Merge Taal into master

.codecov.yml

@@ -1,11 +1,16 @@
 # https://docs.codecov.io/docs/codecovyml-reference
 
-# We have 6 * 3 parallel jobs in ci.yml
+# We have
+#   6 * [number of basic OS] + 2 * [number of additional OS]
+# with
+# [number of basic OS] = 1 (Linux)
+# [number of additional OS] = 2 (Windows, MacOS)
+# parallel jobs in ci.yml
 codecov:
   notify:
-    after_n_builds: 18
+    after_n_builds: 10
 comment:
-  after_n_builds: 18
+  after_n_builds: 10
 
 coverage:
   range: 70..95

.github/workflows/CompatHelper.yml

@@ -13,4 +13,4 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           COMPATHELPER_PRIV: ${{ secrets.DOCUMENTER_KEY }}  # optional
-        run: julia -e 'using CompatHelper; CompatHelper.main(; subdirs = ["", "test", "docs"])'
+        run: julia -e 'using CompatHelper; CompatHelper.main(; subdirs=["", "docs", "examples", "test"])'

.github/workflows/ci.yml

@@ -4,13 +4,32 @@ on:
   push:
     branches:
       - master
-      - dev
+    paths-ignore:
+      - 'AUTHORS.md'
+      - 'CONTRIBUTING.md'
+      - 'LICENSE.md'
+      - 'README.md'
+      - '.zenodo.json'
+      - '.github/workflows/CompatHelper.yml'
+      - '.github/workflows/TagBot.yml'
+      - 'docs/**'
+      - 'utils/**'
   pull_request:
+    paths-ignore:
+      - 'AUTHORS.md'
+      - 'CONTRIBUTING.md'
+      - 'LICENSE.md'
+      - 'README.md'
+      - '.zenodo.json'
+      - '.github/workflows/CompatHelper.yml'
+      - '.github/workflows/TagBot.yml'
+      - 'docs/**'
+      - 'utils/**'
 
 jobs:
   test:
     if: "!contains(github.event.head_commit.message, 'skip ci')"
-    name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ matrix.trixi_test }} - ${{ github.event_name }}
+    name: ${{ matrix.trixi_test }} - ${{ matrix.os }} - Julia ${{ matrix.version }} - ${{ matrix.arch }} - ${{ github.event_name }}
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
@@ -20,8 +39,6 @@ jobs:
           # - 'nightly'
         os:
           - ubuntu-latest
-          - macOS-latest
-          - windows-latest
         arch:
           - x64
         trixi_test:
@@ -31,6 +48,23 @@ jobs:
           - parallel_2d
           - 1D
           - misc
+        include:
+          - version: 1.5
+            os: macOS-latest
+            arch: x64
+            trixi_test: 2D
+          - version: 1.5
+            os: macOS-latest
+            arch: x64
+            trixi_test: parallel_2d
+          - version: 1.5
+            os: windows-latest
+            arch: x64
+            trixi_test: 2D
+          - version: 1.5
+            os: windows-latest
+            arch: x64
+            trixi_test: parallel_2d
     steps:
       - uses: actions/checkout@v2
       - uses: julia-actions/setup-julia@v1
@@ -54,7 +88,12 @@ jobs:
         env:
           PYTHON: ""
           TRIXI_TEST: ${{ matrix.trixi_test }}
-      - uses: julia-actions/julia-processcoverage@v1
+      # The following step is inspired by the setup of
+      # - uses: julia-actions/julia-processcoverage@v1/
+      # but checks also the examples folder, since the elixirs
+      # contained therein are considered to be a part of Trixi.
+      - run: julia --color=yes -e 'using Pkg; Pkg.activate("coveragetempenv", shared=true); Pkg.add(PackageSpec(name="CoverageTools")); using CoverageTools; pf = process_folder(); append!(pf, process_folder("examples")); LCOV.writefile("lcov.info", pf)'
+        shell: bash
       - uses: codecov/codecov-action@v1
         with:
           file: ./lcov.info

.gitignore

@@ -8,7 +8,7 @@
 *.avi
 *.ogv
 **/Manifest.toml
-out/
+out*/
 docs/build
 docs/src/authors.md
 public/

.travis.yml → .outdated/.travis.yml

@@ -33,8 +33,11 @@ env:
     - COVERALLS_PARALLEL=true
   jobs:
     - TRIXI_TEST=2D
+    - TRIXI_TEST=2D_OLD
     - TRIXI_TEST=3D
+    - TRIXI_TEST=3D_OLD
     - TRIXI_TEST=paper-self-gravitating-gas-dynamics
+    - TRIXI_TEST=paper-self-gravitating-gas-dynamics-old
     - TRIXI_TEST=parallel_2d
     - TRIXI_TEST=1D
     - TRIXI_TEST=misc

AUTHORS.md

@@ -24,5 +24,6 @@ are listed in alphabetical order:
 * Gregor Gassner
 * Julia Odenthal
 * Hendrik Ranocha
+* Andrés M. Rueda-Ramírez
 * Michael Schlottke-Lakemper
 * Andrew Winters

Project.toml

@@ -1,27 +1,28 @@
 name = "Trixi"
 uuid = "a7f1ee26-1774-49b1-8366-f1abc58fbfcb"
 authors = ["Michael Schlottke-Lakemper <mschlott@math.uni-koeln.de>", "Gregor Gassner <ggassner@uni-koeln.de>", "Hendrik Ranocha <mail@ranocha.de>", "Andrew R. Winters <andrew.ross.winters@liu.se>"]
-version = "0.2.7-pre"
+version = "0.3.0-pre"
 
 [deps]
+DiffEqBase = "2b5f629d-d688-5b77-993f-72d75c75574e"
+DiffEqCallbacks = "459566f4-90b8-5000-8ac3-15dfb0a30def"
 EllipsisNotation = "da5c29d0-fa7d-589e-88eb-ea29b0a81949"
 HDF5 = "f67ccb44-e63f-5c2f-98bd-6dc0ccc4ba2f"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 LinearMaps = "7a12625a-238d-50fd-b39a-03d52299707e"
 LoopVectorization = "bdcacae8-1622-11e9-2a5c-532679323890"
 MPI = "da04e1cc-30fd-572f-bb4f-1f8673147195"
 OffsetArrays = "6fe1bfb0-de20-5000-8ca7-80f57d26f881"
-Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
 Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
-Profile = "9abbd945-dff8-562f-b5e8-e1ebf5ef1b79"
-Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
 TimerOutputs = "a759f4b9-e2f1-59dc-863e-4aeb61b1ea8f"
 Tullio = "bc48ee85-29a4-5162-ae0b-a64e1601d4bc"
 UnPack = "3a884ed6-31ef-47d7-9d2a-63182c4928ed"
 
 [compat]
-EllipsisNotation = "0.4, 1.0"
+DiffEqBase = "6.47"
+DiffEqCallbacks = "2.14"
+EllipsisNotation = "1.0"
 HDF5 = "0.13, 0.14"
 LinearMaps = "2.7"
 LoopVectorization = "0.8.25"

README.md

@@ -3,7 +3,6 @@
 [![Docs-stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://trixi-framework.github.io/Trixi.jl/stable)
 [![Docs-dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://trixi-framework.github.io/Trixi.jl/dev)
 [![Build Status](https://github.com/trixi-framework/Trixi.jl/workflows/CI/badge.svg)](https://github.com/trixi-framework/Trixi.jl/actions?query=workflow%3ACI)
-[![Build Windows](https://ci.appveyor.com/api/projects/status/uu0xds4hyc1i10n8/branch/master?svg=true)](https://ci.appveyor.com/project/ranocha/trixi-jl/branch/master)
 [![Coveralls](https://coveralls.io/repos/github/trixi-framework/Trixi.jl/badge.svg?branch=master)](https://coveralls.io/github/trixi-framework/Trixi.jl?branch=master)
 [![License: MIT](https://img.shields.io/badge/License-MIT-success.svg)](https://opensource.org/licenses/MIT)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3996439.svg)](https://doi.org/10.5281/zenodo.3996439)
@@ -29,7 +28,10 @@ installation and postprocessing procedures. Its features include:
   * Kinetic energy-preserving and entropy-stable split forms
   * Entropy-stable shock capturing
   * Positivity-preserving limiting
-* Explicit low-storage Runge-Kutta time integration
+* 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))
+  * CFL-based and error-based time step control
 * Square/cubic domains with periodic and weakly-enforced boundary conditions
 * Multiple governing equations:
   * Compressible Euler equations
@@ -39,7 +41,8 @@ installation and postprocessing procedures. Its features include:
 * Multi-physics simulations
   * [Self-gravitating gas dynamics](https://github.com/trixi-framework/paper-self-gravitating-gas-dynamics)
 * Shared-memory parallelization via multithreading
-* Visualization of results with Julia-only tools (2D) or ParaView/VisIt (2D/3D)
+* Visualization of results with Julia-only tools ([Trixi2Img](https://github.com/trixi-framework/Trixi2Img.jl))
+  or ParaView/VisIt ([Trixi2Vtk](https://github.com/trixi-framework/Trixi2Vtk.jl))
 
 
 ## Installation
@@ -49,30 +52,35 @@ with Julia v1.5.
 
 ### For users
 Trixi and related postprocessing tools are registered Julia packages. Hence, you
-can install Trixi, [Trixi2Vtk](https://github.com/trixi-framework/Trixi2Vtk.jl),
-and [Trixi2Img](https://github.com/trixi-framework/Trixi2Img.jl) by executing
-the following commands in the Julia REPL:
+can install Trixi, the visualization tools
+[Trixi2Vtk](https://github.com/trixi-framework/Trixi2Vtk.jl)
+and [Trixi2Img](https://github.com/trixi-framework/Trixi2Img.jl), and the
+[OrdinaryDiffEq.jl](https://github.com/SciML/OrdinaryDiffEq.jl) package by
+executing the following commands in the Julia REPL:
 ```julia
 julia> import Pkg
 
-julia> Pkg.add("Trixi"); Pkg.add("Trixi2Vtk"); Pkg.add("Trixi2Img")
+julia> Pkg.add("Trixi"); Pkg.add("Trixi2Vtk"); Pkg.add("Trixi2Img"); Pkg.add("OrdinaryDiffEq")
 ```
 Note that 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.
 
 ### For developers
 If you plan on editing Trixi itself, you can download Trixi locally and run it from
 within the cloned directory:
 ```bash
 git clone git@github.com:trixi-framework/Trixi.jl.git
 cd Trixi.jl
-julia --project=. -e 'import Pkg; Pkg.instantiate()' # Install Trixi's dependencies
+julia --project=@. -e 'import Pkg; Pkg.instantiate()' # Install Trixi's dependencies
 julia -e 'import Pkg; Pkg.add("Trixi2Vtk"); Pkg.add("Trixi2Img")' # Install postprocessing tools
+julia -e 'import Pkg; Pkg.add("OrdinaryDiffEq")' # Install time integration schemes
 ```
 If you installed Trixi this way, you always have to start Julia with the `--project`
 flag set to your local Trixi clone, e.g.,
 ```bash
-julia --project=.
+julia --project=@.
 ```
 Further details can be found in the [documentation](#documentation).
 
@@ -84,7 +92,7 @@ julia> using Trixi
 ```
 Then start a simulation by executing
 ```julia
-julia> Trixi.run(default_example())
+julia> trixi_include(default_example())
 ```
 To visualize the results, load the package Trixi2Img
 ```julia
@@ -100,21 +108,23 @@ that can be opened with any image viewer:
   <img width="300px" src="docs/src/assets/solution_000040_scalar_resized.png">
 </p>
 
-The method `Trixi.run(...)` expects a single string argument with the path to a
-Trixi parameter file. To quickly see Trixi in action, `default_example()`
-returns the path to an example parameter file with a short, two-dimensional
-problem setup. A list of all example parameter files packaged with Trixi can be
+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()`
+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
 obtained by running `get_examples()`. Alternatively, you can also browse the
-[`examples/`](examples/) subdirectory. If you want to
-modify one of the parameter files to set up your own simulation, download it to
-your machine, edit the configuration, and pass the file path to `Trixi.run(...)`.
+[`examples/`](examples/) subdirectory.
+If you want to modify one of the elixirs to set up your own simulation,
+download it to your machine, edit the configuration, and pass the file path to
+`trixi_include(...)`.
 
 *Note on performance:* Julia uses just-in-time compilation to transform its
 source code to native, optimized machine code at the *time of execution* and
 caches the compiled methods for further use. That means that the first execution
 of a Julia method is typically slow, with subsequent runs being much faster. For
-instance, in the example above the first execution of `Trixi.run` takes about 15
-seconds, while subsequent runs require less than 50 *milli*seconds.
+instance, in the example above the first execution of `trixi_include` takes about
+20 seconds, while subsequent runs require less than 60 *milli*seconds.
 
 
 ## Documentation

docs/make.jl

@@ -43,8 +43,11 @@ makedocs(
     # Explicitly specify documentation structure
     pages = [
         "Home" => "index.md",
-        "Development" => "development.md",
         "Visualization" => "visualization.md",
+        "Conventions" => "conventions.md",
+        "Time integration" => "time_integration.md",
+        "Development" => "development.md",
+        "Performance" => "performance.md",
         "Parallelization" => "parallelization.md",
         "Style guide" => "styleguide.md",
         "GitHub & Git" => "github-git.md",

docs/src/conventions.md

@@ -0,0 +1,15 @@
+# Conventions
+
+## Spatial dimensions and directions
+
+We use the following numbering schemes on Cartesian meshes.
+- The `orientation`s are numbered as
+  `1 => x, 2 => y, 3 => z`.
+  For example, numerical fluxes such as
+  `flux_central(u_ll, u_rr, orientation, equations::AbstractEquations)`
+  use the `orientation` in this way.
+- The `direction`s are numbered as
+  `1 => -x, 2 => +x, 3 => -y, 4 => +y, 5 => -z, 6 => +z`.
+  For example, the `boundary_conditions` are ordered in this way
+  when a `Tuple` of boundary conditions per direction is passed
+  to the constructor of a `SemidiscretizationHyperbolic`.