1,1)]) + dp = allocate_in_domain(A[Block(2,2)]) + dj = allocate_in_domain(A[Block(3,3)]) + dφ = allocate_in_domain(A[Block(4,4)]) return du, dp, dj, dφ end diff --git a/src/Li2019/solver.jl b/src/Li2019/solver.jl index 7383aad..4824243 100644 --- a/src/Li2019/solver.jl +++ b/src/Li2019/solver.jl @@ -155,7 +155,7 @@ function test_preconditioner(op,P) # Test preconditioner i_am_main(parts) && println(repeat("=",50)) ns = numerical_setup(symbolic_setup(P,A),A) - x = allocate_col_vector(A) + x = allocate_in_domain(A) solve!(x,ns,b) e = norm(x) i_am_main(parts) && println("P error: ",e) @@ -168,8 +168,8 @@ function test_block_solvers(parts,block_solvers,block_mats) function test_solver(s,m) ns = numerical_setup(symbolic_setup(s,m),m) - x = allocate_col_vector(m) - b = allocate_col_vector(m) + x = allocate_in_domain(m) + b = allocate_in_domain(m) fill!(b,1.0) x = solve!(x,ns,b) return norm(b - m*x) diff --git a/src/Main.jl b/src/Main.jl index 145676e..8f9c5d7 100644 --- a/src/Main.jl +++ b/src/Main.jl @@ -291,8 +291,13 @@ end function weak_form(params,k) fluid = params[:fluid] - Ωf = _interior(params[:model],fluid[:domain]) - dΩf = Measure(Ωf,2*k) + Ωf = _interior(params[:model],fluid[:domain]) + dΩf = Measure(Ωf,2*k) + + α, β, γ, σf = fluid[:α], fluid[:β], fluid[:γ], fluid[:σ] + f = fluid[:f] + B = fluid[:B] + ζ = params[:ζ] solid = params[:solid] if solid !== nothing @@ -301,14 +306,6 @@ function weak_form(params,k) σs = solid[:σ] end - α = fluid[:α] - β = fluid[:β] - γ = fluid[:γ] - f = fluid[:f] - B = fluid[:B] - σf = fluid[:σ] - ζ = params[:ζ] - bcs = params[:bcs] params_φ = [] @@ -466,6 +463,3 @@ function a_B(x,dy,γ,B,dΩ) v_u, v_p, v_j, v_φ = dy ∫( -(γ*(j×B)⋅v_u) - (u×B)⋅v_j )*dΩ end - - - diff --git a/test/dev/Dj_solver.jl b/test/dev/Dj_solver.jl index 825bd15..e61ddf1 100644 --- a/test/dev/Dj_solver.jl +++ b/test/dev/Dj_solver.jl @@ -9,9 +9,9 @@ using Gridap.ReferenceFEs function test_smoother(s,D_j) ns = numerical_setup(symbolic_setup(s,D_j),D_j) - b = GridapSolvers.allocate_col_vector(D_j) - x = GridapSolvers.allocate_col_vector(D_j) - y = GridapSolvers.allocate_row_vector(D_j) + b = GridapSolvers.allocate_in_domain(D_j) + x = GridapSolvers.allocate_in_domain(D_j) + y = GridapSolvers.allocate_in_range(D_j) fill!(b,1.0) y = b - D_j*x @@ -24,8 +24,8 @@ end function test_solver(s,D_j) ns = numerical_setup(symbolic_setup(s,D_j),D_j) - b = GridapSolvers.allocate_col_vector(D_j) - x = GridapSolvers.allocate_col_vector(D_j) + b = GridapSolvers.allocate_in_domain(D_j) + x = GridapSolvers.allocate_in_domain(D_j) fill!(b,1.0) solve!(x,ns,b) diff --git a/test/dev/Dj_solver_gmg.jl b/test/dev/Dj_solver_gmg.jl index 3b36716..20155f5 100644 --- a/test/dev/Dj_solver_gmg.jl +++ b/test/dev/Dj_solver_gmg.jl @@ -105,8 +105,8 @@ end function test_solver(s,D_j) ns = numerical_setup(symbolic_setup(s,D_j),D_j) - b = GridapSolvers.allocate_col_vector(D_j) - x = GridapSolvers.allocate_col_vector(D_j) + b = GridapSolvers.allocate_in_domain(D_j) + x = GridapSolvers.allocate_in_domain(D_j) fill!(b,1.0) solve!(x,ns,b) @@ -117,9 +117,9 @@ end function test_smoother(s,D_j) ns = numerical_setup(symbolic_setup(s,D_j),D_j) - b = GridapSolvers.allocate_col_vector(D_j) - x = GridapSolvers.allocate_col_vector(D_j) - r = GridapSolvers.allocate_row_vector(D_j) + b = GridapSolvers.allocate_in_domain(D_j) + x = GridapSolvers.allocate_in_domain(D_j) + r = GridapSolvers.allocate_in_range(D_j) fill!(b,1.0) fill!(x,1.0) mul!(r,D_j,x) @@ -226,12 +226,12 @@ gmg = GMGLinearSolver(mh, solver = FGMRESSolver(100,gmg;rtol=1e-6,verbose=true) ns = numerical_setup(symbolic_setup(solver,A),A) -x = GridapSolvers.allocate_col_vector(A) +x = GridapSolvers.allocate_in_domain(A) solve!(x,ns,b) Pl = LinearSolvers.IdentitySolver() solver2 = GMRESSolver(1000;Pl=Pl,rtol=1e-6,verbose=true) ns2 = numerical_setup(symbolic_setup(solver2,A),A) -x2 = GridapSolvers.allocate_col_vector(A) +x2 = GridapSolvers.allocate_in_domain(A) solve!(x2,ns2,b) diff --git a/test/dev/Dj_solver_petsc.jl b/test/dev/Dj_solver_petsc.jl index 0c7bd4e..a168804 100644 --- a/test/dev/Dj_solver_petsc.jl +++ b/test/dev/Dj_solver_petsc.jl @@ -41,8 +41,8 @@ end function test_solver(s,D_j) ns = numerical_setup(symbolic_setup(s,D_j),D_j) - b = GridapSolvers.allocate_col_vector(D_j) - x = GridapSolvers.allocate_col_vector(D_j) + b = GridapSolvers.allocate_in_domain(D_j) + x = GridapSolvers.allocate_in_domain(D_j) fill!(b,1.0) solve!(x,ns,b) diff --git a/test/dev/Lp_solver.jl b/test/dev/Lp_solver.jl index af534f7..6338778 100644 --- a/test/dev/Lp_solver.jl +++ b/test/dev/Lp_solver.jl @@ -116,8 +116,8 @@ a_dg(p,v_p) = a_cg(p,v_p) + aΛ(p,v_p) + aΓ(p,v_p) Δp = assemble_matrix(a_dg,U_p,V_p) # Solver -b = GridapSolvers.allocate_col_vector(Δp) -x = GridapSolvers.allocate_col_vector(Δp) +b = GridapSolvers.allocate_in_domain(Δp) +x = GridapSolvers.allocate_in_domain(Δp) fill!(x,0.0) fill!(b,1.0)