From fc488f11426199b462c47aa0d072fbad26efd93e Mon Sep 17 00:00:00 2001 From: termi-official Date: Fri, 14 Jun 2024 18:58:59 +0200 Subject: [PATCH] Update monodomain discretizer to use heat discretizer and reresolve Manifests with new compats. --- Project.toml | 4 +- docs/Manifest.toml | 22 +- examples-gpu/Manifest.toml | 2171 +++++++++++++++++++++++++++++ examples-gpu/Project.toml | 2 - examples-gpu/spiral-wave.jl | 1 + examples/Manifest.toml | 172 ++- examples/Project.toml | 1 - examples/spiral-wave.jl | 3 +- src/discretization/fem.jl | 25 +- src/modeling/common.jl | 1 + src/modeling/core/diffusion.jl | 2 +- src/modeling/electrophysiology.jl | 88 +- 12 files changed, 2330 insertions(+), 162 deletions(-) create mode 100644 examples-gpu/Manifest.toml diff --git a/Project.toml b/Project.toml index 0d928e07..e2e6255d 100644 --- a/Project.toml +++ b/Project.toml @@ -38,9 +38,11 @@ CuThunderboltExt = "CUDA" [compat] Aqua = "0.8" BlockArrays = "1" +DiffEqBase = "6.151.3" +julia = "1.10" LinearSolve = "2" ModelingToolkit = "9" -julia = "1.10" +UnPack = "1" [extras] Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595" diff --git a/docs/Manifest.toml b/docs/Manifest.toml index 14e7a739..55652263 100644 --- a/docs/Manifest.toml +++ b/docs/Manifest.toml @@ -318,9 +318,9 @@ uuid = "ade2ca70-3891-5945-98fb-dc099432e06a" [[deps.DiffEqBase]] deps = ["ArrayInterface", "ConcreteStructs", "DataStructures", "DocStringExtensions", "EnumX", "EnzymeCore", "FastBroadcast", "FastClosures", "ForwardDiff", "FunctionWrappers", "FunctionWrappersWrappers", "LinearAlgebra", "Logging", "Markdown", "MuladdMacro", "Parameters", "PreallocationTools", "PrecompileTools", "Printf", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "Setfield", "SparseArrays", "Static", "StaticArraysCore", "Statistics", "Tricks", "TruncatedStacktraces"] -git-tree-sha1 = "37d49a1f8eedfe68b7622075ff3ebe3dd0e8f327" +git-tree-sha1 = "89d57776cafee3b69f594af8b8a0659cb03422c8" uuid = "2b5f629d-d688-5b77-993f-72d75c75574e" -version = "6.151.2" +version = "6.151.3" [deps.DiffEqBase.extensions] DiffEqBaseCUDAExt = "CUDA" @@ -558,8 +558,8 @@ version = "2.0.4" [[deps.Ferrite]] deps = ["EnumX", "ForwardDiff", "LinearAlgebra", "NearestNeighbors", "OrderedCollections", "Preferences", "Reexport", "SparseArrays", "StaticArrays", "Tensors", "WriteVTK"] -git-tree-sha1 = "faf7547ae49922f7381925a9f0bd638853c4fa36" -repo-rev = "bdd5b41" +git-tree-sha1 = "3ed81140fa5116369d88a9b24f3d4d710a9ef158" +repo-rev = "6dfa0e4" repo-url = "https://github.com/Ferrite-FEM/Ferrite.jl.git" uuid = "c061ca5d-56c9-439f-9c0e-210fe06d3992" version = "0.3.14" @@ -1229,9 +1229,9 @@ 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 = "339bd35be201372b0ce259dc49aacf4991ba671d" +git-tree-sha1 = "8d43517ec8d9895f7d5f661167c05f54146a769d" uuid = "961ee093-0014-501f-94e3-6117800e7a78" -version = "9.18.1" +version = "9.19.0" [deps.ModelingToolkit.extensions] MTKBifurcationKitExt = "BifurcationKit" @@ -1495,9 +1495,9 @@ version = "1.3.4" [[deps.RecursiveArrayTools]] deps = ["Adapt", "ArrayInterface", "DocStringExtensions", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "SparseArrays", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"] -git-tree-sha1 = "3400ce27995422fb88ffcd3af9945565aad947f0" +git-tree-sha1 = "980aabbeac7aee70d0e452a72b0c68b5b266cc7b" uuid = "731186ca-8d62-57ce-b412-fbd966d074cd" -version = "3.23.1" +version = "3.24.0" [deps.RecursiveArrayTools.extensions] RecursiveArrayToolsFastBroadcastExt = "FastBroadcast" @@ -1816,9 +1816,9 @@ version = "7.2.1+1" [[deps.SymbolicIndexingInterface]] deps = ["Accessors", "ArrayInterface", "RuntimeGeneratedFunctions", "StaticArraysCore"] -git-tree-sha1 = "a5f6f138b740c9d93d76f0feddd3092e6ef002b7" +git-tree-sha1 = "9bda3c1e2b771ab45fcbc264a078f612ca7ef427" uuid = "2efcf032-c050-4f8e-a9bb-153293bab1f5" -version = "0.3.22" +version = "0.3.23" [[deps.SymbolicLimits]] deps = ["SymbolicUtils"] @@ -1894,7 +1894,7 @@ uuid = "8290d209-cae3-49c0-8002-c8c24d57dab5" version = "0.5.2" [[deps.Thunderbolt]] -deps = ["Adapt", "BlockArrays", "CommonSolve", "DataStructures", "DiffEqBase", "Ferrite", "FerriteGmsh", "JLD2", "LinearAlgebra", "LinearSolve", "ModelingToolkit", "OrderedCollections", "Polyester", "ReadVTK", "Reexport", "SparseArrays", "SparseMatricesCSR", "StaticArrays", "SymbolicIndexingInterface", "Tensors", "TimerOutputs", "UnPack", "Unrolled", "WriteVTK"] +deps = ["Adapt", "BlockArrays", "CommonSolve", "DataStructures", "DiffEqBase", "Ferrite", "FerriteGmsh", "GPUArraysCore", "JLD2", "LinearAlgebra", "LinearSolve", "ModelingToolkit", "OrderedCollections", "Polyester", "ReadVTK", "Reexport", "SparseArrays", "SparseMatricesCSR", "StaticArrays", "SymbolicIndexingInterface", "Tensors", "TimerOutputs", "UnPack", "Unrolled", "WriteVTK"] path = ".." uuid = "909927c2-98d5-4a67-bba9-79f03a9ad49b" version = "0.0.1-DEV" diff --git a/examples-gpu/Manifest.toml b/examples-gpu/Manifest.toml new file mode 100644 index 00000000..1cb9978b --- /dev/null +++ b/examples-gpu/Manifest.toml @@ -0,0 +1,2171 @@ +# This 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+[[deps.libpng_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Zlib_jll"] +git-tree-sha1 = "d7015d2e18a5fd9a4f47de711837e980519781a4" +uuid = "b53b4c65-9356-5827-b1ea-8c7a1a84506f" +version = "1.6.43+1" + +[[deps.nghttp2_jll]] +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" +version = "17.4.0+2" diff --git a/examples-gpu/Project.toml b/examples-gpu/Project.toml index 311892d8..f331e7a5 100644 --- a/examples-gpu/Project.toml +++ b/examples-gpu/Project.toml @@ -1,6 +1,4 @@ [deps] -Adapt = "79e6a3ab-5dfb-504d-930d-738a2a938a0e" CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" -DiffEqBase = "2b5f629d-d688-5b77-993f-72d75c75574e" Ferrite = "c061ca5d-56c9-439f-9c0e-210fe06d3992" Thunderbolt = "909927c2-98d5-4a67-bba9-79f03a9ad49b" diff --git a/examples-gpu/spiral-wave.jl b/examples-gpu/spiral-wave.jl index 0e402bf9..fa069c31 100644 --- a/examples-gpu/spiral-wave.jl +++ b/examples-gpu/spiral-wave.jl @@ -40,6 +40,7 @@ model = MonodomainModel( ConstantCoefficient(SymmetricTensor{2,2,Float32}((4.5e-5, 0, 2.0e-5))), NoStimulationProtocol(), Thunderbolt.ParametrizedFHNModel{Float32}(), + :φₘ, :s, ) mesh = generate_mesh(Quadrilateral, (2^7, 2^7), Vec{2}((0.0,0.0)), Vec{2}((2.5,2.5))) diff --git a/examples/Manifest.toml b/examples/Manifest.toml index 3478837a..e7a70f69 100644 --- a/examples/Manifest.toml +++ b/examples/Manifest.toml @@ -2,12 +2,12 @@ julia_version = "1.10.2" manifest_format = "2.0" -project_hash = "133703943726468e289a34e92674dcd4c441f969" +project_hash = "ff62a7543d0f412dc8108396fe6f60ec2a468b13" [[deps.ADTypes]] -git-tree-sha1 = "daf26bbdec60d9ca1c0003b70f389d821ddb4224" +git-tree-sha1 = "fc02d55798c1af91123d07915a990fbb9a10d146" uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b" -version = "1.2.1" +version = "1.3.0" weakdeps = ["ChainRulesCore", "EnzymeCore"] [deps.ADTypes.extensions] @@ -113,9 +113,9 @@ version = "7.11.0" [[deps.ArrayLayouts]] deps = ["FillArrays", "LinearAlgebra"] -git-tree-sha1 = "29649b61e0313db0a7ad5ecf41210e4e85aea234" +git-tree-sha1 = "420e2853770f50e5306b9d96b5a66f26e7c73bc6" uuid = "4c555306-a7a7-4459-81d9-ec55ddd5c99a" -version = "1.9.3" +version = "1.9.4" weakdeps = ["SparseArrays"] [deps.ArrayLayouts.extensions] @@ -158,9 +158,15 @@ version = "0.1.5" [[deps.BlockArrays]] deps = ["ArrayLayouts", "FillArrays", "LinearAlgebra"] -git-tree-sha1 = "9a9610fbe5779636f75229e423e367124034af41" +git-tree-sha1 = "35d4ec59c771dacfa7b5a916d50109537f6292ce" uuid = "8e7c35d0-a365-5155-bbbb-fb81a777f24e" -version = "0.16.43" +version = "1.0.1" + + [deps.BlockArrays.extensions] + BlockArraysBandedMatricesExt = "BandedMatrices" + + [deps.BlockArrays.weakdeps] + BandedMatrices = "aae01518-5342-5314-be14-df237901396f" [[deps.Bzip2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -224,7 +230,7 @@ weakdeps = ["SparseArrays"] [[deps.CirculatorySystemModels]] deps = ["CSV", "DataFrames", "ModelingToolkit"] -git-tree-sha1 = "1035bcbd5cde32c6fe9ee1b4c45214033688ff50" +git-tree-sha1 = "190e4a0e80a6f99a5b4c65393ca307874f2a1634" repo-rev = "do/diffeq-to-odediffeq" repo-url = "https://github.com/termi-official/CirculatorySystemModels.jl" uuid = "4211d73e-f4e8-40c4-b600-92e4b82f0e1a" @@ -393,11 +399,9 @@ version = "1.0.3" [[deps.DiffEqBase]] deps = ["ArrayInterface", "ConcreteStructs", "DataStructures", "DocStringExtensions", "EnumX", "EnzymeCore", "FastBroadcast", "FastClosures", "ForwardDiff", "FunctionWrappers", "FunctionWrappersWrappers", "LinearAlgebra", "Logging", "Markdown", "MuladdMacro", "Parameters", "PreallocationTools", "PrecompileTools", "Printf", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "Setfield", "SparseArrays", "Static", "StaticArraysCore", "Statistics", "Tricks", "TruncatedStacktraces"] -git-tree-sha1 = "19ad3b93ddcf848ce82fc03c875cb78b08d11b4d" -repo-rev = "master" -repo-url = "https://github.com/SciML/DiffEqBase.jl.git" +git-tree-sha1 = "89d57776cafee3b69f594af8b8a0659cb03422c8" uuid = "2b5f629d-d688-5b77-993f-72d75c75574e" -version = "6.151.2" +version = "6.151.3" [deps.DiffEqBase.extensions] DiffEqBaseCUDAExt = "CUDA" @@ -449,9 +453,9 @@ version = "1.15.1" [[deps.DifferentiationInterface]] deps = ["ADTypes", "Compat", "DocStringExtensions", "FillArrays", "LinearAlgebra", "PackageExtensionCompat", "SparseArrays", "SparseMatrixColorings"] -git-tree-sha1 = "b4ce591b91f500126c9c5030aa5b8a710c7db7a0" +git-tree-sha1 = "23c6df13ad8fcffde4b0596d798911d2e309fc2c" uuid = "a0c0ee7d-e4b9-4e03-894e-1c5f64a51d63" -version = "0.4.2" +version = "0.5.5" [deps.DifferentiationInterface.extensions] DifferentiationInterfaceChainRulesCoreExt = "ChainRulesCore" @@ -466,7 +470,7 @@ version = "0.4.2" DifferentiationInterfaceSymbolicsExt = "Symbolics" DifferentiationInterfaceTapirExt = "Tapir" DifferentiationInterfaceTrackerExt = "Tracker" - DifferentiationInterfaceZygoteExt = "Zygote" + DifferentiationInterfaceZygoteExt = ["Zygote", "ForwardDiff"] [deps.DifferentiationInterface.weakdeps] ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" @@ -577,9 +581,9 @@ uuid = "4e289a0a-7415-4d19-859d-a7e5c4648b56" version = "1.0.4" [[deps.EnzymeCore]] -git-tree-sha1 = "0910982db2490a20f81dc7db5d4bbea236c027b3" +git-tree-sha1 = "88bc63137eb033acc3afe1b9875717889c718c46" uuid = "f151be2c-9106-41f4-ab19-57ee4f262869" -version = "0.7.3" +version = "0.7.5" weakdeps = ["Adapt"] [deps.EnzymeCore.extensions] @@ -597,21 +601,15 @@ git-tree-sha1 = "1c6317308b9dc757616f0b5cb379db10494443a7" uuid = "2e619515-83b5-522b-bb60-26c02a35a201" version = "2.6.2+0" -[[deps.ExponentialUtilities]] -deps = ["Adapt", "ArrayInterface", "GPUArraysCore", "GenericSchur", "LinearAlgebra", "PrecompileTools", "Printf", "SparseArrays", "libblastrampoline_jll"] -git-tree-sha1 = "8e18940a5ba7f4ddb41fe2b79b6acaac50880a86" -uuid = "d4d017d3-3776-5f7e-afef-a10c40355c18" -version = "1.26.1" - [[deps.ExprTools]] git-tree-sha1 = "27415f162e6028e81c72b82ef756bf321213b6ec" 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.FFMPEG_jll]] deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "JLLWrappers", "LAME_jll", "Libdl", "Ogg_jll", "OpenSSL_jll", "Opus_jll", "PCRE2_jll", "Zlib_jll", "libaom_jll", "libass_jll", "libfdk_aac_jll", "libvorbis_jll", "x264_jll", "x265_jll"] @@ -639,9 +637,9 @@ version = "1.3.8+0" [[deps.FastBroadcast]] deps = ["ArrayInterface", "LinearAlgebra", "Polyester", "Static", "StaticArrayInterface", "StrideArraysCore"] -git-tree-sha1 = "e17367f052035620d832499496080f792fa7ea47" +git-tree-sha1 = "2be93e36303143c6fffd07e2222bbade35194d9e" uuid = "7034ab61-46d4-4ed7-9d0f-46aef9175898" -version = "0.3.2" +version = "0.3.3" [[deps.FastClosures]] git-tree-sha1 = "acebe244d53ee1b461970f8910c235b259e772ef" @@ -656,8 +654,8 @@ version = "2.0.4" [[deps.Ferrite]] deps = ["EnumX", "ForwardDiff", "LinearAlgebra", "NearestNeighbors", "OrderedCollections", "Preferences", "Reexport", "SparseArrays", "StaticArrays", "Tensors", "WriteVTK"] -git-tree-sha1 = "e608f28615d999ae7be3172e5af186236030a0d0" -repo-rev = "master" +git-tree-sha1 = "3ed81140fa5116369d88a9b24f3d4d710a9ef158" +repo-rev = "6dfa0e4" repo-url = "https://github.com/Ferrite-FEM/Ferrite.jl.git" uuid = "c061ca5d-56c9-439f-9c0e-210fe06d3992" version = "0.3.14" @@ -837,12 +835,6 @@ git-tree-sha1 = "ec632f177c0d990e64d955ccc1b8c04c485a0950" uuid = "46192b85-c4d5-4398-a991-12ede77f4527" version = "0.1.6" -[[deps.GenericSchur]] -deps = ["LinearAlgebra", "Printf"] -git-tree-sha1 = "af49a0851f8113fcfae2ef5027c6d49d0acec39b" -uuid = "c145ed77-6b09-5dd9-b285-bf645a82121e" -version = "0.5.4" - [[deps.GeoInterface]] deps = ["Extents"] git-tree-sha1 = "801aef8228f7f04972e596b09d4dba481807c913" @@ -886,9 +878,9 @@ version = "1.3.14+0" [[deps.Graphs]] deps = ["ArnoldiMethod", "Compat", "DataStructures", "Distributed", "Inflate", "LinearAlgebra", "Random", "SharedArrays", "SimpleTraits", "SparseArrays", "Statistics"] -git-tree-sha1 = "4f2b57488ac7ee16124396de4f2bbdd51b2602ad" +git-tree-sha1 = "334d300809ae0a68ceee3444c6e99ded412bf0b3" uuid = "86223c79-3864-5bf0-83f7-82e725a168b6" -version = "1.11.0" +version = "1.11.1" [[deps.GridLayoutBase]] deps = ["GeometryBasics", "InteractiveUtils", "Observables"] @@ -1010,9 +1002,9 @@ weakdeps = ["Unitful"] [[deps.IntervalArithmetic]] deps = ["CRlibm_jll", "MacroTools", "RoundingEmulator"] -git-tree-sha1 = "90709228dc114e599a2b62b7d23482a4f50938ee" +git-tree-sha1 = "433b0bb201cd76cb087b017e49244f10394ebe9c" uuid = "d1acc4aa-44c8-5952-acd4-ba5d80a2a253" -version = "0.22.13" +version = "0.22.14" weakdeps = ["DiffRules", "ForwardDiff", "RecipesBase"] [deps.IntervalArithmetic.extensions] @@ -1186,15 +1178,23 @@ uuid = "10f19ff3-798f-405d-979b-55457f8fc047" version = "0.1.15" [[deps.LazyArrays]] -deps = ["ArrayLayouts", "FillArrays", "LinearAlgebra", "MacroTools", "MatrixFactorizations", "SparseArrays"] -git-tree-sha1 = "35079a6a869eecace778bcda8641f9a54ca3a828" +deps = ["ArrayLayouts", "FillArrays", "LinearAlgebra", "MacroTools", "SparseArrays"] +git-tree-sha1 = "899d44fa1a575653df5721a7fccb4988f7f09b62" uuid = "5078a376-72f3-5289-bfd5-ec5146d43c02" -version = "1.10.0" -weakdeps = ["StaticArrays"] +version = "2.0.4" [deps.LazyArrays.extensions] + LazyArraysBandedMatricesExt = "BandedMatrices" + LazyArraysBlockArraysExt = "BlockArrays" + LazyArraysBlockBandedMatricesExt = "BlockBandedMatrices" LazyArraysStaticArraysExt = "StaticArrays" + [deps.LazyArrays.weakdeps] + BandedMatrices = "aae01518-5342-5314-be14-df237901396f" + BlockArrays = "8e7c35d0-a365-5155-bbbb-fb81a777f24e" + BlockBandedMatrices = "ffab5731-97b5-5995-9138-79e8c1846df0" + StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" + [[deps.LazyArtifacts]] deps = ["Artifacts", "Pkg"] uuid = "4af54fe1-eca0-43a8-85a7-787d91b784e3" @@ -1297,7 +1297,7 @@ version = "5.0.0+0" [[deps.LinearSolve]] deps = ["ArrayInterface", "ChainRulesCore", "ConcreteStructs", "DocStringExtensions", "EnumX", "FastLapackInterface", "GPUArraysCore", "InteractiveUtils", "KLU", "Krylov", "LazyArrays", "Libdl", "LinearAlgebra", "MKL_jll", "Markdown", "PrecompileTools", "Preferences", "RecursiveFactorization", "Reexport", "SciMLBase", "SciMLOperators", "Setfield", "SparseArrays", "Sparspak", "StaticArraysCore", "UnPack"] -git-tree-sha1 = "ba21beb1c549599192b3016f12718c58895b82e5" +git-tree-sha1 = "7bcfe3fa968f3c0f68f8ee869851f85cf2ebb7f6" repo-rev = "main" repo-url = "https://github.com/SciML/LinearSolve.jl.git" uuid = "7ed4a6bd-45f5-4d41-b270-4a48e9bafcae" @@ -1443,12 +1443,6 @@ git-tree-sha1 = "1865d0b8a2d91477c8b16b49152a32764c7b1f5f" uuid = "0a4f8689-d25c-4efe-a92b-7142dfc1aa53" version = "0.6.0" -[[deps.MatrixFactorizations]] -deps = ["ArrayLayouts", "LinearAlgebra", "Printf", "Random"] -git-tree-sha1 = "6731e0574fa5ee21c02733e397beb133df90de35" -uuid = "a3b82374-2e81-5b9e-98ce-41277c0e4c87" -version = "2.2.0" - [[deps.MaybeInplace]] deps = ["ArrayInterface", "LinearAlgebra", "MacroTools", "SparseArrays"] git-tree-sha1 = "1b9e613f2ca3b6cdcbfe36381e17ca2b66d4b3a1" @@ -1482,10 +1476,10 @@ 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", "OrderedCollections", "OrdinaryDiffEq", "PrecompileTools", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLBase", "SciMLStructures", "Serialization", "Setfield", "SimpleNonlinearSolve", "SparseArrays", "SpecialFunctions", "StaticArrays", "SymbolicIndexingInterface", "SymbolicUtils", "Symbolics", "URIs", "UnPack", "Unitful"] -git-tree-sha1 = "1a05837e1b9f24db3e516f694b6a3ac40916fb5a" +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 = "8d43517ec8d9895f7d5f661167c05f54146a769d" uuid = "961ee093-0014-501f-94e3-6117800e7a78" -version = "9.16.0" +version = "9.19.0" [deps.ModelingToolkit.extensions] MTKBifurcationKitExt = "BifurcationKit" @@ -1518,15 +1512,15 @@ version = "0.2.4" [[deps.MultivariatePolynomials]] deps = ["ChainRulesCore", "DataStructures", "LinearAlgebra", "MutableArithmetics"] -git-tree-sha1 = "dad7be0c92b688bf8f24af170825ccedc104b116" +git-tree-sha1 = "5c1d1d9361e1417e5a065e1f84dc3686cbdaea21" uuid = "102ac46a-7ee4-5c85-9060-abc95bfdeaa3" -version = "0.5.5" +version = "0.5.6" [[deps.MutableArithmetics]] deps = ["LinearAlgebra", "SparseArrays", "Test"] -git-tree-sha1 = "a3589efe0005fc4718775d8641b2de9060d23f73" +git-tree-sha1 = "898c56fbf8bf71afb0c02146ef26f3a454e88873" uuid = "d8a4904e-b15c-11e9-3269-09a3773c0cb0" -version = "1.4.4" +version = "1.4.5" [[deps.NLSolversBase]] deps = ["DiffResults", "Distributed", "FiniteDiff", "ForwardDiff"] @@ -1542,9 +1536,9 @@ version = "1.0.2" [[deps.NearestNeighbors]] deps = ["Distances", "StaticArrays"] -git-tree-sha1 = "ded64ff6d4fdd1cb68dfcbb818c69e144a5b2e4c" +git-tree-sha1 = "e4a9d37f0ee694da969def1f0dd4654642dfb51c" uuid = "b8a86587-4115-5ab1-83bc-aa920d37bbce" -version = "0.4.16" +version = "0.4.17" [[deps.Netpbm]] deps = ["FileIO", "ImageCore", "ImageMetadata"] @@ -1644,9 +1638,9 @@ 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"] @@ -1665,12 +1659,6 @@ git-tree-sha1 = "dfdf5519f235516220579f949664f1bf44e741c5" uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d" version = "1.6.3" -[[deps.OrdinaryDiffEq]] -deps = ["ADTypes", "Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "EnumX", "ExponentialUtilities", "FastBroadcast", "FastClosures", "FillArrays", "FiniteDiff", "ForwardDiff", "FunctionWrappersWrappers", "IfElse", "InteractiveUtils", "LineSearches", "LinearAlgebra", "LinearSolve", "Logging", "MacroTools", "MuladdMacro", "NonlinearSolve", "Polyester", "PreallocationTools", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SciMLStructures", "SimpleNonlinearSolve", "SimpleUnPack", "SparseArrays", "SparseDiffTools", "StaticArrayInterface", "StaticArrays", "TruncatedStacktraces"] -git-tree-sha1 = "78486623c0b7f6779beafadf2a00a095b4b687ef" -uuid = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed" -version = "6.81.1" - [[deps.PCRE2_jll]] deps = ["Artifacts", "Libdl"] uuid = "efcefdf7-47ab-520b-bdef-62a2eaa19f15" @@ -1870,9 +1858,9 @@ version = "1.3.4" [[deps.RecursiveArrayTools]] deps = ["Adapt", "ArrayInterface", "DocStringExtensions", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "SparseArrays", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"] -git-tree-sha1 = "2cea01606a852c2431ded77293eb533b511b19e6" +git-tree-sha1 = "980aabbeac7aee70d0e452a72b0c68b5b266cc7b" uuid = "731186ca-8d62-57ce-b412-fbd966d074cd" -version = "3.22.0" +version = "3.24.0" [deps.RecursiveArrayTools.extensions] RecursiveArrayToolsFastBroadcastExt = "FastBroadcast" @@ -1967,9 +1955,9 @@ version = "0.6.42" [[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 = "1d1d1ff37d2917cad263fa186cbc19ce4b587ccf" +git-tree-sha1 = "7a6c5c8c38d2e37f45d4686c3598c20c1aebf48e" uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462" -version = "2.40.0" +version = "2.41.3" [deps.SciMLBase.extensions] SciMLBaseChainRulesCoreExt = "ChainRulesCore" @@ -1997,9 +1985,10 @@ uuid = "c0aeaf25-5076-4817-a8d5-81caf7dfa961" version = "0.3.8" [[deps.SciMLStructures]] -git-tree-sha1 = "d778a74df2f64059c38453b34abad1953b2b8722" +deps = ["ArrayInterface"] +git-tree-sha1 = "6ab4beaf88dcdd2639bead916f2347f81dcacd0e" uuid = "53ae85a6-f571-4167-b2af-e1d143709226" -version = "1.2.0" +version = "1.3.0" [[deps.Scratch]] deps = ["Dates"] @@ -2046,9 +2035,9 @@ version = "0.4.0" [[deps.SimpleNonlinearSolve]] deps = ["ADTypes", "ArrayInterface", "ConcreteStructs", "DiffEqBase", "DiffResults", "DifferentiationInterface", "FastClosures", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "MaybeInplace", "PrecompileTools", "Reexport", "SciMLBase", "Setfield", "StaticArraysCore"] -git-tree-sha1 = "f3c50acd5145f2c6ee85343ce6f433dd2caab41e" +git-tree-sha1 = "913754ccbbc78720a4542b56a6bdfbab1c84c8f2" uuid = "727e6d20-b764-4bd8-a329-72de5adea6c7" -version = "1.9.0" +version = "1.10.0" [deps.SimpleNonlinearSolve.extensions] SimpleNonlinearSolveChainRulesCoreExt = "ChainRulesCore" @@ -2068,11 +2057,6 @@ git-tree-sha1 = "5d7e3f4e11935503d3ecaf7186eac40602e7d231" uuid = "699a6c99-e7fa-54fc-8d76-47d257e15c1d" version = "0.9.4" -[[deps.SimpleUnPack]] -git-tree-sha1 = "58e6353e72cde29b90a69527e56df1b5c3d8c437" -uuid = "ce78b400-467f-4804-87d8-8f486da07d0a" -version = "1.1.0" - [[deps.Sixel]] deps = ["Dates", "FileIO", "ImageCore", "IndirectArrays", "OffsetArrays", "REPL", "libsixel_jll"] git-tree-sha1 = "2da10356e31327c7096832eb9cd86307a50b1eb6" @@ -2121,9 +2105,9 @@ version = "0.6.7" [[deps.SparseMatrixColorings]] deps = ["ADTypes", "Compat", "DocStringExtensions", "LinearAlgebra", "Random", "SparseArrays"] -git-tree-sha1 = "d4adedbcc8776c567e0e22ef19f13cf10cb6ecaa" +git-tree-sha1 = "eed2446b3c3dd58f6ded3168998b8b2cb3fc9229" uuid = "0a514795-09f3-496d-8182-132a7b665d35" -version = "0.3.2" +version = "0.3.3" [[deps.Sparspak]] deps = ["Libdl", "LinearAlgebra", "Logging", "OffsetArrays", "Printf", "SparseArrays", "Test"] @@ -2166,9 +2150,9 @@ weakdeps = ["OffsetArrays", "StaticArrays"] [[deps.StaticArrays]] deps = ["LinearAlgebra", "PrecompileTools", "Random", "StaticArraysCore"] -git-tree-sha1 = "9ae599cd7529cfce7fea36cf00a62cfc56f0f37c" +git-tree-sha1 = "6e00379a24597be4ae1ee6b2d882e15392040132" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.9.4" +version = "1.9.5" weakdeps = ["ChainRulesCore", "Statistics"] [deps.StaticArrays.extensions] @@ -2176,9 +2160,9 @@ 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.Statistics]] deps = ["LinearAlgebra", "SparseArrays"] @@ -2244,9 +2228,9 @@ version = "7.2.1+1" [[deps.SymbolicIndexingInterface]] deps = ["Accessors", "ArrayInterface", "RuntimeGeneratedFunctions", "StaticArraysCore"] -git-tree-sha1 = "a5f6f138b740c9d93d76f0feddd3092e6ef002b7" +git-tree-sha1 = "9bda3c1e2b771ab45fcbc264a078f612ca7ef427" uuid = "2efcf032-c050-4f8e-a9bb-153293bab1f5" -version = "0.3.22" +version = "0.3.23" [[deps.SymbolicLimits]] deps = ["SymbolicUtils"] @@ -2262,9 +2246,9 @@ version = "2.0.2" [[deps.Symbolics]] deps = ["ADTypes", "ArrayInterface", "Bijections", "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", "StaticArrays", "SymbolicIndexingInterface", "SymbolicLimits", "SymbolicUtils", "TermInterface"] -git-tree-sha1 = "2448b5d1d4cf09a028492a150080a2390086d36b" +git-tree-sha1 = "3669f8eba2720c595e16b038f33cb880c12ef7f7" uuid = "0c5d862f-8b57-4792-8d23-62f2024744c7" -version = "5.30.1" +version = "5.30.3" [deps.Symbolics.extensions] SymbolicsGroebnerExt = "Groebner" @@ -2328,11 +2312,17 @@ uuid = "8290d209-cae3-49c0-8002-c8c24d57dab5" version = "0.5.2" [[deps.Thunderbolt]] -deps = ["BlockArrays", "CommonSolve", "DataStructures", "DiffEqBase", "Ferrite", "FerriteGmsh", "JLD2", "LinearAlgebra", "LinearSolve", "ModelingToolkit", "OrderedCollections", "Polyester", "ReadVTK", "Reexport", "SparseArrays", "SparseMatricesCSR", "StaticArrays", "SymbolicIndexingInterface", "Tensors", "TimerOutputs", "UnPack", "Unrolled", "WriteVTK"] +deps = ["Adapt", "BlockArrays", "CommonSolve", "DataStructures", "DiffEqBase", "Ferrite", "FerriteGmsh", "GPUArraysCore", "JLD2", "LinearAlgebra", "LinearSolve", "ModelingToolkit", "OrderedCollections", "Polyester", "ReadVTK", "Reexport", "SparseArrays", "SparseMatricesCSR", "StaticArrays", "SymbolicIndexingInterface", "Tensors", "TimerOutputs", "UnPack", "Unrolled", "WriteVTK"] path = ".." uuid = "909927c2-98d5-4a67-bba9-79f03a9ad49b" version = "0.0.1-DEV" + [deps.Thunderbolt.extensions] + CuThunderboltExt = "CUDA" + + [deps.Thunderbolt.weakdeps] + CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" + [[deps.TiffImages]] deps = ["ColorTypes", "DataStructures", "DocStringExtensions", "FileIO", "FixedPointNumbers", "IndirectArrays", "Inflate", "Mmap", "OffsetArrays", "PkgVersion", "ProgressMeter", "SIMD", "UUIDs"] git-tree-sha1 = "bc7fd5c91041f44636b2c134041f7e5263ce58ae" diff --git a/examples/Project.toml b/examples/Project.toml index 7abd6444..0c2c46a1 100644 --- a/examples/Project.toml +++ b/examples/Project.toml @@ -1,6 +1,5 @@ [deps] CirculatorySystemModels = "4211d73e-f4e8-40c4-b600-92e4b82f0e1a" -DiffEqBase = "2b5f629d-d688-5b77-993f-72d75c75574e" Ferrite = "c061ca5d-56c9-439f-9c0e-210fe06d3992" FerriteGmsh = "4f95f4f8-b27c-4ae5-9a39-ea55e634e36b" GLMakie = "e9467ef8-e4e7-5192-8a1a-b1aee30e663a" diff --git a/examples/spiral-wave.jl b/examples/spiral-wave.jl index 9610761d..3af640d4 100644 --- a/examples/spiral-wave.jl +++ b/examples/spiral-wave.jl @@ -39,7 +39,8 @@ model = MonodomainModel( ConstantCoefficient(1.0), ConstantCoefficient(SymmetricTensor{2,2,Float64}((4.5e-5, 0, 2.0e-5))), NoStimulationProtocol(), - Thunderbolt.FHNModel() + Thunderbolt.FHNModel(), + :φₘ, :s, ) mesh = generate_mesh(Quadrilateral, (2^7, 2^7), Vec{2}((0.0,0.0)), Vec{2}((2.5,2.5))) diff --git a/src/discretization/fem.jl b/src/discretization/fem.jl index 888f964c..62eef88c 100644 --- a/src/discretization/fem.jl +++ b/src/discretization/fem.jl @@ -40,32 +40,35 @@ end function semidiscretize(split::ReactionDiffusionSplit{<:MonodomainModel}, discretization::FiniteElementDiscretization, grid::AbstractGrid) epmodel = split.model - + φsym = epmodel.transmembrane_solution_symbol ets = elementtypes(grid) @assert length(ets) == 1 - # TODO factor this out to make a isolated transient heat problem and call semidiscretize here. This should simplify testing. - ip = getinterpolation(discretization.interpolations[:φₘ], getcells(grid, 1)) - dh = DofHandler(grid) - Ferrite.add!(dh, :φₘ, ip) - close!(dh); - heatfun = TransientHeatFunction( + heat_model = TransientHeatModel( ConductivityToDiffusivityCoefficient(epmodel.κ, epmodel.Cₘ, epmodel.χ), epmodel.stim, - dh + φsym, ) + + heatfun = semidiscretize( + heat_model, + discretization, + grid, + ) + + dh = heatfun.dh ndofsφ = ndofs(dh) - heat_dofrange = 1:ndofsφ # TODO we need some information about the discretization of this one, e.g. dofs a nodes vs dofs at quadrature points - # TODO we should call semidiscretize here too + # TODO we should call semidiscretize here too - This is a placeholder for the nodal discretization odefun = PointwiseODEFunction( # TODO epmodel.Cₘ(x) and coordinates - ndofs(dh), + ndofsφ, epmodel.ion ) # TODO This is a faulty assumption. We can have varying ndofs per cell. nstates_per_cell = num_states(odefun.ode) # TODO this assumes that the transmembrane potential is the first field. Relax this. + heat_dofrange = 1:ndofsφ ode_dofrange = 1:nstates_per_cell*ndofsφ # semidiscrete_ode = GenericSplitFunction( diff --git a/src/modeling/common.jl b/src/modeling/common.jl index 81b1be47..6e53927e 100644 --- a/src/modeling/common.jl +++ b/src/modeling/common.jl @@ -7,6 +7,7 @@ include("core/coefficients.jl") include("core/boundary_conditions.jl") +abstract type AbstractSourceTerm end abstract type AbstractBilinearIntegrator end include("core/mass.jl") include("core/diffusion.jl") diff --git a/src/modeling/core/diffusion.jl b/src/modeling/core/diffusion.jl index ac769051..de4eb01e 100644 --- a/src/modeling/core/diffusion.jl +++ b/src/modeling/core/diffusion.jl @@ -37,7 +37,7 @@ end setup_element_cache(element_model::BilinearDiffusionIntegrator, qr, ip, ip_geo) = BilinearDiffusionElementCache(element_model, CellValues(qr, ip, ip_geo)) -struct TransientHeatModel{ConductivityCoefficientType, SourceType} +struct TransientHeatModel{ConductivityCoefficientType, SourceType <: AbstractSourceTerm} κ::ConductivityCoefficientType source::SourceType solution_variable_symbol::Symbol diff --git a/src/modeling/electrophysiology.jl b/src/modeling/electrophysiology.jl index c01180c5..b6e56f84 100644 --- a/src/modeling/electrophysiology.jl +++ b/src/modeling/electrophysiology.jl @@ -126,7 +126,7 @@ struct FitzHughNagumoModel <: HodgkinHuxleyTypeModel end; abstract type AbstractEPModel end; -abstract type AbstractStimulationProtocol end; +abstract type AbstractStimulationProtocol <: AbstractSourceTerm end; @doc raw""" Supertype for all stimulation protocols fulfilling $I_{\rm{stim,e}} = I_{\rm{stim,i}}$. @@ -146,48 +146,48 @@ struct AnalyticalTransmembraneStimulationProtocol{F <: AnalyticalCoefficient, T} nonzero_intervals::Vector{SVector{2,T}} # helper to speed up rhs end -""" -The original model formulation (TODO citation) with the structure - - χCₘ∂ₜφₘ = ∇⋅κᵢ∇φᵢ + χ(Iᵢₒₙ(φₘ,𝐬,x) + Iₛₜᵢₘ,ᵢ(x,t)) - χCₘ∂ₜφₘ = ∇⋅κₑ∇φₑ - χ(Iᵢₒₙ(φₘ,𝐬,x) + Iₛₜᵢₘ,ₑ(x,t)) - ∂ₜ𝐬 = g(φₘ,𝐬,x) - φᵢ - φₑ = φₘ - -!!! note - Not implemented yet. -""" -struct ParabolicParabolicBidomainModel <: AbstractEPModel - χ - Cₘ - κᵢ - κₑ - stim::AbstractStimulationProtocol - ion::AbstractIonicModel -end - -""" -Transformed bidomain model with the structure - - χCₘ∂ₜφₘ = ∇⋅κᵢ∇φₘ + ∇⋅κᵢ∇φₑ + χ(Iᵢₒₙ(φₘ,𝐬,x) + Iₛₜᵢₘ(x,t)) - 0 = ∇⋅κᵢ∇φₘ + ∇⋅(κᵢ+κₑ)∇φₑ + Iₛₜᵢₘ,ₑ(t) - Iₛₜᵢₘ,ᵢ(t) - ∂ₜ𝐬 = g(φₘ,𝐬,x) - φᵢ = φₘ + φₑ - -This formulation is a transformation of the parabolic-parabolic -form (c.f. TODO citation) and has been derived by (TODO citation) first. - -!!! note - Not implemented yet. -""" -struct ParabolicEllipticBidomainModel <: AbstractEPModel - χ - Cₘ - κᵢ - κₑ - stim::AbstractStimulationProtocol - ion::AbstractIonicModel -end +# """ +# The original model formulation (TODO citation) with the structure + +# χCₘ∂ₜφₘ = ∇⋅κᵢ∇φᵢ + χ(Iᵢₒₙ(φₘ,𝐬,x) + Iₛₜᵢₘ,ᵢ(x,t)) +# χCₘ∂ₜφₘ = ∇⋅κₑ∇φₑ - χ(Iᵢₒₙ(φₘ,𝐬,x) + Iₛₜᵢₘ,ₑ(x,t)) +# ∂ₜ𝐬 = g(φₘ,𝐬,x) +# φᵢ - φₑ = φₘ + +# !!! note +# Not implemented yet. +# """ +# struct ParabolicParabolicBidomainModel <: AbstractEPModel +# χ +# Cₘ +# κᵢ +# κₑ +# stim::AbstractStimulationProtocol +# ion::AbstractIonicModel +# end + +# """ +# Transformed bidomain model with the structure + +# χCₘ∂ₜφₘ = ∇⋅κᵢ∇φₘ + ∇⋅κᵢ∇φₑ + χ(Iᵢₒₙ(φₘ,𝐬,x) + Iₛₜᵢₘ(x,t)) +# 0 = ∇⋅κᵢ∇φₘ + ∇⋅(κᵢ+κₑ)∇φₑ + Iₛₜᵢₘ,ₑ(t) - Iₛₜᵢₘ,ᵢ(t) +# ∂ₜ𝐬 = g(φₘ,𝐬,x) +# φᵢ = φₘ + φₑ + +# This formulation is a transformation of the parabolic-parabolic +# form (c.f. TODO citation) and has been derived by (TODO citation) first. + +# !!! note +# Not implemented yet. +# """ +# struct ParabolicEllipticBidomainModel <: AbstractEPModel +# χ +# Cₘ +# κᵢ +# κₑ +# stim::AbstractStimulationProtocol +# ion::AbstractIonicModel +# end """ Simplification of the bidomain model with the structure @@ -205,6 +205,8 @@ struct MonodomainModel{F1,F2,F3,STIM<:TransmembraneStimulationProtocol,ION<:Abst κ::F3 stim::STIM ion::ION + transmembrane_solution_symbol::Symbol + internal_state_symbol::Symbol end """