Merge branch 'main' into sc/mhd-treemesh-2d

.github/workflows/FormatCheck.yml

@@ -29,7 +29,7 @@ jobs:
         # TODO: Change the call below to
         #       format(".")
         run: |
-          julia  -e 'using Pkg; Pkg.add(PackageSpec(name = "JuliaFormatter"))'
+          julia  -e 'using Pkg; Pkg.add(PackageSpec(name = "JuliaFormatter", version="1.0.45"))'
           julia  -e 'using JuliaFormatter; format(["benchmark", "examples", "ext", "src", "test", "utils"])'
       - name: Format check
         run: |

.github/workflows/SpellCheck.yml

@@ -10,4 +10,4 @@ jobs:
       - name: Checkout Actions Repository
         uses: actions/checkout@v4
       - name: Check spelling
-        uses: crate-ci/typos@v1.16.26
+        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:

.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
@@ -100,6 +101,10 @@ jobs:
             os: windows-latest
             arch: x64
             trixi_test: threaded
+          - version: '1.9'
+            os: macos-14
+            arch: arm64
+            trixi_test: threaded
     steps:
       - uses: actions/checkout@v4
       - uses: julia-actions/setup-julia@v1
@@ -128,12 +133,13 @@ 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
           name: codecov-umbrella
-          fail_ci_if_error: false
+          fail_ci_if_error: true
+          verbose: true
           token: ${{ secrets.CODECOV_TOKEN }}
       # The standard setup of Coveralls is just annoying for parallel builds, see, e.g.,
       # https://github.com/trixi-framework/Trixi.jl/issues/691
@@ -194,7 +200,7 @@ jobs:
           coverage = merge_coverage_counts(coverage)
           @show covered_lines, total_lines = get_summary(coverage)
           LCOV.writefile("./lcov.info", coverage)
-      - uses: coverallsapp/github-action@master
+      - uses: coverallsapp/github-action@v2
         with:
           github-token: ${{ secrets.GITHUB_TOKEN }}
           path-to-lcov: ./lcov.info

.gitignore

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

NEWS.md

@@ -9,6 +9,9 @@ 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 <[email protected]>", "Gregor Gassner <[email protected]>", "Hendrik Ranocha <[email protected]>", "Andrew R. Winters <[email protected]>", "Jesse Chan <[email protected]>"]
-version = "0.6.7-pre"
+version = "0.6.10-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"
@@ -44,6 +45,7 @@ TimerOutputs = "a759f4b9-e2f1-59dc-863e-4aeb61b1ea8f"
 Triangulate = "f7e6ffb2-c36d-4f8f-a77e-16e897189344"
 TriplotBase = "981d1d27-644d-49a2-9326-4793e63143c3"
 TriplotRecipes = "808ab39a-a642-4abf-81ff-4cb34ebbffa3"
+TrixiBase = "9a0f1c46-06d5-4909-a5a3-ce25d3fa3284"
 
 [weakdeps]
 Makie = "ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a"
@@ -57,6 +59,7 @@ 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"
@@ -66,7 +69,7 @@ LinearAlgebra = "1"
 LinearMaps = "2.7, 3.0"
 LoopVectorization = "0.12.118"
 MPI = "0.20"
-Makie = "0.19"
+Makie = "0.19, 0.20"
 MuladdMacro = "0.2.2"
 Octavian = "0.3.5"
 OffsetArrays = "1.3"
@@ -93,6 +96,7 @@ TimerOutputs = "0.5.7"
 Triangulate = "2.0"
 TriplotBase = "0.1"
 TriplotRecipes = "0.1"
+TrixiBase = "0.1.1"
 julia = "1.8"
 
 [extras]

benchmark/benchmarks.jl

@@ -55,5 +55,5 @@ let
   SUITE["latency"]["euler_2d"] = @benchmarkable run(
     `$(Base.julia_cmd()) -e 'using Trixi; trixi_include(joinpath(examples_dir(), "tree_2d_dgsem", "elixir_euler_kelvin_helmholtz_instability.jl"), tspan=(0.0, 1.0e-10), save_restart=TrivialCallback(), save_solution=TrivialCallback())'`) seconds=60
   SUITE["latency"]["mhd_2d"] = @benchmarkable run(
-    `$(Base.julia_cmd()) -e 'using Trixi; trixi_include(joinpath(examples_dir(), "tree_2d_dgsem", "elixir_mhd_blast_wave.jl"), tspan=(0.0, 1.0e-10), save_restart=TrivialCallback(), save_solution=TrivialCallback())'`) seconds=60
+    `$(Base.julia_cmd()) -e 'using Trixi; trixi_include(joinpath(examples_dir(), "tree_2d_dgsem", "elixir_mhd_blast_wave.jl"), tspan=(0.0, 1.0e-10), save_solution=TrivialCallback())'`) seconds=60
 end

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/Project.toml

@@ -10,9 +10,10 @@ OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 Trixi2Vtk = "bc1476a1-1ca6-4cc3-950b-c312b255ff95"
+TrixiBase = "9a0f1c46-06d5-4909-a5a3-ce25d3fa3284"
 
 [compat]
-CairoMakie = "0.6, 0.7, 0.8, 0.9, 0.10"
+CairoMakie = "0.6, 0.7, 0.8, 0.9, 0.10, 0.11"
 Documenter = "1"
 ForwardDiff = "0.10"
 HOHQMesh = "0.1, 0.2"
@@ -23,3 +24,4 @@ OrdinaryDiffEq = "6.49.1"
 Plots = "1.9"
 Test = "1"
 Trixi2Vtk = "0.3"
+TrixiBase = "0.1.1"

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.