Merge branch 'main' into t8codemesh-FV-1order

.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

@@ -129,7 +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

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 = "0.6.9-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/src/files/index.jl

@@ -108,20 +108,26 @@
 # software in the Trixi.jl ecosystem, and then run a simulation using Trixi.jl on said mesh.
 # In the end, the tutorial briefly explains how to simulate an example using AMR via `P4estMesh`.
 
-# ### [15 Explicit time stepping](@ref time_stepping)
+# ### [15 P4est mesh from gmsh](@ref p4est_from_gmsh)
+#-
+# This tutorial describes how to obtain a [`P4estMesh`](@ref) from an existing mesh generated
+# by [`gmsh`](https://gmsh.info/) or any other meshing software that can export to the Abaqus
+# input `.inp` format. The tutorial demonstrates how edges/faces can be associated with boundary conditions based on the physical nodesets.
+
+# ### [16 Explicit time stepping](@ref time_stepping)
 #-
 # This tutorial is about time integration using [OrdinaryDiffEq.jl](https://github.com/SciML/OrdinaryDiffEq.jl).
 # It explains how to use their algorithms and presents two types of time step choices - with error-based
 # and CFL-based adaptive step size control.
 
-# ### [16 Differentiable programming](@ref differentiable_programming)
+# ### [17 Differentiable programming](@ref differentiable_programming)
 #-
 # This part deals with some basic differentiable programming topics. For example, a Jacobian, its
 # eigenvalues and a curve of total energy (through the simulation) are calculated and plotted for
 # a few semidiscretizations. Moreover, we calculate an example for propagating errors with Measurement.jl
 # at the end.
 
-# ### [17 Custom semidiscretization](@ref custom_semidiscretization)
+# ### [18 Custom semidiscretization](@ref custom_semidiscretization)
 #-
 # This tutorial describes the [semidiscretiations](@ref overview-semidiscretizations) of Trixi.jl
 # and explains how to extend them for custom tasks.

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.