Merge branch 'main' into hr/ci_julia110

.github/review-checklist.md

@@ -0,0 +1,38 @@
+### Review checklist
+
+This checklist is meant to assist creators of PRs (to let them know what reviewers will typically look for) and reviewers (to guide them in a structured review process). Items do not need to be checked explicitly for a PR to be eligible for merging.
+
+#### Purpose and scope
+- [ ] The PR has a single goal that is clear from the PR title and/or description.
+- [ ] All code changes represent a single set of modifications that logically belong together.
+- [ ] No more than 500 lines of code are changed or there is no obvious way to split the PR into multiple PRs.
+
+#### Code quality
+- [ ] The code can be understood easily.
+- [ ] Newly introduced names for variables etc. are self-descriptive and consistent with existing naming conventions.
+- [ ] There are no redundancies that can be removed by simple modularization/refactoring.
+- [ ] There are no leftover debug statements or commented code sections.
+- [ ] The code adheres to our [conventions](https://trixi-framework.github.io/Trixi.jl/stable/conventions/) and [style guide](https://trixi-framework.github.io/Trixi.jl/stable/styleguide/), and to the [Julia guidelines](https://docs.julialang.org/en/v1/manual/style-guide/).
+
+#### Documentation
+- [ ] New functions and types are documented with a docstring or top-level comment.
+- [ ] Relevant publications are referenced in docstrings (see [example](https://github.com/trixi-framework/Trixi.jl/blob/7f83a1a938eecd9b841efe215a6e482e67cfdcc1/src/equations/compressible_euler_2d.jl#L601-L615) for formatting).
+- [ ] Inline comments are used to document longer or unusual code sections.
+- [ ] Comments describe intent ("why?") and not just functionality ("what?").
+- [ ] If the PR introduces a significant change or new feature, it is documented in `NEWS.md`.
+
+#### Testing
+- [ ] The PR passes all tests.
+- [ ] New or modified lines of code are covered by tests.
+- [ ] New or modified tests run in less then 10 seconds.
+
+#### Performance
+- [ ] There are no type instabilities or memory allocations in performance-critical parts.
+- [ ] If the PR intent is to improve performance, before/after [time measurements](https://trixi-framework.github.io/Trixi.jl/stable/performance/#Manual-benchmarking) are posted in the PR.
+
+#### Verification
+- [ ] The correctness of the code was verified using appropriate tests.
+- [ ] If new equations/methods are added, a convergence test has been run and the results
+  are posted in the PR.
+
+*Created with :heart: by the Trixi.jl community.*

.github/workflows/ReviewChecklist.yml

@@ -0,0 +1,20 @@
+name: Add review checklist
+
+on:
+  pull_request_target:
+    types: [opened]
+
+permissions:
+  pull-requests: write
+
+jobs:
+  add-review-checklist:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v3
+      - name: Add review checklist
+        uses: trixi-framework/add-pr-review-checklist@v1
+        with:
+          file: '.github/review-checklist.md'
+          no-checklist-keyword: '[no checklist]'

.github/workflows/SpellCheck.yml

@@ -10,4 +10,4 @@ jobs:
       - name: Checkout Actions Repository
         uses: actions/checkout@v3
       - name: Check spelling
-        uses: crate-ci/[email protected].5
+        uses: crate-ci/[email protected].9

.zenodo.json

@@ -15,7 +15,7 @@
             "orcid": "0000-0002-1752-1158"
         },
         {
-            "affiliation": "Applied Mathematics, University of Hamburg, Germany",
+            "affiliation": "Numerical Mathematics, Johannes Gutenberg University Mainz, Germany",
             "name": "Ranocha, Hendrik",
             "orcid": "0000-0002-3456-2277"
         },

AUTHORS.md

@@ -12,7 +12,7 @@ provided substantial additions or modifications. Together, these two groups form
 * [Gregor Gassner](https://www.mi.uni-koeln.de/NumSim/gregor-gassner),
   University of Cologne, Germany
 * [Hendrik Ranocha](https://ranocha.de),
-  University of Hamburg, Germany
+  Johannes Gutenberg University Mainz, Germany
 * [Andrew Winters](https://liu.se/en/employee/andwi94),
   Linköping University, Sweden
 * [Jesse Chan](https://jlchan.github.io),

NEWS.md

@@ -12,6 +12,7 @@ for human readability.
 - Non-uniform `TreeMesh` available for hyperbolic-parabolic equations.
 - Capability to set truly discontinuous initial conditions in 1D.
 - Wetting and drying feature and examples for 1D and 2D shallow water equations
+- Subcell positivity limiting support for conservative variables in 2D for `TreeMesh`
 
 #### Changed
 

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 = "0.5.39-pre"
+version = "0.5.42-pre"
 
 [deps]
 CodeTracking = "da1fd8a2-8d9e-5ec2-8556-3022fb5608a2"
@@ -56,7 +56,7 @@ DiffEqCallbacks = "2.25"
 EllipsisNotation = "1.0"
 FillArrays = "0.13.2, 1"
 ForwardDiff = "0.10.18"
-HDF5 = "0.14, 0.15, 0.16"
+HDF5 = "0.14, 0.15, 0.16, 0.17"
 IfElse = "0.1"
 LinearMaps = "2.7, 3.0"
 LoopVectorization = "0.12.118"

README.md

@@ -247,7 +247,7 @@ Schlottke-Lakemper](https://lakemper.eu)
 (RWTH Aachen University/High-Performance Computing Center Stuttgart (HLRS), Germany) and
 [Gregor Gassner](https://www.mi.uni-koeln.de/NumSim/gregor-gassner)
 (University of Cologne, Germany). Together with [Hendrik Ranocha](https://ranocha.de)
-(University of Hamburg, Germany), [Andrew Winters](https://liu.se/en/employee/andwi94)
+(Johannes Gutenberg University Mainz, Germany), [Andrew Winters](https://liu.se/en/employee/andwi94)
 (Linköping University, Sweden), and [Jesse Chan](https://jlchan.github.io) (Rice University, US),
 they are the principal developers of Trixi.jl.
 The full list of contributors can be found in [AUTHORS.md](AUTHORS.md).

docs/literate/src/files/differentiable_programming.jl

@@ -128,7 +128,7 @@ condition_number = cond(V)
 # you can compute the gradient of an entropy-dissipative semidiscretization with respect to the
 # ideal gas constant of the compressible Euler equations as described in the following. This example
 # is also available as the elixir
-# [examples/special\_elixirs/elixir\_euler\_ad.jl](https://github.com/trixi-framework/Trixi.jl/blob/main/examples/special_elixirs/elixir_euler_ad.jl)
+# [`examples/special_elixirs/elixir_euler_ad.jl`](https://github.com/trixi-framework/Trixi.jl/blob/main/examples/special_elixirs/elixir_euler_ad.jl)
 
 # First, we create a semidiscretization of the compressible Euler equations.
 

docs/literate/src/files/index.jl

@@ -116,7 +116,7 @@
 
 # ## Examples in Trixi.jl
 # Trixi.jl already contains several more coding examples, the so-called `elixirs`. You can find them
-# in the folder [`examples`](https://github.com/trixi-framework/Trixi.jl/blob/main/examples/).
+# in the folder [`examples/`](https://github.com/trixi-framework/Trixi.jl/blob/main/examples/).
 # They are structured by the underlying mesh type and the respective number of spatial dimensions.
 # The name of an elixir is composed of the underlying system of conservation equations (for instance
 # `advection` or `euler`) and other special characteristics like the initial condition

docs/src/callbacks.md

@@ -15,7 +15,7 @@ control, adaptive mesh refinement, I/O, and more.
 
 ### CFL-based time step control
 Time step control can be performed with a [`StepsizeCallback`](@ref). An example making use
-of this can be found at [examples/tree_2d_dgsem/elixir\_advection\_basic.jl](https://github.com/trixi-framework/Trixi.jl/blob/main/examples/tree_2d_dgsem/elixir_advection_basic.jl)
+of this can be found at [`examples/tree_2d_dgsem/elixir_advection_basic.jl`](https://github.com/trixi-framework/Trixi.jl/blob/main/examples/tree_2d_dgsem/elixir_advection_basic.jl)
 
 ### Adaptive mesh refinement
 Trixi.jl uses a hierarchical Cartesian mesh which can be locally refined in a solution-adaptive way.
@@ -24,12 +24,12 @@ passing an [`AMRCallback`](@ref) to the ODE solver. The `AMRCallback` requires a
 [`ControllerThreeLevel`](@ref) or [`ControllerThreeLevelCombined`](@ref) to tell the AMR
 algorithm which cells to refine/coarsen.
 
-An example elixir using AMR can be found at [examples/tree_2d_dgsem/elixir\_advection\_amr.jl](https://github.com/trixi-framework/Trixi.jl/blob/main/examples/tree_2d_dgsem/elixir_advection_amr.jl).
+An example elixir using AMR can be found at [`examples/tree_2d_dgsem/elixir_advection_amr.jl`](https://github.com/trixi-framework/Trixi.jl/blob/main/examples/tree_2d_dgsem/elixir_advection_amr.jl).
 
 ### Analyzing the numerical solution
 The [`AnalysisCallback`](@ref) can be used to analyze the numerical solution, e.g. calculate
 errors or user-specified integrals, and print the results to the screen. The results can also be
-saved in a file. An example can be found at [examples/tree_2d_dgsem/elixir\_euler\_vortex.jl](https://github.com/trixi-framework/Trixi.jl/blob/main/examples/tree_2d_dgsem/elixir_euler_vortex.jl).
+saved in a file. An example can be found at [`examples/tree_2d_dgsem/elixir_euler_vortex.jl`](https://github.com/trixi-framework/Trixi.jl/blob/main/examples/tree_2d_dgsem/elixir_euler_vortex.jl).
 In [Performance metrics of the `AnalysisCallback`](@ref) you can find a detailed
 description of the different performance metrics the `AnalysisCallback` computes.
 
@@ -38,15 +38,15 @@ description of the different performance metrics the `AnalysisCallback` computes
 #### Solution and restart files
 To save the solution in regular intervals you can use a [`SaveSolutionCallback`](@ref). It is also
 possible to create restart files using the [`SaveRestartCallback`](@ref). An example making use
-of these can be found at [examples/tree_2d_dgsem/elixir\_advection\_extended.jl](https://github.com/trixi-framework/Trixi.jl/blob/main/examples/tree_2d_dgsem/elixir_advection_extended.jl).
+of these can be found at [`examples/tree_2d_dgsem/elixir_advection_extended.jl`](https://github.com/trixi-framework/Trixi.jl/blob/main/examples/tree_2d_dgsem/elixir_advection_extended.jl).
 An example showing how to restart a simulation from a restart file can be found at
-[examples/tree_2d_dgsem/elixir\_advection\_restart.jl](https://github.com/trixi-framework/Trixi.jl/blob/main/examples/tree_2d_dgsem/elixir_advection_restart.jl).
+[`examples/tree_2d_dgsem/elixir_advection_restart.jl`](https://github.com/trixi-framework/Trixi.jl/blob/main/examples/tree_2d_dgsem/elixir_advection_restart.jl).
 
 #### Time series
 Sometimes it is useful to record the evaluations of state variables over time at
 a given set of points. This can be achieved by the [`TimeSeriesCallback`](@ref), which is used,
 e.g., in
-[examples/tree_2d_dgsem/elixir\_acoustics\_gaussian\_source.jl](https://github.com/trixi-framework/Trixi.jl/blob/main/examples/tree_2d_dgsem/elixir_acoustics_gaussian_source.jl).
+[`examples/tree_2d_dgsem/elixir_acoustics_gaussian_source.jl`](https://github.com/trixi-framework/Trixi.jl/blob/main/examples/tree_2d_dgsem/elixir_acoustics_gaussian_source.jl).
 The `TimeSeriesCallback` constructor expects a semidiscretization and a list of points at
 which the solution should be recorded in regular time step intervals. After the
 last time step, the entire record is stored in an HDF5 file.
@@ -113,12 +113,12 @@ will yield the following plot:
 Some callbacks provided by Trixi.jl implement specific features for certain equations:
 * The [`LBMCollisionCallback`](@ref) implements the Lattice-Boltzmann method (LBM) collision
   operator and should only be used when solving the Lattice-Boltzmann equations. See e.g.
-  [examples/tree_2d_dgsem/elixir\_lbm\_constant.jl](https://github.com/trixi-framework/Trixi.jl/blob/main/examples/tree_2d_dgsem/elixir_lbm_constant.jl)
+  [`examples/tree_2d_dgsem/elixir_lbm_constant.jl`](https://github.com/trixi-framework/Trixi.jl/blob/main/examples/tree_2d_dgsem/elixir_lbm_constant.jl)
 * The [`SteadyStateCallback`](@ref) terminates the time integration when the residual steady state
   falls below a certain threshold. This checks the convergence of the potential ``\phi`` for
-  hyperbolic diffusion. See e.g. [examples/tree_2d_dgsem/elixir\_hypdiff\_nonperiodic.jl](https://github.com/trixi-framework/Trixi.jl/blob/main/examples/tree_2d_dgsem/elixir_hypdiff_nonperiodic.jl).
+  hyperbolic diffusion. See e.g. [`examples/tree_2d_dgsem/elixir_hypdiff_nonperiodic.jl`](https://github.com/trixi-framework/Trixi.jl/blob/main/examples/tree_2d_dgsem/elixir_hypdiff_nonperiodic.jl).
 * The [`GlmSpeedCallback`](@ref) updates the divergence cleaning wave speed `c_h` for the ideal
-  GLM-MHD equations. See e.g. [examples/tree_2d_dgsem/elixir\_mhd\_alfven\_wave.jl](https://github.com/trixi-framework/Trixi.jl/blob/main/examples/tree_2d_dgsem/elixir_mhd_alfven_wave.jl).
+  GLM-MHD equations. See e.g. [`examples/tree_2d_dgsem/elixir_mhd_alfven_wave.jl`](https://github.com/trixi-framework/Trixi.jl/blob/main/examples/tree_2d_dgsem/elixir_mhd_alfven_wave.jl).
 
 ## Usage of step callbacks
 Step callbacks are passed to the `solve` method from the ODE solver via the keyword argument
@@ -152,7 +152,7 @@ more callbacks, you need to turn them into a `CallbackSet` first by calling
 ## Stage callbacks
 [`PositivityPreservingLimiterZhangShu`](@ref) is a positivity-preserving limiter, used to enforce
 physical constraints. An example elixir using this feature can be found at
-[examples/tree_2d_dgsem/elixir\_euler\_positivity.jl](https://github.com/trixi-framework/Trixi.jl/blob/main/examples/tree_2d_dgsem/elixir_euler_positivity.jl).
+[`examples/tree_2d_dgsem/elixir_euler_positivity.jl`](https://github.com/trixi-framework/Trixi.jl/blob/main/examples/tree_2d_dgsem/elixir_euler_positivity.jl).
 
 ## Implementing new callbacks
 Since Trixi.jl is compatible with [OrdinaryDiffEq.jl](https://github.com/SciML/OrdinaryDiffEq.jl),
@@ -162,4 +162,4 @@ Step callbacks are just called [callbacks](https://diffeq.sciml.ai/latest/featur
 Stage callbacks are called [`stage_limiter!`](https://diffeq.sciml.ai/latest/solvers/ode_solve/#Explicit-Strong-Stability-Preserving-Runge-Kutta-Methods-for-Hyperbolic-PDEs-(Conservation-Laws)).
 
 An example elixir showing how to implement a new simple stage callback and a new simple step
-callback can be found at [examples/tree_2d_dgsem/elixir\_advection\_callbacks.jl](https://github.com/trixi-framework/Trixi.jl/blob/main/examples/tree_2d_dgsem/elixir_advection_callbacks.jl).
+callback can be found at [`examples/tree_2d_dgsem/elixir_advection_callbacks.jl`](https://github.com/trixi-framework/Trixi.jl/blob/main/examples/tree_2d_dgsem/elixir_advection_callbacks.jl).

docs/src/index.md

@@ -324,7 +324,7 @@ Schlottke-Lakemper](https://lakemper.eu)
 (RWTH Aachen University/High-Performance Computing Center Stuttgart (HLRS), Germany) and
 [Gregor Gassner](https://www.mi.uni-koeln.de/NumSim/gregor-gassner)
 (University of Cologne, Germany). Together with [Hendrik Ranocha](https://ranocha.de)
-(University of Hamburg, Germany) and [Andrew Winters](https://liu.se/en/employee/andwi94)
+(Johannes Gutenberg University Mainz, Germany) and [Andrew Winters](https://liu.se/en/employee/andwi94)
 (Linköping University, Sweden), and [Jesse Chan](https://jlchan.github.io) (Rice University, US),
 they are the principal developers of Trixi.jl.
 The full list of contributors can be found under [Authors](@ref).

docs/src/meshes/dgmulti_mesh.md

@@ -81,16 +81,20 @@ type, but will be more efficient at high orders of approximation.
 ## Trixi.jl elixirs on simplicial and tensor product element meshes
 
 Example elixirs with triangular, quadrilateral, and tetrahedral meshes can be found in
-the `examples/dgmulti_2d` and `examples/dgmulti_3d` folders. Some key elixirs to look at:
+the [`examples/dgmulti_2d/`](https://github.com/trixi-framework/Trixi.jl/blob/main/examples/dgmulti_2d/)
+and [`examples/dgmulti_3d/`](https://github.com/trixi-framework/Trixi.jl/blob/main/examples/dgmulti_3d/)
+folders. Some key elixirs to look at:
 
-* `examples/dgmulti_2d/elixir_euler_weakform.jl`: basic weak form DG discretization on a uniform triangular mesh.
+* [`examples/dgmulti_2d/elixir_euler_weakform.jl`](https://github.com/trixi-framework/Trixi.jl/blob/main/examples/dgmulti_2d/elixir_euler_weakform.jl):
+  basic weak form DG discretization on a uniform triangular mesh.
   Changing `element_type = Quad()` or `approximation_type = SBP()` will switch to a quadrilateral mesh
   or an SBP-type discretization. Changing `surface_integral = SurfaceIntegralWeakForm(flux_ec)` and
   `volume_integral = VolumeIntegralFluxDifferencing(flux_ec)` for some entropy conservative flux
   (e.g., [`flux_chandrashekar`](@ref) or [`flux_ranocha`](@ref)) will switch to an entropy conservative formulation.
-* `examples/dgmulti_2d/elixir_euler_triangulate_pkg_mesh.jl`: uses an unstructured mesh generated by
-  [Triangulate.jl](https://github.com/JuliaGeometry/Triangulate.jl).
-* `examples/dgmulti_3d/elixir_euler_weakform.jl`: basic weak form DG discretization on a uniform tetrahedral mesh.
+* [`examples/dgmulti_2d/elixir_euler_triangulate_pkg_mesh.jl`](https://github.com/trixi-framework/Trixi.jl/blob/main/examples/dgmulti_2d/elixir_euler_triangulate_pkg_mesh.jl):
+  uses an unstructured mesh generated by [Triangulate.jl](https://github.com/JuliaGeometry/Triangulate.jl).
+* [`examples/dgmulti_3d/elixir_euler_weakform.jl`](https://github.com/trixi-framework/Trixi.jl/blob/main/examples/dgmulti_3d/elixir_euler_weakform.jl):
+  ´basic weak form DG discretization on a uniform tetrahedral mesh.
   Changing `element_type = Hex()` will switch to a hexahedral mesh. Changing
   `surface_integral = SurfaceIntegralWeakForm(flux_ec)` and
   `volume_integral = VolumeIntegralFluxDifferencing(flux_ec)` for some entropy conservative flux

docs/src/overview.md

@@ -5,7 +5,7 @@ conservation laws. Thus, it is not a monolithic PDE solver that is configured at
 via parameter files, as it is often found in classical numerical simulation codes.
 Instead, each simulation is configured by pure Julia code. Many examples of such
 simulation setups, called *elixirs* in Trixi.jl, are provided in the
-[examples](https://github.com/trixi-framework/Trixi.jl/blob/main/examples)
+[`examples/`](https://github.com/trixi-framework/Trixi.jl/blob/main/examples)
 folder.
 
 Trixi.jl uses the method of lines, i.e., the full space-time discretization is separated into two steps;
@@ -77,7 +77,7 @@ Further information can be found in the
 ## Next steps
 
 We explicitly encourage people interested in Trixi.jl to have a look at the
-[examples](https://github.com/trixi-framework/Trixi.jl/blob/main/examples)
+[`examples/`](https://github.com/trixi-framework/Trixi.jl/blob/main/examples)
 bundled with Trixi.jl to get an impression of what is possible and the general
 look and feel of Trixi.jl.
 Before doing that, it is usually good to get an idea of