Merge branch 'main' into multi_ion_mhd

.github/workflows/SpellCheck.yml

@@ -0,0 +1,13 @@
+name: Spell Check
+
+on: [pull_request, workflow_dispatch]
+
+jobs:
+  typos-check:
+    name: Spell Check with Typos
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout Actions Repository
+        uses: actions/checkout@v3
+      - name: Check spelling
+        uses: crate-ci/[email protected]

.github/workflows/ci.yml

@@ -73,7 +73,8 @@ jobs:
           - paper_self_gravitating_gas_dynamics
           - misc_part1
           - misc_part2
-          - misc_part3
+          - performance_specializations_part1
+          - performance_specializations_part2
           - mpi
           - threaded
         include:

.gitignore

@@ -26,3 +26,6 @@ coverage_report/
 .vscode/
 
 .DS_Store
+
+run
+run/*

.typos.toml

@@ -0,0 +1,4 @@
+[default.extend-words]
+rcall = "rcall"
+claus = "claus"
+dum = "dum"

AUTHORS.md

@@ -1,14 +1,14 @@
 # Authors
 
-Trixi's development is coordinated by a group of *principal developers*,
+Trixi.jl's development is coordinated by a group of *principal developers*,
 who are also its main contributors and who can be contacted in case of
-questions about Trixi. In addition, there are *contributors* who have
+questions about Trixi.jl. In addition, there are *contributors* who have
 provided substantial additions or modifications. Together, these two groups form
-"The Trixi Authors" as mentioned in the [LICENSE.md](LICENSE.md) file.
+"The Trixi.jl Authors" as mentioned in the [LICENSE.md](LICENSE.md) file.
 
 ## Principal Developers
 * [Michael Schlottke-Lakemper](https://lakemper.eu),
-  RWTH Aachen University, Germany
+  RWTH Aachen University/High-Performance Computing Center Stuttgart (HLRS), Germany
 * [Gregor Gassner](https://www.mi.uni-koeln.de/NumSim/gregor-gassner),
   University of Cologne, Germany
 * [Hendrik Ranocha](https://ranocha.de),
@@ -19,20 +19,22 @@ provided substantial additions or modifications. Together, these two groups form
   Rice University, US
 
 ## Contributors
-The following people contributed major additions or modifications to Trixi and
+The following people contributed major additions or modifications to Trixi.jl and
 are listed in alphabetical order:
 
 * Maximilian D. Bertrand
 * Benjamin Bolm
 * Jesse Chan
 * Lars Christmann
 * Christof Czernik
+* Patrick Ersing
 * Erik Faulhaber
 * Gregor Gassner
 * Lucas Gemein
 * Sven Goldberg
 * Joshua Lampert
 * Julia Odenthal
+* Sigrun Ortleb
 * Hendrik Ranocha
 * Andrés M. Rueda-Ramírez
 * Felipe Santillan

CONTRIBUTING.md

@@ -1,12 +1,12 @@
 # Contributing
 
-Trixi is an open-source project and we are very happy to accept contributions
+Trixi.jl is an open-source project and we are very happy to accept contributions
 from the community. Please feel free to open issues or submit patches (preferably
-as merge requests) any time. For planned larger contributions, it is often
+as pull requests) any time. For planned larger contributions, it is often
 beneficial to get in contact with one of the principal developers first (see
 [AUTHORS.md](AUTHORS.md)).
 
-Trixi and its contributions are licensed under the MIT license (see
+Trixi.jl and its contributions are licensed under the MIT license (see
 [LICENSE.md](LICENSE.md)). As a contributor, you certify that all your
 contributions are in conformance with the *Developer Certificate of Origin
 (Version 1.1)*, which is reproduced below.

LICENSE.md

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2020-present The Trixi Authors (see [AUTHORS.md](AUTHORS.md))
+Copyright (c) 2020-present The Trixi.jl Authors (see [AUTHORS.md](AUTHORS.md))
 
 Permission is hereby granted, free of charge, to any person obtaining a copy  
 of this software and associated documentation files (the "Software"), to deal  

NEWS.md

@@ -19,6 +19,9 @@ for human readability.
 - The macro `@unpack` (re-exported originally from UnPack.jl) is deprecated and
   will be removed. Consider using Julia's standard destructuring syntax
   `(; a, b) = stuff` instead of `@unpack a, b = stuff`.
+- The constructor `DGMultiMesh(dg; cells_per_dimension, kwargs...)` is deprecated
+  and will be removed. The new constructor `DGMultiMesh(dg, cells_per_dimension; kwargs...)`
+  does not have `cells_per_dimesion` as a keyword argument.
 
 #### Removed
 
@@ -164,7 +167,7 @@ for human readability.
   `flux_lax_friedrichs(u_ll, u_rr, orientation, equations::LatticeBoltzmannEquations3D)`
   were actually using the logic of `flux_godunov`. Thus, they were renamed accordingly
   in [#493](https://github.com/trixi-framework/Trixi.jl/pull/493). This is considered a bugfix
-  (released in Trixi v0.3.22).
+  (released in Trixi.jl v0.3.22).
 - The required Julia version is updated to v1.6.
 
 #### Deprecated

Project.toml

@@ -1,11 +1,12 @@
 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 = "0.5.15-pre"
+version = "0.5.23-pre"
 
 [deps]
 CodeTracking = "da1fd8a2-8d9e-5ec2-8556-3022fb5608a2"
 ConstructionBase = "187b0558-2788-49d3-abe0-74a17ed4e7c9"
+DiffEqCallbacks = "459566f4-90b8-5000-8ac3-15dfb0a30def"
 EllipsisNotation = "da5c29d0-fa7d-589e-88eb-ea29b0a81949"
 FillArrays = "1a297f60-69ca-5386-bcde-b61e274b549b"
 ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
@@ -20,6 +21,7 @@ Octavian = "6fd5a793-0b7e-452c-907f-f8bfe9c57db4"
 OffsetArrays = "6fe1bfb0-de20-5000-8ca7-80f57d26f881"
 P4est = "7d669430-f675-4ae7-b43e-fab78ec5a902"
 Polyester = "f517fe37-dbe3-4b94-8317-1923a5111588"
+PrecompileTools = "aea7be01-6a6a-4083-8856-8a6e6704d82a"
 Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
 RecipesBase = "3cdcf5f2-1ef4-517c-9805-6587b60abb01"
 Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
@@ -30,6 +32,7 @@ SimpleUnPack = "ce78b400-467f-4804-87d8-8f486da07d0a"
 SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 StartUpDG = "472ebc20-7c99-4d4b-9470-8fde4e9faa0f"
 Static = "aedffcd0-7271-4cad-89d0-dc628f76c6d3"
+StaticArrayInterface = "0d7ed370-da01-4f52-bd93-41d350b8b718"
 StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
 StrideArrays = "d1fa6d79-ef01-42a6-86c9-f7c551f8593b"
 StructArrays = "09ab397b-f2b6-538f-b94a-2f83cf4a842a"
@@ -42,8 +45,9 @@ TriplotRecipes = "808ab39a-a642-4abf-81ff-4cb34ebbffa3"
 [compat]
 CodeTracking = "1.0.5"
 ConstructionBase = "1.3"
+DiffEqCallbacks = "2.25"
 EllipsisNotation = "1.0"
-FillArrays = "0.13.2"
+FillArrays = "0.13.2, 1"
 ForwardDiff = "0.10.18"
 HDF5 = "0.14, 0.15, 0.16"
 IfElse = "0.1"
@@ -55,14 +59,16 @@ Octavian = "0.3.5"
 OffsetArrays = "1.3"
 P4est = "0.4"
 Polyester = "0.3.4, 0.5, 0.6, 0.7"
+PrecompileTools = "1.1"
 RecipesBase = "1.1"
 Reexport = "1.0"
 Requires = "1.1"
 SciMLBase = "1.90"
 Setfield = "0.8, 1"
 SimpleUnPack = "1.1"
-StartUpDG = "0.15"
+StartUpDG = "0.16"
 Static = "0.3, 0.4, 0.5, 0.6, 0.7, 0.8"
+StaticArrayInterface = "1.4"
 StaticArrays = "1"
 StrideArrays = "0.1.18"
 StructArrays = "0.6"

README.md

@@ -20,7 +20,7 @@
 **Trixi.jl** is a numerical simulation framework for hyperbolic conservation
 laws written in [Julia](https://julialang.org). A key objective for the
 framework is to be useful to both scientists and students. Therefore, next to
-having an extensible design with a fast implementation, Trixi is
+having an extensible design with a fast implementation, Trixi.jl is
 focused on being easy to use for new or inexperienced users, including the
 installation and postprocessing procedures. Its features include:
 
@@ -35,7 +35,7 @@ installation and postprocessing procedures. Its features include:
   * Kinetic energy-preserving and entropy-stable methods based on flux differencing
   * Entropy-stable shock capturing
   * Positivity-preserving limiting
-  * Finite difference summation by parts (SBP) methods
+  * [Finite difference summation by parts (SBP) methods](https://github.com/ranocha/SummationByPartsOperators.jl)
 * Compatible with the [SciML ecosystem for ordinary differential equations](https://diffeq.sciml.ai/latest/)
   * [Explicit low-storage Runge-Kutta time integration](https://diffeq.sciml.ai/latest/solvers/ode_solve/#Low-Storage-Methods)
   * [Strong stability preserving methods](https://diffeq.sciml.ai/latest/solvers/ode_solve/#Explicit-Strong-Stability-Preserving-Runge-Kutta-Methods-for-Hyperbolic-PDEs-(Conservation-Laws))
@@ -63,61 +63,66 @@ installation and postprocessing procedures. Its features include:
 
 ## Installation
 If you have not yet installed Julia, please [follow the instructions for your
-operating system](https://julialang.org/downloads/platform/). Trixi works
+operating system](https://julialang.org/downloads/platform/). Trixi.jl works
 with Julia v1.8.
 
 ### For users
-Trixi and its related tools are registered Julia packages. Hence, you
-can install Trixi, the visualization tool
+Trixi.jl and its related tools are registered Julia packages. Hence, you
+can install Trixi.jl, the visualization tool
 [Trixi2Vtk](https://github.com/trixi-framework/Trixi2Vtk.jl),
 [OrdinaryDiffEq.jl](https://github.com/SciML/OrdinaryDiffEq.jl), and
 [Plots.jl](https://github.com/JuliaPlots/Plots.jl)
 by executing the following commands in the Julia REPL:
 ```julia
-julia> import Pkg
+julia> using Pkg
 
 julia> Pkg.add(["Trixi", "Trixi2Vtk", "OrdinaryDiffEq", "Plots"])
 ```
 You can copy and paste all commands to the REPL *including* the leading
 `julia>` prompts - they will automatically be stripped away by Julia.
 The package [OrdinaryDiffEq.jl](https://github.com/SciML/OrdinaryDiffEq.jl)
-provides time integration schemes used by Trixi, while
+provides time integration schemes used by Trixi.jl, while
 [Plots.jl](https://github.com/JuliaPlots/Plots.jl) can be used to directly
-visualize Trixi's results from the REPL.
+visualize Trixi.jl's results from the REPL.
 
-*Note on package versions:* If some of the examples for how to use Trixi do not
-work, verify that you are using a recent Trixi release by comparing the
-installed Trixi version from
+*Note on package versions:* If some of the examples for how to use Trixi.jl do not
+work, verify that you are using a recent Trixi.jl release by comparing the
+installed Trixi.jl version from
 ```julia
-julia> import Pkg; Pkg.update("Trixi"); Pkg.status("Trixi")
+julia> using Pkg; Pkg.update("Trixi"); Pkg.status("Trixi")
 ```
 to the [latest release](https://github.com/trixi-framework/Trixi.jl/releases/latest).
 If the installed version does not match the current release, please check the
 *Troubleshooting* section in the [documentation](#documentation).
 
-The commands above can also be used to update Trixi. A brief list of notable
-changes to Trixi is available in [`NEWS.md`](NEWS.md).
+The commands above can also be used to update Trixi.jl. A brief list of notable
+changes to Trixi.jl is available in [`NEWS.md`](NEWS.md).
 
 ### For developers
-If you plan on editing Trixi itself, you can download Trixi locally and run it from
-within the cloned directory:
+If you plan on editing Trixi.jl itself, you can download Trixi.jl locally and use the
+code from the cloned directory:
 ```bash
 git clone [email protected]:trixi-framework/Trixi.jl.git
 cd Trixi.jl
-julia --project=@. -e 'import Pkg; Pkg.instantiate()' # Install Trixi's dependencies
-julia -e 'import Pkg; Pkg.add(["Trixi2Vtk", "Plots"])' # Install postprocessing tools
-julia -e 'import Pkg; Pkg.add("OrdinaryDiffEq")' # Install time integration schemes
+mkdir run
+cd run
+julia --project=. -e 'using Pkg; Pkg.develop(PackageSpec(path=".."))' # Install local Trixi.jl clone
+julia --project=. -e 'using Pkg; Pkg.add(["OrdinaryDiffEq", "Trixi2Vtk", "Plots"])' # Install additional packages
 ```
-If you installed Trixi this way, you always have to start Julia with the `--project`
-flag set to your local Trixi clone, e.g.,
+Note that the postprocessing tools Trixi2Vtk.jl and Plots.jl are optional and
+can be omitted.
+
+If you installed Trixi.jl this way, you always have to start Julia with the `--project`
+flag set to your `run` directory, e.g.,
 ```bash
-julia --project=@.
+julia --project=.
 ```
+if already inside the `run` directory.
 Further details can be found in the [documentation](#documentation).
 
 
 ## Usage
-In the Julia REPL, first load the package Trixi
+In the Julia REPL, first load the package Trixi.jl
 ```julia
 julia> using Trixi
 ```
@@ -140,10 +145,10 @@ This will open a new window with a 2D visualization of the final solution:
 </p>
 
 The method `trixi_include(...)` expects a single string argument with the path to a
-Trixi elixir, i.e., a text file containing Julia code necessary to set up and run a
-simulation. To quickly see Trixi in action, `default_example()`
+Trixi.jl elixir, i.e., a text file containing Julia code necessary to set up and run a
+simulation. To quickly see Trixi.jl in action, `default_example()`
 returns the path to an example elixir with a short, two-dimensional
-problem setup. A list of all example elixirs packaged with Trixi can be
+problem setup. A list of all example elixirs packaged with Trixi.jl can be
 obtained by running `get_examples()`. Alternatively, you can also browse the
 [`examples/`](examples/) subdirectory.
 If you want to modify one of the elixirs to set up your own simulation,
@@ -159,23 +164,23 @@ instance, in the example above the first execution of `trixi_include` takes abou
 
 ### Showcase of advanced features
 The presentation [From Mesh Generation to Adaptive Simulation: A Journey in Julia](https://youtu.be/_N4ozHr-t9E),
-originally given as part of JuliaCon 2022, outlines how to use Trixi for an adaptive simulation
+originally given as part of JuliaCon 2022, outlines how to use Trixi.jl for an adaptive simulation
 of the compressible Euler equations in two spatial dimensions on a complex domain. More details
 as well as code to run the simulation presented can be found at the
 [reproducibility repository](https://github.com/trixi-framework/talk-2022-juliacon_toolchain)
 for the presentation.
 
 ## Documentation
 Additional documentation is available that contains more information on how to
-modify/extend Trixi's implementation, how to visualize output files etc. It
+modify/extend Trixi.jl's implementation, how to visualize output files etc. It
 also includes a section on our preferred development workflow and some tips for
 using Git. The latest documentation can be accessed either
 [online](https://trixi-framework.github.io/Trixi.jl/stable) or under [`docs/src`](docs/src).
 
 
 ## Referencing
-If you use Trixi in your own research or write a paper using results obtained
-with the help of Trixi, please cite the following articles:
+If you use Trixi.jl in your own research or write a paper using results obtained
+with the help of Trixi.jl, please cite the following articles:
 ```bibtex
 @article{ranocha2022adaptive,
   title={Adaptive numerical simulations with {T}rixi.jl:
@@ -211,7 +216,7 @@ with the help of Trixi, please cite the following articles:
 }
 ```
 
-In addition, you can also refer to Trixi directly as
+In addition, you can also refer to Trixi.jl directly as
 ```bibtex
 @misc{schlottkelakemper2020trixi,
   title={{T}rixi.jl: {A}daptive high-order numerical simulations
@@ -227,19 +232,19 @@ In addition, you can also refer to Trixi directly as
 
 
 ## Authors
-Trixi was initiated by [Michael
+Trixi.jl was initiated by [Michael
 Schlottke-Lakemper](https://lakemper.eu)
-(RWTH Aachen University, Germany) and
+(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)
 (Linköping University, Sweden), and [Jesse Chan](https://jlchan.github.io) (Rice University, US),
-they are the principal developers of Trixi.
+they are the principal developers of Trixi.jl.
 The full list of contributors can be found in [AUTHORS.md](AUTHORS.md).
 
 
 ## License and contributing
-Trixi is licensed under the MIT license (see [LICENSE.md](LICENSE.md)). Since Trixi is
+Trixi.jl is licensed under the MIT license (see [LICENSE.md](LICENSE.md)). Since Trixi.jl is
 an open-source project, we are very happy to accept contributions from the
 community. Please refer to [CONTRIBUTING.md](CONTRIBUTING.md) for more details.
 Note that we strive to be a friendly, inclusive open-source community and ask all members
@@ -250,17 +255,31 @@ or [create an issue](https://github.com/trixi-framework/Trixi.jl/issues/new).
 
 
 ## Acknowledgments
+<p align="center">
+  <img align="middle" src="https://user-images.githubusercontent.com/3637659/233821022-84910be7-8649-4999-a0ff-22d5e20f0b90.jpg" width=auto/>
+</p>
+
 This project has benefited from funding by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation)
 under Germany's Excellence Strategy EXC 2044-390685587, Mathematics Münster:
 Dynamics-Geometry-Structure.
 
+This project has benefited from funding by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation)
+through the research unit FOR 5409 "Structure-Preserving Numerical Methods for Bulk- and
+Interface Coupling of Heterogeneous Models (SNuBIC)" (project number 463312734).
+
 This project has benefited from funding from the European Research Council through the
 ERC Starting Grant "An Exascale aware and Un-crashable Space-Time-Adaptive
 Discontinuous Spectral Element Solver for Non-Linear Conservation Laws" (Extreme),
 ERC grant agreement no. 714487.
 
-This project has benefited from funding from Vetenskapsrådet (VR, Swedish Research Council), Sweden grant
-agreement 2020-03642 VR.
+This project has benefited from funding from Vetenskapsrådet (VR, Swedish Research Council), Sweden
+through the VR Starting Grant "Shallow water flows including sediment transport and morphodynamics",
+VR grant agreement 2020-03642 VR.
 
 This project has benefited from funding from the United States National Science Foundation under awards
 DMS-1719818 and DMS-1943186.
+
+This project has benefited from funding from the German Federal Ministry of
+Education and Research through the project grant "Adaptive earth system modeling
+with significantly reduced computation time for exascale supercomputers
+(ADAPTEX)" (funding id: 16ME0668K).