diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index dec5f26c..91e1e736 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -30,7 +30,7 @@ jobs: - uses: julia-actions/julia-buildpkg@v1 - uses: julia-actions/julia-runtest@v1 - uses: julia-actions/julia-processcoverage@v1 - - uses: codecov/codecov-action@v1 + - uses: codecov/codecov-action@v2 if: ${{ matrix.version == '1' && matrix.os == 'ubuntu-latest' }} with: file: lcov.info diff --git a/Project.toml b/Project.toml index fe1829a3..16bd73d0 100644 --- a/Project.toml +++ b/Project.toml @@ -1,6 +1,6 @@ name = "CoherentStructures" uuid = "0c1513b4-3a13-56f1-9cd2-8312eaec88c4" -version = "0.4.6" +version = "0.4.7" [deps] ArnoldiMethod = "ec485272-7323-5ecc-a04f-4719b315124d" @@ -38,10 +38,10 @@ Interpolations = "0.11, 0.12, 0.13" IterativeSolvers = "0.7, 0.8, 0.9" LinearMaps = "2, 3" NearestNeighbors = "0.4.4" -OrdinaryDiffEq = "5.61.1" +OrdinaryDiffEq = "6" ProgressMeter = "1" RecipesBase = "0.7, 0.8, 1" -StaticArrays = "0.10, 0.11, 0.12, 1.0" +StaticArrays = "1.1" Tensors = "1.8" VoronoiDelaunay = "0.4" julia = "1.6" diff --git a/docs/Manifest.toml b/docs/Manifest.toml index 14773abd..99578e86 100644 --- a/docs/Manifest.toml +++ b/docs/Manifest.toml @@ -1,1110 +1,1149 @@ # This file is machine-generated - editing it directly is not advised -[[ANSIColoredPrinters]] +julia_version = "1.7.0" +manifest_format = "2.0" + +[[deps.ANSIColoredPrinters]] git-tree-sha1 = "574baf8110975760d391c710b6341da1afa48d8c" uuid = "a4c015fc-c6ff-483c-b24f-f7ea428134e9" version = "0.0.1" -[[Adapt]] +[[deps.Adapt]] deps = ["LinearAlgebra"] git-tree-sha1 = "84918055d15b3114ede17ac6a7182f68870c16f7" uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e" version = "3.3.1" -[[ArgTools]] +[[deps.ArgTools]] uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f" -[[ArnoldiMethod]] +[[deps.ArnoldiMethod]] deps = ["LinearAlgebra", "Random", "StaticArrays"] -git-tree-sha1 = "f87e559f87a45bece9c9ed97458d3afe98b1ebb9" +git-tree-sha1 = "62e51b39331de8911e4a7ff6f5aaf38a5f4cc0ae" uuid = "ec485272-7323-5ecc-a04f-4719b315124d" -version = "0.1.0" +version = "0.2.0" -[[Arpack]] +[[deps.Arpack]] deps = ["Arpack_jll", "Libdl", "LinearAlgebra"] git-tree-sha1 = "2ff92b71ba1747c5fdd541f8fc87736d82f40ec9" uuid = "7d9fca2a-8960-54d3-9f78-7d1dccf2cb97" version = "0.4.0" -[[Arpack_jll]] +[[deps.Arpack_jll]] deps = ["Libdl", "OpenBLAS_jll", "Pkg"] git-tree-sha1 = "e214a9b9bd1b4e1b4f15b22c0994862b66af7ff7" uuid = "68821587-b530-5797-8361-c406ea357684" version = "3.5.0+3" -[[ArrayInterface]] +[[deps.ArrayInterface]] deps = ["Compat", "IfElse", "LinearAlgebra", "Requires", "SparseArrays", "Static"] -git-tree-sha1 = "e527b258413e0c6d4f66ade574744c94edef81f8" +git-tree-sha1 = "265b06e2b1f6a216e0e8f183d28e4d354eab3220" uuid = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9" -version = "3.1.40" +version = "3.2.1" -[[Artifacts]] +[[deps.Artifacts]] uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" -[[AxisAlgorithms]] +[[deps.AxisAlgorithms]] deps = ["LinearAlgebra", "Random", "SparseArrays", "WoodburyMatrices"] git-tree-sha1 = "66771c8d21c8ff5e3a93379480a2307ac36863f7" uuid = "13072b0f-2c55-5437-9ae7-d433b7a33950" version = "1.0.1" -[[AxisArrays]] +[[deps.AxisArrays]] deps = ["Dates", "IntervalSets", "IterTools", "RangeArrays"] git-tree-sha1 = "d127d5e4d86c7680b20c35d40b503c74b9a39b5e" uuid = "39de3d68-74b9-583c-8d2d-e117c070f3a9" version = "0.4.4" -[[Base64]] +[[deps.Base64]] uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f" -[[BitTwiddlingConvenienceFunctions]] +[[deps.BitTwiddlingConvenienceFunctions]] deps = ["Static"] git-tree-sha1 = "bc1317f71de8dce26ea67fcdf7eccc0d0693b75b" uuid = "62783981-4cbd-42fc-bca8-16325de8dc4b" version = "0.1.1" -[[Bzip2_jll]] +[[deps.Bzip2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] git-tree-sha1 = "19a35467a82e236ff51bc17a3a44b69ef35185a2" uuid = "6e34b625-4abd-537c-b88f-471c36dfa7a0" version = "1.0.8+0" -[[CPUSummary]] +[[deps.CPUSummary]] deps = ["Hwloc", "IfElse", "Static"] git-tree-sha1 = "87b0c9c6ee0124d6c1f4ce8cb035dcaf9f90b803" uuid = "2a0fbf3d-bb9c-48f3-b0a9-814d99fd7ab9" version = "0.1.6" -[[Cairo_jll]] +[[deps.Cairo_jll]] deps = ["Artifacts", "Bzip2_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "JLLWrappers", "LZO_jll", "Libdl", "Pixman_jll", "Pkg", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Zlib_jll", "libpng_jll"] -git-tree-sha1 = "f2202b55d816427cd385a9a4f3ffb226bee80f99" +git-tree-sha1 = "4b859a208b2397a7a623a03449e4636bdb17bcf2" uuid = "83423d85-b0ee-5818-9007-b63ccbeb887a" -version = "1.16.1+0" +version = "1.16.1+1" -[[ChainRulesCore]] +[[deps.ChainRulesCore]] deps = ["Compat", "LinearAlgebra", "SparseArrays"] -git-tree-sha1 = "f885e7e7c124f8c92650d61b9477b9ac2ee607dd" +git-tree-sha1 = "4c26b4e9e91ca528ea212927326ece5918a04b47" uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" -version = "1.11.1" +version = "1.11.2" + +[[deps.ChangesOfVariables]] +deps = ["ChainRulesCore", "LinearAlgebra", "Test"] +git-tree-sha1 = "bf98fa45a0a4cee295de98d4c1462be26345b9a1" +uuid = "9e997f8a-9a97-42d5-a9f1-ce6bfc15e2c0" +version = "0.1.2" -[[CloseOpenIntervals]] +[[deps.CloseOpenIntervals]] deps = ["ArrayInterface", "Static"] git-tree-sha1 = "7b8f09d58294dc8aa13d91a8544b37c8a1dcbc06" uuid = "fb6a15b2-703c-40df-9091-08a04967cfa9" version = "0.1.4" -[[Clustering]] +[[deps.Clustering]] deps = ["Distances", "LinearAlgebra", "NearestNeighbors", "Printf", "SparseArrays", "Statistics", "StatsBase"] git-tree-sha1 = "75479b7df4167267d75294d14b58244695beb2ac" uuid = "aaaa29a8-35af-508c-8bc3-b662a17a0fe5" version = "0.14.2" -[[CodecZlib]] +[[deps.CodecZlib]] deps = ["TranscodingStreams", "Zlib_jll"] git-tree-sha1 = "ded953804d019afa9a3f98981d99b33e3db7b6da" uuid = "944b1d66-785c-5afd-91f1-9de20f533193" version = "0.7.0" -[[CoherentStructures]] +[[deps.CoherentStructures]] deps = ["ArnoldiMethod", "AxisArrays", "ColorTypes", "DiffEqBase", "Distances", "Distributed", "Ferrite", "GeometricalPredicates", "Interpolations", "IterativeSolvers", "LinearAlgebra", "LinearMaps", "NearestNeighbors", "OrdinaryDiffEq", "ProgressMeter", "RecipesBase", "SharedArrays", "SparseArrays", "StaticArrays", "Statistics", "Tensors", "VoronoiDelaunay"] path = ".." uuid = "0c1513b4-3a13-56f1-9cd2-8312eaec88c4" -version = "0.4.6" +version = "0.4.7" -[[ColorSchemes]] +[[deps.ColorSchemes]] deps = ["ColorTypes", "Colors", "FixedPointNumbers", "Random"] git-tree-sha1 = "a851fec56cb73cfdf43762999ec72eff5b86882a" uuid = "35d6a980-a343-548e-a6ea-1d62b119f2f4" version = "3.15.0" -[[ColorTypes]] +[[deps.ColorTypes]] deps = ["FixedPointNumbers", "Random"] git-tree-sha1 = "024fe24d83e4a5bf5fc80501a314ce0d1aa35597" uuid = "3da002f7-5984-5a60-b8a6-cbb66c0b333f" version = "0.11.0" -[[Colors]] +[[deps.Colors]] deps = ["ColorTypes", "FixedPointNumbers", "Reexport"] git-tree-sha1 = "417b0ed7b8b838aa6ca0a87aadf1bb9eb111ce40" uuid = "5ae59095-9a9b-59fe-a467-6f913c188581" version = "0.12.8" -[[CommonSolve]] +[[deps.CommonSolve]] git-tree-sha1 = "68a0743f578349ada8bc911a5cbd5a2ef6ed6d1f" uuid = "38540f10-b2f7-11e9-35d8-d573e4eb0ff2" version = "0.2.0" -[[CommonSubexpressions]] +[[deps.CommonSubexpressions]] deps = ["MacroTools", "Test"] git-tree-sha1 = "7b8a93dba8af7e3b42fecabf646260105ac373f7" uuid = "bbf7d656-a473-5ed7-a52c-81e309532950" version = "0.3.0" -[[Compat]] +[[deps.Compat]] deps = ["Base64", "Dates", "DelimitedFiles", "Distributed", "InteractiveUtils", "LibGit2", "Libdl", "LinearAlgebra", "Markdown", "Mmap", "Pkg", "Printf", "REPL", "Random", "SHA", "Serialization", "SharedArrays", "Sockets", "SparseArrays", "Statistics", "Test", "UUIDs", "Unicode"] -git-tree-sha1 = "dce3e3fea680869eaa0b774b2e8343e9ff442313" +git-tree-sha1 = "44c37b4636bc54afac5c574d2d02b625349d6582" uuid = "34da2185-b29b-5c13-b0c7-acf172513d20" -version = "3.40.0" +version = "3.41.0" -[[CompilerSupportLibraries_jll]] +[[deps.CompilerSupportLibraries_jll]] deps = ["Artifacts", "Libdl"] uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae" -[[ConstructionBase]] +[[deps.ConstructionBase]] deps = ["LinearAlgebra"] git-tree-sha1 = "f74e9d5388b8620b4cee35d4c5a618dd4dc547f4" uuid = "187b0558-2788-49d3-abe0-74a17ed4e7c9" version = "1.3.0" -[[Contour]] +[[deps.Contour]] deps = ["StaticArrays"] git-tree-sha1 = "9f02045d934dc030edad45944ea80dbd1f0ebea7" uuid = "d38c429a-6771-53c6-b99e-75d170b6e991" version = "0.5.7" -[[DEDataArrays]] +[[deps.DEDataArrays]] deps = ["ArrayInterface", "DocStringExtensions", "LinearAlgebra", "RecursiveArrayTools", "SciMLBase", "StaticArrays"] git-tree-sha1 = "31186e61936fbbccb41d809ad4338c9f7addf7ae" uuid = "754358af-613d-5f8d-9788-280bf1605d4c" version = "0.2.0" -[[DataAPI]] +[[deps.DataAPI]] git-tree-sha1 = "cc70b17275652eb47bc9e5f81635981f13cea5c8" uuid = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a" version = "1.9.0" -[[DataStructures]] +[[deps.DataStructures]] deps = ["Compat", "InteractiveUtils", "OrderedCollections"] -git-tree-sha1 = "7d9d316f04214f7efdbb6398d545446e246eff02" +git-tree-sha1 = 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"Xorg_xcb_util_jll"] git-tree-sha1 = "d1151e2c45a544f32441a567d1690e701ec89b00" uuid = "975044d2-76e6-5fbe-bf08-97ce7c6574c7" version = "0.4.0+1" -[[Xorg_xcb_util_renderutil_jll]] +[[deps.Xorg_xcb_util_renderutil_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xcb_util_jll"] git-tree-sha1 = "dfd7a8f38d4613b6a575253b3174dd991ca6183e" uuid = "0d47668e-0667-5a69-a72c-f761630bfb7e" version = "0.3.9+1" -[[Xorg_xcb_util_wm_jll]] +[[deps.Xorg_xcb_util_wm_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xcb_util_jll"] git-tree-sha1 = "e78d10aab01a4a154142c5006ed44fd9e8e31b67" uuid = "c22f9ab0-d5fe-5066-847c-f4bb1cd4e361" version = "0.4.1+1" -[[Xorg_xkbcomp_jll]] +[[deps.Xorg_xkbcomp_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libxkbfile_jll"] git-tree-sha1 = "4bcbf660f6c2e714f87e960a171b119d06ee163b" uuid = "35661453-b289-5fab-8a00-3d9160c6a3a4" version = "1.4.2+4" -[[Xorg_xkeyboard_config_jll]] +[[deps.Xorg_xkeyboard_config_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xkbcomp_jll"] git-tree-sha1 = "5c8424f8a67c3f2209646d4425f3d415fee5931d" uuid = "33bec58e-1273-512f-9401-5d533626f822" version = "2.27.0+4" -[[Xorg_xtrans_jll]] +[[deps.Xorg_xtrans_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] git-tree-sha1 = "79c31e7844f6ecf779705fbc12146eb190b7d845" uuid = "c5fb5394-a638-5e4d-96e5-b29de1b5cf10" version = "1.4.0+3" -[[Zlib_jll]] +[[deps.Zlib_jll]] deps = ["Libdl"] uuid = "83775a58-1f1d-513f-b197-d71354ab007a" -[[Zstd_jll]] +[[deps.Zstd_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] git-tree-sha1 = "cc4bf3fdde8b7e3e9fa0351bdeedba1cf3b7f6e6" uuid = "3161d3a3-bdf6-5164-811a-617609db77b4" version = "1.5.0+0" -[[ZygoteRules]] +[[deps.ZygoteRules]] deps = ["MacroTools"] git-tree-sha1 = "8c1a8e4dfacb1fd631745552c8db35d0deb09ea0" uuid = "700de1a5-db45-46bc-99cf-38207098b444" version = "0.2.2" -[[libass_jll]] +[[deps.libass_jll]] deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "HarfBuzz_jll", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] git-tree-sha1 = "5982a94fcba20f02f42ace44b9894ee2b140fe47" uuid = "0ac62f75-1d6f-5e53-bd7c-93b484bb37c0" version = "0.15.1+0" -[[libfdk_aac_jll]] +[[deps.libblastrampoline_jll]] +deps = ["Artifacts", "Libdl", "OpenBLAS_jll"] +uuid = "8e850b90-86db-534c-a0d3-1478176c7d93" + +[[deps.libfdk_aac_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] git-tree-sha1 = "daacc84a041563f965be61859a36e17c4e4fcd55" uuid = "f638f0a6-7fb0-5443-88ba-1cc74229b280" version = "2.0.2+0" -[[libpng_jll]] +[[deps.libpng_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] git-tree-sha1 = "94d180a6d2b5e55e447e2d27a29ed04fe79eb30c" uuid = "b53b4c65-9356-5827-b1ea-8c7a1a84506f" version = "1.6.38+0" -[[libvorbis_jll]] +[[deps.libvorbis_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Ogg_jll", "Pkg"] git-tree-sha1 = "c45f4e40e7aafe9d086379e5578947ec8b95a8fb" uuid = "f27f6e37-5d2b-51aa-960f-b287f2bc3b7a" version = "1.3.7+0" -[[nghttp2_jll]] +[[deps.nghttp2_jll]] deps = ["Artifacts", "Libdl"] uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d" -[[p7zip_jll]] +[[deps.p7zip_jll]] deps = ["Artifacts", "Libdl"] uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0" -[[x264_jll]] +[[deps.x264_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] git-tree-sha1 = "4fea590b89e6ec504593146bf8b988b2c00922b2" uuid = "1270edf5-f2f9-52d2-97e9-ab00b5d0237a" version = "2021.5.5+0" -[[x265_jll]] +[[deps.x265_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] git-tree-sha1 = "ee567a171cce03570d77ad3a43e90218e38937a9" uuid = "dfaa095f-4041-5dcd-9319-2fabd8486b76" version = "3.5.0+0" -[[xkbcommon_jll]] +[[deps.xkbcommon_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Wayland_jll", "Wayland_protocols_jll", "Xorg_libxcb_jll", "Xorg_xkeyboard_config_jll"] git-tree-sha1 = "ece2350174195bb31de1a63bea3a41ae1aa593b6" uuid = "d8fb68d0-12a3-5cfd-a85a-d49703b185fd" diff --git a/docs/Project.toml b/docs/Project.toml index 74ddde13..a1fe80c6 100644 --- a/docs/Project.toml +++ b/docs/Project.toml @@ -25,7 +25,7 @@ Documenter = "0.24, 0.25, 0.26, 0.27" Interpolations = "0.13" JLD2 = "0.1.11, 02, 0.3, 0.4" Literate = "2.2.1" -OrdinaryDiffEq = "5.61.1" +OrdinaryDiffEq = "6" Plots = "0.29, 1" StaticArrays = "1.1" -Tensors = "1.4" +Tensors = "1.8" diff --git a/docs/examples/OceanFlow.jl b/docs/examples/OceanFlow.jl index f1a27bcc..bbd6300e 100644 --- a/docs/examples/OceanFlow.jl +++ b/docs/examples/OceanFlow.jl @@ -4,14 +4,14 @@ using Distributed, BenchmarkTools, Test, JLD2 nprocs() == 1 && addprocs() @everywhere using CoherentStructures -JLD2.@load "docs/examples/Ocean_geostrophic_velocity.jld2" Lon Lat Time UT VT +lon, lat, time, us, vs = load(OCEAN_FLOW_FILE, "Lon", "Lat", "Time", "UT", "VT") -t_initial = minimum(Time) +t_initial = minimum(time) t_final = t_initial + 90 LL = (-4.0, -34.0) UR = (6.0, -28.0) -const p = interpolateVF(Lon, Lat, Time, UT, VT) +const p = interpolateVF(lon, lat, time, us, vs) ctx, _ = regularP2TriangularGrid((100, 60), LL, UR, quadrature_order=2) # ctx.mass_weights = [cos(deg2rad(x[2])) for x in ctx.quadrature_points] diff --git a/docs/examples/Ocean_geostrophic_velocity.jld2 b/docs/examples/Ocean_geostrophic_velocity.jld2 index ba41edc1..2b3fe66a 100644 Binary files a/docs/examples/Ocean_geostrophic_velocity.jld2 and b/docs/examples/Ocean_geostrophic_velocity.jld2 differ diff --git a/docs/examples/diffbarriers.jl b/docs/examples/diffbarriers.jl index ef233b9d..034cb608 100644 --- a/docs/examples/diffbarriers.jl +++ b/docs/examples/diffbarriers.jl @@ -117,14 +117,14 @@ nprocs() == 1 && addprocs() # `Lon`, `Lat`, `Time`, `UT`, `VT`. using JLD2 -JLD2.@load("docs/examples/Ocean_geostrophic_velocity.jld2") -const VI = interpolateVF(Lon, Lat, Time, UT, VT) +lon, lat, time, us, vs = load("docs/examples/Ocean_geostrophic_velocity.jld2", "Lon", "Lat", "Time", "UT", "VT") +const VI = interpolateVF(lon, lat, time, us, vs) # Since we want to use parallel computing, we set up the integration LCSParameters # on all workers, i.e., `@everywhere`. q = 91 -t_initial = minimum(Time) +t_initial = minimum(time) t_final = t_initial + 90 const ts = range(t_initial, stop=t_final, length=q) xmin, xmax, ymin, ymax = -4.0, 7.5, -37.0, -28.0 diff --git a/docs/examples/ocean_flow.jl b/docs/examples/ocean_flow.jl index 9eeca62f..914382d3 100644 --- a/docs/examples/ocean_flow.jl +++ b/docs/examples/ocean_flow.jl @@ -32,17 +32,16 @@ nprocs() == 1 && addprocs() @everywhere using CoherentStructures, OrdinaryDiffEq -# Next, we load and interpolate the velocity data sets. Loading the data sets defines -# `Lon`, `Lat`, `Time`, `UT`, `VT`. +# Next, we load and interpolate the velocity data sets. using JLD2 -JLD2.@load(OCEAN_FLOW_FILE) -const uv = interpolateVF(Lon, Lat, Time, UT, VT) +xs, ys, ts, us, vs = load(OCEAN_FLOW_FILE, "Lon", "Lat", "Time", "UT", "VT") +const uv = interpolateVF(xs, ys, ts, us, vs) # Now, we set up the computational problem. q = 91 -t_initial = minimum(Time) +t_initial = minimum(ts) t_final = t_initial + 90 const tspan = range(t_initial, stop=t_final, length=q) xmin, xmax, ymin, ymax = -4.0, 7.5, -37.0, -28.0 @@ -81,7 +80,7 @@ DISPLAY_PLOT(fig, ocean_flow_geodesic_vortices) using Interpolations, Tensors, StaticArrays -const V = scale(interpolate(SVector{2}.(UT[:,:,1], VT[:,:,1]), BSpline(Quadratic(Free(OnGrid())))), Lon, Lat) +const V = scale(interpolate(SVector{2}.(us[:,:,1], vs[:,:,1]), BSpline(Quadratic(Free(OnGrid())))), xs, ys) rate_of_strain_tensor(xin) = let V=V x, y = xin @@ -122,13 +121,13 @@ DISPLAY_PLOT(fig, ocean_flow_oecs) using CoherentStructures import JLD2, OrdinaryDiffEq, Plots -JLD2.@load(OCEAN_FLOW_FILE) +xs, ys, ts, us, vs = load(OCEAN_FLOW_FILE, "Lon", "Lat", "Time", "UT", "VT") -const UV = interpolateVF(Lon, Lat, Time, UT, VT) +const UV = interpolateVF(xs, ys, ts, us, vs) # Next, we define a flow function from it. -t_initial = minimum(Time) +t_initial = minimum(ts) t_final = t_initial + 90 const times = [t_initial, t_final] flow_map(u0) = flow(interp_rhs, u0, times; p=UV, tolerance=1e-5, solver=OrdinaryDiffEq.BS5())[end] diff --git a/src/odesolvers.jl b/src/odesolvers.jl index 02f0d120..a88175c1 100644 --- a/src/odesolvers.jl +++ b/src/odesolvers.jl @@ -4,12 +4,13 @@ ### LinearImplicitEuler: ################################################################################ -struct LinearImplicitEuler{CS,AD,F} <: OrdinaryDiffEqNewtonAlgorithm{CS,AD,Nothing} +struct LinearImplicitEuler{CS,AD,F} <: OrdinaryDiffEqNewtonAlgorithm{CS,AD,Nothing,Val{true}} linsolve::F end LinearImplicitEuler(; chunk_size = 0, autodiff = false, + standardtag = Val(true), linsolve = DEFAULT_LINSOLVE, ) = LinearImplicitEuler{chunk_size,autodiff,typeof(linsolve)}(linsolve) OrdinaryDiffEq.alg_order(::LinearImplicitEuler) = 1 @@ -92,10 +93,10 @@ end ### LinearMEBDF2: ################################################################################ -struct LinearMEBDF2{CS,AD,F} <: OrdinaryDiffEqNewtonAlgorithm{CS,AD,Nothing} +struct LinearMEBDF2{CS,AD,F} <: OrdinaryDiffEqNewtonAlgorithm{CS,AD,Nothing,Val{true}} linsolve::F end -LinearMEBDF2(; chunk_size=0, autodiff=false, linsolve=DEFAULT_LINSOLVE) = +LinearMEBDF2(; chunk_size=0, autodiff=false, standardtag = Val(true), linsolve=DEFAULT_LINSOLVE) = LinearMEBDF2{chunk_size,autodiff,typeof(linsolve)}(linsolve) OrdinaryDiffEq.alg_order(::LinearMEBDF2) = 2 OrdinaryDiffEq.is_mass_matrix_alg(::LinearMEBDF2) = true diff --git a/test/test_odesolvers.jl b/test/test_odesolvers.jl index e4ee06df..ca4b9fa5 100644 --- a/test/test_odesolvers.jl +++ b/test/test_odesolvers.jl @@ -3,30 +3,33 @@ using OrdinaryDiffEq, DiffEqDevTools, SparseArrays, LinearAlgebra @testset "odesolvers" begin dts = 0.5 .^(12:-1:7) - u0 = sin.(range(0, pi, length = 100)) tspan = (0.0, 1.0) @testset "autonomous ODEs, no mass matrix" begin - A = spdiagm(-1 => ones(99) , 0 => fill(-2.0, 100) , 1 => ones(99)) + N = 50 + u0 = sin.(range(0, pi, length = N)) + A = N^2*SymTridiagonal(fill(-2.0, N), ones(N-1)) f = DiffEqArrayOperator(A) sol_analytic = (u0,p,t) -> exp(t*Matrix(A)) * u0 prob = ODEProblem(ODEFunction(f; analytic=sol_analytic), u0, tspan) - sim1 = test_convergence(dts, prob, LinearImplicitEuler(linsolve=LinSolveFactorize(lu))) - @test sim1.𝒪est[:final] ≈ 1 rtol=1e-3 + sim1 = test_convergence(dts, prob, LinearImplicitEuler(linsolve=LinSolveFactorize(factorize))) + @test sim1.𝒪est[:final] ≈ 1 rtol=5e-2 - sim2 = test_convergence(dts, prob, LinearMEBDF2(linsolve=LinSolveFactorize(lu))) - @test sim2.𝒪est[:final] ≈ 2 rtol=1e-2 + sim2 = test_convergence(dts, prob, LinearMEBDF2(linsolve=LinSolveFactorize(factorize))) + @test sim2.𝒪est[:final] ≈ 2 rtol=5e-2 end @testset "nonautonomous ODEs with mass matrix" begin - M = 0.5Diagonal(ones(100)) - A = spdiagm(0 => ones(100)) - update_func = (_A, u, p, t) -> _A.nzval .= t + N = 100 + M = 0.5Diagonal(ones(N)) + A = spdiagm(0 => ones(N)) + u0 = sin.(range(0, pi, length = N)) + update_func = (_A, u, p, t) -> (nzv = nonzeros(_A); nzv .= t; _A) f = DiffEqArrayOperator(A; update_func=update_func) sol_analytic = (u0, p, t) -> exp(t^2/(2*0.5)) .* u0 - prob = ODEProblem(ODEFunction(f; analytic=sol_analytic, mass_matrix=M), u0, tspan) + prob = ODEProblem(ODEFunction(f; jac=update_func, jac_prototype=A, analytic=sol_analytic, mass_matrix=M), u0, tspan) sim1 = test_convergence(dts, prob, LinearImplicitEuler(linsolve=LinSolveFactorize(lu))) @test sim1.𝒪est[:final] ≈ 1 rtol=1e-2 @@ -34,15 +37,14 @@ using OrdinaryDiffEq, DiffEqDevTools, SparseArrays, LinearAlgebra sim2 = test_convergence(dts, prob, LinearMEBDF2(linsolve=LinSolveFactorize(lu))) @test sim2.𝒪est[:final] ≈ 2 rtol=1e-2 - solve(prob, LinearImplicitEuler(linsolve=LinSolveFactorize(lu)), dt=0.1) - solve(prob, LinearMEBDF2(linsolve=LinSolveFactorize(lu)), dt=0.1) - - # solve(prob, ImplicitEuler(linsolve=LinSolveFactorize(lu))) + # solve(prob, LinearImplicitEuler(linsolve=LinSolveFactorize(lu)), dt=0.1) + # solve(prob, LinearMEBDF2(linsolve=LinSolveFactorize(lu)), dt=0.1) + # solve(prob, ImplicitEuler(linsolve=LinSolveFactorize(lu)), dt=0.1) # solve(prob, MEBDF2(linsolve=LinSolveFactorize(lu)), dt=0.1) - # @time solve(prob, LinearImplicitEuler(linsolve=LinSolveFactorize(lu)), dt=0.1) - # @time solve(prob, ImplicitEuler(linsolve=LinSolveFactorize(lu))) - # @time solve(prob, LinearMEBDF2(linsolve=LinSolveFactorize(lu)), dt=0.1) - # @time solve(prob, MEBDF2(linsolve=LinSolveFactorize(lu)), dt=0.1) + # @time solve(prob, LinearImplicitEuler(linsolve=LinSolveFactorize(lu)), dt=0.1); + # @time solve(prob, ImplicitEuler(linsolve=LinSolveFactorize(lu))); + # @time solve(prob, LinearMEBDF2(linsolve=LinSolveFactorize(lu)), dt=0.1); + # @time solve(prob, MEBDF2(linsolve=LinSolveFactorize(lu)), dt=0.1); end @testset "ADE in rotating double gyre" begin @@ -58,19 +60,21 @@ using OrdinaryDiffEq, DiffEqDevTools, SparseArrays, LinearAlgebra A = assemble(Stiffness(), ctx) function update_coeffs!(A, u, p, t) - vals = SparseArrays.nzvalview(A) - vals .= CoherentStructures.stiffnessMatrixTimeT(ctx, sol, t, δ).nzval - vals .*= ϵ - A + let ϵ=ϵ, δ=δ, sol=sol, ctx=ctx + vals = nonzeros(A) + vals .= nonzeros(CoherentStructures.stiffnessMatrixTimeT(ctx, sol, t, δ)) + rmul!(vals, ϵ) + return A + end end f = DiffEqArrayOperator(A; update_func=update_coeffs!) u0 = nodal_interpolation(ctx, circleFun) - prob = ODEProblem(ODEFunction(f; mass_matrix=M), u0, tspan) + prob = ODEProblem(ODEFunction(f; jac=update_coeffs!, jac_prototype=A, mass_matrix=M), u0, tspan) - sol1 = solve(prob, LinearImplicitEuler(linsolve=LinSolveFactorize(lu)), dt=0.1) - sol2 = solve(prob, LinearMEBDF2(linsolve=LinSolveFactorize(lu)), dt=0.1) + sol1 = solve(prob, LinearImplicitEuler(linsolve=LinSolveFactorize(lu)), dt=0.01) + sol2 = solve(prob, LinearMEBDF2(linsolve=LinSolveFactorize(lu)), dt=0.01) # solve(prob, ImplicitEuler(linsolve=LinSolveFactorize(lu)), dt=0.1) # solve(prob, MEBDF2(linsolve=LinSolveFactorize(lu)), dt=0.1) @@ -81,6 +85,6 @@ using OrdinaryDiffEq, DiffEqDevTools, SparseArrays, LinearAlgebra @test sol1.retcode === :Success @test sol2.retcode === :Success - @test sol1.u[end] ≈ sol2.u[end] atol=1e-1 + @test sol1.u[end] ≈ sol2.u[end] rtol=1e-3 end end