Merge branch 'main' into lc/gpu-develop

.github/workflows/FormatCheck.yml

@@ -1,4 +1,4 @@
-name: format-check
+name: Format suggestions
 
 on:
   push:
@@ -8,37 +8,10 @@ on:
   pull_request:
 
 jobs:
-  check-format:
-    runs-on: ${{ matrix.os }}
-    strategy:
-      matrix:
-        julia-version: [1]
-        julia-arch: [x86]
-        os: [ubuntu-latest]
+  format-suggestions:
+    runs-on: ubuntu-latest
     steps:
-      - uses: julia-actions/setup-julia@latest
-        with:
-          version: ${{ matrix.julia-version }}
-
       - uses: actions/checkout@v4
-      - name: Install JuliaFormatter and format
-        # This will use the latest version by default but you can set the version like so:
-        #
-        # julia  -e 'using Pkg; Pkg.add(PackageSpec(name = "JuliaFormatter", version = "0.13.0"))'
-        #
-        # TODO: Change the call below to
-        #       format(".")
-        run: |
-          julia  -e 'using Pkg; Pkg.add(PackageSpec(name = "JuliaFormatter", version="1.0.60"))'
-          julia  -e 'using JuliaFormatter; format(["benchmark", "examples", "ext", "src", "test", "utils"])'
-      - name: Format check
-        run: |
-          julia -e '
-          out = Cmd(`git diff --name-only`) |> read |> String
-          if out == ""
-              exit(0)
-          else
-              @error "Some files have not been formatted !!!"
-              write(stdout, out)
-              exit(1)
-          end'
+      - uses: julia-actions/julia-format@v3
+        with:
+          version: "1.0.60"

.github/workflows/SpellCheck.yml

@@ -10,4 +10,4 @@ jobs:
       - name: Checkout Actions Repository
         uses: actions/checkout@v4
       - name: Check spelling
-        uses: crate-ci/typos@v1.25.0
+        uses: crate-ci/typos@v1.27.0

NEWS.md

@@ -4,6 +4,14 @@ Trixi.jl follows the interpretation of [semantic versioning (semver)](https://ju
 used in the Julia ecosystem. Notable changes will be documented in this file
 for human readability.
 
+## Changes in the v0.9 lifecycle
+
+#### Added
+
+- New time integrator `PairedExplicitRK3`, implementing the third-order paired explicit Runge-Kutta
+  method with [Convex.jl](https://github.com/jump-dev/Convex.jl), [ECOS.jl](https://github.com/jump-dev/ECOS.jl),
+  and [NLsolve.jl](https://github.com/JuliaNLSolvers/NLsolve.jl) ([#2008])
+
 ## Changes when updating to v0.9 from v0.8.x
 
 #### Added

Project.toml

@@ -1,7 +1,7 @@
 name = "Trixi"
 uuid = "a7f1ee26-1774-49b1-8366-f1abc58fbfcb"
 authors = ["Michael Schlottke-Lakemper <[email protected]>", "Gregor Gassner <[email protected]>", "Hendrik Ranocha <[email protected]>", "Andrew R. Winters <[email protected]>", "Jesse Chan <[email protected]>"]
-version = "0.9.2-DEV"
+version = "0.9.7-DEV"
 
 [deps]
 Adapt = "79e6a3ab-5dfb-504d-930d-738a2a938a0e"
@@ -37,6 +37,7 @@ Requires = "ae029012-a4dd-5104-9daa-d747884805df"
 SciMLBase = "0bca4576-84f4-4d90-8ffe-ffa030f20462"
 SimpleUnPack = "ce78b400-467f-4804-87d8-8f486da07d0a"
 SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
+StableRNGs = "860ef19b-820b-49d6-a774-d7a799459cd3"
 StartUpDG = "472ebc20-7c99-4d4b-9470-8fde4e9faa0f"
 Static = "aedffcd0-7271-4cad-89d0-dc628f76c6d3"
 StaticArrayInterface = "0d7ed370-da01-4f52-bd93-41d350b8b718"
@@ -56,10 +57,12 @@ UUIDs = "cf7118a7-6976-5b1a-9a39-7adc72f591a4"
 Convex = "f65535da-76fb-5f13-bab9-19810c17039a"
 ECOS = "e2685f51-7e38-5353-a97d-a921fd2c8199"
 Makie = "ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a"
+NLsolve = "2774e3e8-f4cf-5e23-947b-6d7e65073b56"
 
 [extensions]
 TrixiConvexECOSExt = ["Convex", "ECOS"]
 TrixiMakieExt = "Makie"
+TrixiNLsolveExt = "NLsolve"
 
 [compat]
 Adapt = "3.7, 4.0"
@@ -82,9 +85,10 @@ KernelAbstractions = "0.9"
 LinearAlgebra = "1"
 LinearMaps = "2.7, 3.0"
 LoopVectorization = "0.12.151"
-MPI = "0.20"
+MPI = "0.20.6"
 Makie = "0.19, 0.20"
 MuladdMacro = "0.2.2"
+NLsolve = "4.5.1"
 Octavian = "0.3.21"
 OffsetArrays = "1.12"
 P4est = "0.4.9"
@@ -98,14 +102,15 @@ Requires = "1.1"
 SciMLBase = "1.90, 2"
 SimpleUnPack = "1.1"
 SparseArrays = "1"
+StableRNGs = "1.0.2"
 StartUpDG = "0.17.7, 1.1.5"
 Static = "0.8.7, 1"
 StaticArrayInterface = "1.4"
 StaticArrays = "1.5"
 StrideArrays = "0.1.26"
 StructArrays = "0.6.11"
 SummationByPartsOperators = "0.5.41"
-T8code = "0.6"
+T8code = "0.7"
 TimerOutputs = "0.5.7"
 Triangulate = "2.2"
 TriplotBase = "0.1"
@@ -118,3 +123,4 @@ julia = "1.8"
 Convex = "f65535da-76fb-5f13-bab9-19810c17039a"
 ECOS = "e2685f51-7e38-5353-a97d-a921fd2c8199"
 Makie = "ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a"
+NLsolve = "2774e3e8-f4cf-5e23-947b-6d7e65073b56"

README.md

@@ -36,9 +36,11 @@ installation and postprocessing procedures. Its features include:
 * Discontinuous Galerkin methods
   * Kinetic energy-preserving and entropy-stable methods based on flux differencing
   * Entropy-stable shock capturing
+  * [Finite difference summation by parts (SBP) methods](https://github.com/ranocha/SummationByPartsOperators.jl)
+* Advanced limiting strategies
   * Positivity-preserving limiting
   * Subcell invariant domain-preserving (IDP) limiting
-  * [Finite difference summation by parts (SBP) methods](https://github.com/ranocha/SummationByPartsOperators.jl)
+  * Entropy-bounded limiting
 * Compatible with the [SciML ecosystem for ordinary differential equations](https://diffeq.sciml.ai/latest/)
   * [Explicit low-storage Runge-Kutta time integration](https://diffeq.sciml.ai/latest/solvers/ode_solve/#Low-Storage-Methods)
   * [Strong stability preserving methods](https://diffeq.sciml.ai/latest/solvers/ode_solve/#Explicit-Strong-Stability-Preserving-Runge-Kutta-Methods-for-Hyperbolic-PDEs-(Conservation-Laws))

docs/literate/make.jl

@@ -3,22 +3,22 @@ using Test: @testset
 import Pkg
 
 # Create markdown and notebook files for `file`
-function create_files(title, file, repo_src, pages_dir, notebooks_dir; folder="")
+function create_files(title, file, repo_src, pages_dir, notebooks_dir; folder = "")
     notebook_filename = first(splitext(file)) * ".ipynb"
     if !isempty(folder)
         notebook_filename = joinpath(folder, notebook_filename)
     end
 
-    binder_logo   = "https://mybinder.org/badge_logo.svg"
+    binder_logo = "https://mybinder.org/badge_logo.svg"
     nbviewer_logo = "https://img.shields.io/badge/render-nbviewer-f37726"
     raw_notebook_logo = "https://img.shields.io/badge/raw-notebook-4cc61e"
 
     notebook_path = "tutorials/notebooks/$notebook_filename"
-    binder_url   = "https://mybinder.org/v2/gh/trixi-framework/Trixi.jl/tutorial_notebooks?filepath=$notebook_path"
+    binder_url = "https://mybinder.org/v2/gh/trixi-framework/Trixi.jl/tutorial_notebooks?filepath=$notebook_path"
     nbviewer_url = "https://nbviewer.jupyter.org/github/trixi-framework/Trixi.jl/blob/tutorial_notebooks/$notebook_path"
     raw_notebook_url = "https://raw.githubusercontent.com/trixi-framework/Trixi.jl/tutorial_notebooks/$notebook_path"
 
-    binder_badge   = "# [![]($binder_logo)]($binder_url)"
+    binder_badge = "# [![]($binder_logo)]($binder_url)"
     nbviewer_badge = "# [![]($nbviewer_logo)]($nbviewer_url)"
     raw_notebook_badge = "# [![]($raw_notebook_logo)]($raw_notebook_url)"
 
@@ -28,25 +28,28 @@ function create_files(title, file, repo_src, pages_dir, notebooks_dir; folder=""
         # available for the latest stable release of Trixi.jl at the time of caching.\n\n"
         return string("# # $title\n\n", warning, content)
     end
-    Literate.notebook(joinpath(repo_src, folder, file), joinpath(notebooks_dir, folder); execute=false, preprocess=preprocess_notebook, credit=false)
+    Literate.notebook(joinpath(repo_src, folder, file), joinpath(notebooks_dir, folder);
+                      execute = false, preprocess = preprocess_notebook, credit = false)
 
     # Generate markdown file
     function preprocess_docs(content)
-        return string("# # [$title](@id $(splitext(file)[1]))\n $binder_badge\n $nbviewer_badge\n $raw_notebook_badge\n\n", content)
+        return string("# # [$title](@id $(splitext(file)[1]))\n $binder_badge\n $nbviewer_badge\n $raw_notebook_badge\n\n",
+                      content)
     end
-    Literate.markdown(joinpath(repo_src, folder, file), joinpath(pages_dir, folder); preprocess=preprocess_docs,)
+    Literate.markdown(joinpath(repo_src, folder, file), joinpath(pages_dir, folder);
+                      preprocess = preprocess_docs,)
 end
 
 # Create tutorials with Literate.jl
 function create_tutorials(files)
-    repo_src        = joinpath(@__DIR__, "src", "files")
+    repo_src = joinpath(@__DIR__, "src", "files")
 
-    pages_dir       = joinpath(@__DIR__, "..", "src", "tutorials")
-    notebooks_dir   = joinpath(pages_dir, "notebooks")
+    pages_dir = joinpath(@__DIR__, "..", "src", "tutorials")
+    notebooks_dir = joinpath(pages_dir, "notebooks")
 
-    Sys.rm(pages_dir;       recursive=true, force=true)
+    Sys.rm(pages_dir; recursive = true, force = true)
 
-    Sys.rm("out"; recursive=true, force=true)
+    Sys.rm("out"; recursive = true, force = true)
 
     # Run tests on all tutorial files
     @testset "TrixiTutorials" begin
@@ -59,15 +62,16 @@ function create_tutorials(files)
                     mod = gensym(filename[j][2][2])
                     @testset "$(filename[j][2][2])" begin
                         @eval module $mod
-                            include(joinpath($repo_src, $(filename[j][2][1]), $(filename[j][2][2])))
+                        include(joinpath($repo_src, $(filename[j][2][1]),
+                                         $(filename[j][2][2])))
                         end
                     end
                 end
             else # Single files
                 mod = gensym(title)
                 @testset "$title" begin
                     @eval module $mod
-                        include(joinpath($repo_src, $filename))
+                    include(joinpath($repo_src, $filename))
                     end
                 end
             end
@@ -85,18 +89,20 @@ function create_tutorials(files)
         end
         return content
     end
-    Literate.markdown(joinpath(repo_src, "index.jl"), pages_dir; name="introduction", preprocess=preprocess_introduction)
+    Literate.markdown(joinpath(repo_src, "index.jl"), pages_dir; name = "introduction",
+                      preprocess = preprocess_introduction)
     # Navigation system for makedocs
-    pages = Any["Introduction" => "tutorials/introduction.md",]
+    pages = Any["Introduction" => "tutorials/introduction.md"]
 
     # Create markdown and notebook files for tutorials
     for (i, (title, filename)) in enumerate(files)
         # Several files of one topic are created separately and pushed to `pages` together.
         if filename isa Vector
             vector = []
             for j in eachindex(filename)
-                create_files("$i.$j: $title: $(filename[j][1])", filename[j][2][2], repo_src,
-                             pages_dir, notebooks_dir; folder=filename[j][2][1])
+                create_files("$i.$j: $title: $(filename[j][1])", filename[j][2][2],
+                             repo_src,
+                             pages_dir, notebooks_dir; folder = filename[j][2][1])
 
                 path = "$(filename[j][2][1])/$(splitext(filename[j][2][2])[1]).md"
                 push!(vector, "$i.$j $(filename[j][1])" => "tutorials/$path")