Merge branch 'main' into subcell-limiting

.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@v1.24.3
+        uses: crate-ci/typos@v1.25.0

NEWS.md

@@ -4,13 +4,39 @@ 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 when updating to v0.9 from v0.8.x
+
+#### Added
+
+- Boundary conditions are now supported on nonconservative terms ([#2062]).
+
+#### Changed
+
+- We removed the first argument `semi` corresponding to a `Semidiscretization` from the 
+  `AnalysisSurfaceIntegral` constructor, as it is no longer needed (see [#1959]).
+  The `AnalysisSurfaceIntegral` now only takes the arguments `boundary_symbols` and `variable`.
+  ([#2069])
+- In functions `rhs!`, `rhs_parabolic!`  we removed the unused argument `initial_condition`. ([#2037])
+  Users should not be affected by this.
+- Nonconservative terms depend only on `normal_direction_average` instead of both 
+  `normal_direction_average` and `normal_direction_ll`, such that the function signature is now 
+  identical with conservative fluxes. This required a change of the `normal_direction` in
+  `flux_nonconservative_powell` ([#2062]).
+
+#### Deprecated
+
+#### Removed
+
+
 ## Changes in the v0.8 lifecycle
 
 #### Changed
 
 - The AMR routines for `P4estMesh` and `T8codeMesh` were changed to work on the product
   of the Jacobian and the conserved variables instead of the conserved variables only
   to make AMR fully conservative ([#2028]). This may change AMR results slightly.
+- Subcell (IDP) limiting is now officially supported and not marked as experimental
+  anymore (see `VolumeIntegralSubcellLimiting`).
 
 ## Changes when updating to v0.8 from v0.7.x
 

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 = "0.8.11-DEV"
+version = "0.9.3-DEV"
 
 [deps]
 Accessors = "7d9f7c33-5ae7-4f3b-8dc6-eff91059b697"

README.md

@@ -36,8 +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
-  * Positivity-preserving limiting
   * [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
+  * 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))

benchmark/Project.toml

@@ -8,4 +8,4 @@ Trixi = "a7f1ee26-1774-49b1-8366-f1abc58fbfcb"
 BenchmarkTools = "0.5, 0.7, 1.0"
 OrdinaryDiffEq = "5.65, 6"
 PkgBenchmark = "0.2.10"
-Trixi = "0.4, 0.5, 0.6, 0.7, 0.8"
+Trixi = "0.4, 0.5, 0.6, 0.7, 0.8, 0.9"

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")

docs/literate/src/files/DGMulti_1.jl

@@ -30,22 +30,22 @@ dg = DGMulti(polydeg = 3,
 cells_per_dimension = (32, 32)
 mesh = DGMultiMesh(dg,
                    cells_per_dimension, # initial_refinement_level = 5
-                   coordinates_min=(-2.0, -2.0),
-                   coordinates_max=( 2.0,  2.0),
-                   periodicity=true)
+                   coordinates_min = (-2.0, -2.0),
+                   coordinates_max = (2.0, 2.0),
+                   periodicity = true)
 
 semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition, dg,
-                                    boundary_conditions=boundary_condition_periodic)
+                                    boundary_conditions = boundary_condition_periodic)
 tspan = (0.0, 0.4)
 ode = semidiscretize(semi, tspan)
 
-alive_callback = AliveCallback(alive_interval=10)
-analysis_callback = AnalysisCallback(semi, interval=100, uEltype=real(dg))
+alive_callback = AliveCallback(alive_interval = 10)
+analysis_callback = AnalysisCallback(semi, interval = 100, uEltype = real(dg))
 callbacks = CallbackSet(analysis_callback, alive_callback);
 
 # Run the simulation with the same time integration algorithm as before.
-sol = solve(ode, RDPK3SpFSAL49(), abstol=1.0e-6, reltol=1.0e-6,
-            callback=callbacks, save_everystep=false);
+sol = solve(ode, RDPK3SpFSAL49(), abstol = 1.0e-6, reltol = 1.0e-6,
+            callback = callbacks, save_everystep = false);
 #-
 using Plots
 pd = PlotData2D(sol)
@@ -60,7 +60,6 @@ plot!(getmesh(pd))
 # (2021) provides a nice runtime comparison between the different mesh types. On the other hand,
 # the functions are more general and thus we have more option we can choose from.
 
-
 # ## Simulation with Gauss nodes
 # For instance, we can change the approximation type of our simulation.
 using Trixi, OrdinaryDiffEq
@@ -78,28 +77,27 @@ dg = DGMulti(polydeg = 3,
 
 cells_per_dimension = (32, 32)
 mesh = DGMultiMesh(dg,
-             cells_per_dimension, # initial_refinement_level = 5
-             coordinates_min=(-2.0, -2.0),
-             coordinates_max=( 2.0,  2.0),
-             periodicity=true)
+                   cells_per_dimension, # initial_refinement_level = 5
+                   coordinates_min = (-2.0, -2.0),
+                   coordinates_max = (2.0, 2.0),
+                   periodicity = true)
 
 semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition, dg,
-                              boundary_conditions=boundary_condition_periodic)
+                                    boundary_conditions = boundary_condition_periodic)
 tspan = (0.0, 0.4)
 ode = semidiscretize(semi, tspan)
 
-alive_callback = AliveCallback(alive_interval=10)
-analysis_callback = AnalysisCallback(semi, interval=100, uEltype=real(dg))
+alive_callback = AliveCallback(alive_interval = 10)
+analysis_callback = AnalysisCallback(semi, interval = 100, uEltype = real(dg))
 callbacks = CallbackSet(analysis_callback, alive_callback);
 
-sol = solve(ode, RDPK3SpFSAL49(); abstol=1.0e-6, reltol=1.0e-6,
-            ode_default_options()..., callback=callbacks);
+sol = solve(ode, RDPK3SpFSAL49(); abstol = 1.0e-6, reltol = 1.0e-6,
+            ode_default_options()..., callback = callbacks);
 #-
 using Plots
 pd = PlotData2D(sol)
 plot(pd)
 
-
 # ## Simulation with triangular elements
 # Also, we can set another element type. We want to use triangles now.
 using Trixi, OrdinaryDiffEq
@@ -119,21 +117,21 @@ dg = DGMulti(polydeg = 3,
 cells_per_dimension = (32, 32)
 mesh = DGMultiMesh(dg,
                    cells_per_dimension, # initial_refinement_level = 5
-                   coordinates_min=(-2.0, -2.0),
-                   coordinates_max=( 2.0,  2.0),
-                   periodicity=true)
+                   coordinates_min = (-2.0, -2.0),
+                   coordinates_max = (2.0, 2.0),
+                   periodicity = true)
 
 semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition, dg,
-                                    boundary_conditions=boundary_condition_periodic)
+                                    boundary_conditions = boundary_condition_periodic)
 tspan = (0.0, 0.4)
 ode = semidiscretize(semi, tspan)
 
-alive_callback = AliveCallback(alive_interval=10)
-analysis_callback = AnalysisCallback(semi, interval=100, uEltype=real(dg))
+alive_callback = AliveCallback(alive_interval = 10)
+analysis_callback = AnalysisCallback(semi, interval = 100, uEltype = real(dg))
 callbacks = CallbackSet(analysis_callback, alive_callback);
 
-sol = solve(ode, RDPK3SpFSAL49(); abstol=1.0e-6, reltol=1.0e-6,
-            ode_default_options()..., callback=callbacks);
+sol = solve(ode, RDPK3SpFSAL49(); abstol = 1.0e-6, reltol = 1.0e-6,
+            ode_default_options()..., callback = callbacks);
 #-
 using Plots
 pd = PlotData2D(sol)
@@ -142,7 +140,6 @@ plot(pd)
 plot(pd["rho"])
 plot!(getmesh(pd))
 
-
 # ## Triangular meshes on non-Cartesian domains
 # To use triangular meshes on a non-Cartesian domain, Trixi.jl uses the package [StartUpDG.jl](https://github.com/jlchan/StartUpDG.jl).
 # The following example is based on [`elixir_euler_triangulate_pkg_mesh.jl`](https://github.com/trixi-framework/Trixi.jl/blob/main/examples/dgmulti_2d/elixir_euler_triangulate_pkg_mesh.jl)
@@ -157,7 +154,7 @@ source_terms = source_terms_convergence_test
 
 # We create the solver `DGMulti` with triangular elements (`Tri()`) as before.
 dg = DGMulti(polydeg = 3, element_type = Tri(),
-             approximation_type=Polynomial(),
+             approximation_type = Polynomial(),
              surface_flux = flux_lax_friedrichs,
              volume_integral = VolumeIntegralFluxDifferencing(flux_ranocha))
 
@@ -168,11 +165,11 @@ meshIO = StartUpDG.triangulate_domain(StartUpDG.RectangularDomainWithHole());
 
 # The pre-defined Triangulate geometry in StartUpDG has integer boundary tags. With [`DGMultiMesh`](@ref)
 # we assign boundary faces based on these integer boundary tags and create a mesh compatible with Trixi.jl.
-mesh = DGMultiMesh(dg, meshIO, Dict(:outer_boundary=>1, :inner_boundary=>2))
+mesh = DGMultiMesh(dg, meshIO, Dict(:outer_boundary => 1, :inner_boundary => 2))
 #-
 boundary_condition_convergence_test = BoundaryConditionDirichlet(initial_condition)
 boundary_conditions = (; :outer_boundary => boundary_condition_convergence_test,
-                         :inner_boundary => boundary_condition_convergence_test)
+                       :inner_boundary => boundary_condition_convergence_test)
 
 semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition, dg,
                                     source_terms = source_terms,
@@ -181,12 +178,12 @@ semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition, dg,
 tspan = (0.0, 0.2)
 ode = semidiscretize(semi, tspan)
 
-alive_callback = AliveCallback(alive_interval=20)
-analysis_callback = AnalysisCallback(semi, interval=200, uEltype=real(dg))
+alive_callback = AliveCallback(alive_interval = 20)
+analysis_callback = AnalysisCallback(semi, interval = 200, uEltype = real(dg))
 callbacks = CallbackSet(alive_callback, analysis_callback);
 
-sol = solve(ode, CarpenterKennedy2N54(williamson_condition=false),
-            dt = 0.5 * estimate_dt(mesh, dg), save_everystep=false, callback=callbacks);
+sol = solve(ode, CarpenterKennedy2N54(williamson_condition = false),
+            dt = 0.5 * estimate_dt(mesh, dg), save_everystep = false, callback = callbacks);
 #-
 using Plots
 pd = PlotData2D(sol)
@@ -195,7 +192,6 @@ plot!(getmesh(pd))
 
 # For more information, please have a look in the [StartUpDG.jl documentation](https://jlchan.github.io/StartUpDG.jl/stable/).
 
-
 # ## Package versions
 
 # These results were obtained using the following versions.
@@ -205,4 +201,4 @@ versioninfo()
 
 using Pkg
 Pkg.status(["Trixi", "StartUpDG", "OrdinaryDiffEq", "Plots"],
-           mode=PKGMODE_MANIFEST)
+           mode = PKGMODE_MANIFEST)