Merge branch 'trixi-framework:main' into main

.github/workflows/Documenter.yml

@@ -38,6 +38,7 @@ jobs:
         with:
           version: '1.9'
           show-versioninfo: true
+      - uses: julia-actions/cache@v1
       - uses: julia-actions/julia-buildpkg@v1
         env:
           PYTHON: ""

.github/workflows/SpellCheck.yml

@@ -10,4 +10,4 @@ jobs:
       - name: Checkout Actions Repository
         uses: actions/checkout@v4
       - name: Check spelling
-        uses: crate-ci/typos@v1.16.23
+        uses: crate-ci/typos@v1.18.0

.github/workflows/benchmark.yml

@@ -26,7 +26,7 @@ jobs:
           version: ${{ matrix.version }}
           arch: ${{ matrix.arch }}
           show-versioninfo: true
-      - uses: actions/cache@v3
+      - uses: actions/cache@v4
         env:
           cache-name: cache-artifacts
         with:
@@ -45,7 +45,7 @@ jobs:
         run: julia --project=benchmark/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
       - name: Run benchmarks
         run: julia --project=benchmark/ --color=yes benchmark/run_benchmarks.jl
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
           name: my-artifact
           path: benchmark/results*.md

.github/workflows/ci.yml

@@ -70,6 +70,7 @@ jobs:
           - p4est_part1
           - p4est_part2
           - t8code_part1
+          - t8code_part2
           - unstructured_dgmulti
           - parabolic
           - paper_self_gravitating_gas_dynamics
@@ -128,7 +129,7 @@ jobs:
       - uses: julia-actions/julia-processcoverage@v1
         with:
           directories: src,examples,ext
-      - uses: codecov/codecov-action@v3
+      - uses: codecov/codecov-action@v4
         with:
           file: ./lcov.info
           flags: unittests
@@ -153,7 +154,7 @@ jobs:
       - shell: bash
         run: |
           cp ./lcov.info ./lcov-${{ matrix.trixi_test }}-${{ matrix.os }}-${{ matrix.version }}-${{ matrix.arch }}.info
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
           name: lcov-${{ matrix.trixi_test }}-${{ matrix.os }}-${{ matrix.version }}-${{ matrix.arch }}
           path: ./lcov-${{ matrix.trixi_test }}-${{ matrix.os }}-${{ matrix.version }}-${{ matrix.arch }}.info
@@ -176,7 +177,7 @@ jobs:
       # At first, we check out the repository and download all artifacts
       # (and list files for debugging).
       - uses: actions/checkout@v4
-      - uses: actions/download-artifact@v3
+      - uses: actions/download-artifact@v4
       - run: ls -R
       # Next, we merge the individual coverage files and upload
       # the combined results to Coveralls.
@@ -199,7 +200,7 @@ jobs:
           github-token: ${{ secrets.GITHUB_TOKEN }}
           path-to-lcov: ./lcov.info
       # Upload merged coverage data as artifact for debugging
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
           name: lcov
           path: ./lcov.info

.gitignore

@@ -10,6 +10,7 @@
 *.mesh
 *.bson
 *.inp
+*.msh
 **/Manifest.toml
 out*/
 docs/build

NEWS.md

@@ -8,6 +8,10 @@ for human readability.
 
 #### Added
 - AMR for hyperbolic-parabolic equations on 3D `P4estMesh`
+- `flux_hllc` on non-cartesian meshes for `CompressibleEulerEquations{2,3}D`
+- Different boundary conditions for quad/hex meshes in Abaqus format, even if not generated by HOHQMesh, 
+  can now be digested by Trixi in 2D and 3D.
+- Subcell (positivity) limiting support for nonlinear variables in 2D for `TreeMesh`
 
 ## Changes when updating to v0.6 from v0.5.x
 

Project.toml

@@ -1,14 +1,15 @@
 name = "Trixi"
 uuid = "a7f1ee26-1774-49b1-8366-f1abc58fbfcb"
 authors = ["Michael Schlottke-Lakemper <m.schlottke-lakemper@hlrs.de>", "Gregor Gassner <ggassner@uni-koeln.de>", "Hendrik Ranocha <mail@ranocha.de>", "Andrew R. Winters <andrew.ross.winters@liu.se>", "Jesse Chan <jesse.chan@rice.edu>"]
-version = "0.6.6-pre"
+version = "0.6.9-pre"
 
 [deps]
 CodeTracking = "da1fd8a2-8d9e-5ec2-8556-3022fb5608a2"
 ConstructionBase = "187b0558-2788-49d3-abe0-74a17ed4e7c9"
 DataStructures = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
 DiffEqBase = "2b5f629d-d688-5b77-993f-72d75c75574e"
 DiffEqCallbacks = "459566f4-90b8-5000-8ac3-15dfb0a30def"
+Downloads = "f43a241f-c20a-4ad4-852c-f6b1247861c6"
 EllipsisNotation = "da5c29d0-fa7d-589e-88eb-ea29b0a81949"
 FillArrays = "1a297f60-69ca-5386-bcde-b61e274b549b"
 ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
@@ -57,6 +58,7 @@ ConstructionBase = "1.3"
 DataStructures = "0.18.15"
 DiffEqBase = "6 - 6.143"
 DiffEqCallbacks = "2.25"
+Downloads = "1.6"
 EllipsisNotation = "1.0"
 FillArrays = "0.13.2, 1"
 ForwardDiff = "0.10.18"

benchmark/elixir_2d_euler_vortex_unstructured.jl

@@ -1,5 +1,4 @@
 
-using Downloads: download
 using OrdinaryDiffEq
 using Trixi
 
@@ -49,11 +48,9 @@ end
 initial_condition = initial_condition_isentropic_vortex
 solver = DGSEM(polydeg = 3, surface_flux = flux_lax_friedrichs)
 
-default_mesh_file = joinpath(@__DIR__, "mesh_uniform_cartesian.mesh")
-isfile(default_mesh_file) ||
-    download("https://gist.githubusercontent.com/ranocha/f4ea19ba3b62348968c971db43d7798b/raw/a506abb9479c020920cf6068c142670fc1a9aadc/mesh_uniform_cartesian.mesh",
-             default_mesh_file)
-mesh_file = default_mesh_file
+mesh_file = Trixi.download("https://gist.githubusercontent.com/ranocha/f4ea19ba3b62348968c971db43d7798b/raw/a506abb9479c020920cf6068c142670fc1a9aadc/mesh_uniform_cartesian.mesh",
+                           joinpath(@__DIR__, "mesh_uniform_cartesian.mesh"))
+
 mesh = UnstructuredMesh2D(mesh_file, periodicity = true)
 
 semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition, solver)

docs/literate/make.jl

@@ -10,17 +10,17 @@ function create_files(title, file, repo_src, pages_dir, notebooks_dir; folder=""
     end
 
     binder_logo   = "https://mybinder.org/badge_logo.svg"
-    nbviewer_logo = "https://raw.githubusercontent.com/jupyter/design/master/logos/Badges/nbviewer_badge.svg"
-    download_logo = "https://camo.githubusercontent.com/aea75103f6d9f690a19cb0e17c06f984ab0f472d9e6fe4eadaa0cc438ba88ada/68747470733a2f2f696d672e736869656c64732e696f2f62616467652f646f776e6c6f61642d6e6f7465626f6f6b2d627269676874677265656e"
+    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"
     nbviewer_url = "https://nbviewer.jupyter.org/github/trixi-framework/Trixi.jl/blob/tutorial_notebooks/$notebook_path"
-    download_url = "https://raw.githubusercontent.com/trixi-framework/Trixi.jl/tutorial_notebooks/$notebook_path"
+    raw_notebook_url = "https://raw.githubusercontent.com/trixi-framework/Trixi.jl/tutorial_notebooks/$notebook_path"
 
     binder_badge   = "# [![]($binder_logo)]($binder_url)"
     nbviewer_badge = "# [![]($nbviewer_logo)]($nbviewer_url)"
-    download_badge = "# [![]($download_logo)]($download_url)"
+    raw_notebook_badge = "# [![]($raw_notebook_logo)]($raw_notebook_url)"
 
     # Generate notebook file
     function preprocess_notebook(content)
@@ -32,7 +32,7 @@ function create_files(title, file, repo_src, pages_dir, notebooks_dir; folder=""
 
     # Generate markdown file
     function preprocess_docs(content)
-        return string("# # [$title](@id $(splitext(file)[1]))\n $binder_badge\n $nbviewer_badge\n $download_badge\n\n", content)
+        return string("# # [$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,)
 end

docs/literate/src/files/index.jl

@@ -5,9 +5,9 @@
 
 # Right now, you are using the classic documentation. The corresponding interactive notebooks can
 # be opened in [Binder](https://mybinder.org/) and viewed in [nbviewer](https://nbviewer.jupyter.org/)
-# via the icons ![](https://mybinder.org/badge_logo.svg) and ![](https://raw.githubusercontent.com/jupyter/design/master/logos/Badges/nbviewer_badge.svg)
+# via the icons ![](https://mybinder.org/badge_logo.svg) and ![](https://img.shields.io/badge/render-nbviewer-f37726)
 # in the respective tutorial.
-# You can download the raw notebooks from GitHub via ![](https://camo.githubusercontent.com/aea75103f6d9f690a19cb0e17c06f984ab0f472d9e6fe4eadaa0cc438ba88ada/68747470733a2f2f696d672e736869656c64732e696f2f62616467652f646f776e6c6f61642d6e6f7465626f6f6b2d627269676874677265656e).
+# You can also open the raw notebook files via ![](https://img.shields.io/badge/raw-notebook-4cc61e).
 
 # **Note:** To improve responsiveness via caching, the notebooks are updated only once a week. They are only
 # available for the latest stable release of Trixi.jl at the time of caching.

docs/literate/src/files/non_periodic_boundaries.jl

@@ -16,6 +16,8 @@
 # state as arguments, and solves an approximate Riemann problem to introduce dissipation (and
 # hence stabilization) at the boundary. Hence, the performance of the Dirichlet BC depends on the
 # fidelity of the numerical surface flux.
+# An easy-to read introductory reference on this topic is the paper by 
+# [Mengaldo et al.](https://doi.org/10.2514/6.2014-2923).
 
 # The passed boundary value function is called with the same arguments as an initial condition
 # function, i.e.