Merge branch 'main' into ranocha-patch-2

.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

@@ -4,6 +4,15 @@ 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 v0.6 lifecycle
+
+#### 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
 
 #### Added
@@ -38,7 +47,7 @@ for human readability.
 - Capability to set truly discontinuous initial conditions in 1D.
 - Wetting and drying feature and examples for 1D and 2D shallow water equations
 - Implementation of the polytropic Euler equations in 2D
-- Implementation of the quasi-1D shallow water equations
+- Implementation of the quasi-1D shallow water and compressible Euler equations
 - Subcell (positivity and local min/max) limiting support for conservative variables
   in 2D for `TreeMesh`
 - AMR for hyperbolic-parabolic equations on 2D/3D `TreeMesh`

Project.toml

@@ -1,13 +1,15 @@
 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 = "0.6.5-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"
@@ -54,7 +56,9 @@ TrixiMakieExt = "Makie"
 CodeTracking = "1.0.5"
 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/first_steps/changing_trixi.jl

@@ -0,0 +1,77 @@
+#src # Changing Trixi.jl itself
+
+# If you plan on editing Trixi.jl itself, you can download Trixi.jl locally and run it from
+# the cloned directory.
+
+
+# ## Cloning Trixi.jl
+
+
+# ### Windows
+
+# If you are using Windows, you can clone Trixi.jl by using the GitHub Desktop tool:
+# - If you do not have a GitHub account yet, create it on
+#   the [GitHub website](https://github.com/join).
+# - Download and install [GitHub Desktop](https://desktop.github.com/) and then log in to
+#   your account.
+# - Open GitHub Desktop, press `Ctrl+Shift+O`.
+# - In the opened window, paste `trixi-framework/Trixi.jl` and choose the path to the folder where
+#   you want to save Trixi.jl. Then click `Clone` and Trixi.jl will be cloned to your computer. 
+
+# Now you cloned Trixi.jl and only need to tell Julia to use the local clone as the package sources:
+# - Open a terminal using `Win+r` and `cmd`. Navigate to the folder with the cloned Trixi.jl using `cd`.
+# - Create a new directory `run`, enter it, and start Julia with the `--project=.` flag:
+#   ```shell
+#   mkdir run 
+#   cd run
+#   julia --project=.
+#   ```
+# - Now run the following commands to install all relevant packages:
+#   ```julia
+#   using Pkg; Pkg.develop(PackageSpec(path="..")) # Tell Julia to use the local Trixi.jl clone
+#   Pkg.add(["OrdinaryDiffEq", "Plots"])  # Install additional packages
+#   ```
+
+# Now you already installed Trixi.jl from your local clone. Note that if you installed Trixi.jl
+# this way, you always have to start Julia with the `--project` flag set to your `run` directory,
+# e.g.,
+# ```shell
+# julia --project=.
+# ```
+# if already inside the `run` directory.
+
+
+# ### Linux
+
+# You can clone Trixi.jl to your computer by executing the following commands:
+# ```shell
+# git clone [email protected]:trixi-framework/Trixi.jl.git 
+# # If an error occurs, try the following:
+# # git clone https://github.com/trixi-framework/Trixi.jl
+# cd Trixi.jl
+# mkdir run 
+# cd run
+# julia --project=. -e 'using Pkg; Pkg.develop(PackageSpec(path=".."))' # Tell Julia to use the local Trixi.jl clone
+# julia --project=. -e 'using Pkg; Pkg.add(["OrdinaryDiffEq", "Plots"])' # Install additional packages
+# ```
+# Note that if you installed Trixi.jl this way,
+# you always have to start Julia with the `--project` flag set to your `run` directory, e.g.,
+# ```shell
+# julia --project=.
+# ```
+# if already inside the `run` directory.
+
+
+# ## Additional reading
+
+# To further delve into Trixi.jl, you may have a look at the following introductory tutorials.
+# - [Introduction to DG methods](@ref scalar_linear_advection_1d) will teach you how to set up a
+#   simple way to approximate the solution of a hyperbolic partial differential equation. It will
+#   be especially useful to learn about the 
+#   [Discontinuous Galerkin method](https://en.wikipedia.org/wiki/Discontinuous_Galerkin_method)
+#   and the way it is implemented in Trixi.jl.
+# - [Adding a new scalar conservation law](@ref adding_new_scalar_equations) and
+#   [Adding a non-conservative equation](@ref adding_nonconservative_equation)
+#   describe how to add new physics models that are not yet included in Trixi.jl.
+# - [Callbacks](@ref callbacks-id) gives an overview of how to regularly execute specific actions
+#   during a simulation, e.g., to store the solution or adapt the mesh.