Revise bounds check for MCL (#118)

* Revise bounds check for MCL * Rename `idp_bounds_delta` for MCL to `mcl_bounds_delta` * Remove comment * Fix allocs (trixi-framework#1695) * Fix allocs * remove unnecessary code * rerun fmt * format * Allocation tests dgmulti 2d (trixi-framework#1698) * HLLE CEE 2D3D NonCartesian Meshes (trixi-framework#1692) * HLLE CEE 2D3D NonCartesian Meshes * format * hlle via hll * format test * format test * format * do not export hlle * Correct test vals * test values CI * Update src/equations/compressible_euler_2d.jl Co-authored-by: Hendrik Ranocha <ranocha@users.noreply.github.com> * Update src/equations/compressible_euler_1d.jl Co-authored-by: Hendrik Ranocha <ranocha@users.noreply.github.com> * Update src/equations/compressible_euler_2d.jl Co-authored-by: Hendrik Ranocha <ranocha@users.noreply.github.com> * Update src/equations/compressible_euler_3d.jl Co-authored-by: Hendrik Ranocha <ranocha@users.noreply.github.com> * Update src/equations/compressible_euler_3d.jl Co-authored-by: Hendrik Ranocha <ranocha@users.noreply.github.com> * apply suggestions * additional sentence * Fix typo * typos * correct test vals --------- Co-authored-by: Hendrik Ranocha <ranocha@users.noreply.github.com> * Bump crate-ci/typos from 1.16.15 to 1.16.21 (trixi-framework#1700) Bumps [crate-ci/typos](https://github.com/crate-ci/typos) from 1.16.15 to 1.16.21. - [Release notes](https://github.com/crate-ci/typos/releases) - [Changelog](https://github.com/crate-ci/typos/blob/master/CHANGELOG.md) - [Commits](crate-ci/typos@v1.16.15...v1.16.21) --- updated-dependencies: - dependency-name: crate-ci/typos dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Add NumFOCUS + ACTRIX to acknowledgments (trixi-framework#1697) * Add NumFOCUS + ACTRIX to acknowledgments * Try to avoid spaces * Another try to avoid gaps between images * Hopefully fix image alignment in docs * Try new logo formats * Use smaller DUBS logo and add DUBS funding statement * Add markdown-based table for logos in docs * Try another table approach * Hopefully get a layout that finally *works*... * Arrrrrrgggggghhhhh * format examples (trixi-framework#1531) * format examples * check formatting of examples in CI * update style guide * fix weird formatting * fix formatting of binary operators * format again * Update differentiable_programming.jl (trixi-framework#1704) * Format subcell elixirs * Add warning for missing bounds check for entropy limiter (MCL) --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: Daniel Doehring <daniel.doehring@rwth-aachen.de> Co-authored-by: Hendrik Ranocha <ranocha@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Michael Schlottke-Lakemper <michael@sloede.com> Co-authored-by: ArseniyKholod <119304909+ArseniyKholod@users.noreply.github.com>
bennibolm · Nov 6, 2023 · cb899fe · cb899fe
1 parent 1c845f6
commit cb899fe
Show file tree

Hide file tree

Showing 381 changed files with 13,696 additions and 13,627 deletions.
diff --git a/.github/workflows/FormatCheck.yml b/.github/workflows/FormatCheck.yml
@@ -30,7 +30,7 @@ jobs:
         #       format(".")
         run: |
           julia  -e 'using Pkg; Pkg.add(PackageSpec(name = "JuliaFormatter"))'
-          julia  -e 'using JuliaFormatter; format(["benchmark", "ext", "src", "test", "utils"])'
+          julia  -e 'using JuliaFormatter; format(["benchmark", "examples", "ext", "src", "test", "utils"])'
       - name: Format check
         run: |
           julia -e '

diff --git a/README.md b/README.md
@@ -256,31 +256,48 @@ 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 align="center" style="font-size:0;"><!--
+  BMBF     --><img align="middle" src="https://github.com/trixi-framework/Trixi.jl/assets/3637659/f59af636-3098-4be6-bf80-c6be3f17cbc6" height="120"><!--
+  DFG      --><img align="middle" src="https://github.com/trixi-framework/Trixi.jl/assets/3637659/e67b9ed3-7699-466a-bdaf-2ba070a29a8e" height="120"><!--
+  SRC      --><img align="middle" src="https://github.com/trixi-framework/Trixi.jl/assets/3637659/48f9da06-6f7a-4586-b23e-739bee3901c0" height="120"><!--
+  ERC      --><img align="middle" src="https://github.com/trixi-framework/Trixi.jl/assets/3637659/9371e7e4-3491-4433-ac5f-b3bfb215f5ca" height="120"><!--
+  NSF      --><img align="middle" src="https://github.com/trixi-framework/Trixi.jl/assets/3637659/5325103c-ae81-4747-b87c-c6e4a1b1d7a8" height="120"><!--
+  DUBS     --><img align="middle" src="https://github.com/trixi-framework/Trixi.jl/assets/3637659/bb021e6e-42e6-4fe1-a414-c847402e1937" height="120"><!--
+  NumFOCUS --><img align="middle" src="https://github.com/trixi-framework/Trixi.jl/assets/3637659/8496ac9e-b586-475f-adb7-69bcfc415185" height="120"><!--
+  -->
 </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 by the [Deutsche
+Forschungsgemeinschaft](https://www.dfg.de/) (DFG, German Research Foundation)
+through the following grants:
+* Excellence Strategy EXC 2044-390685587, Mathematics Münster: Dynamics-Geometry-Structure.
+* Research unit FOR 5409 "Structure-Preserving Numerical Methods for Bulk- and
+  Interface Coupling of Heterogeneous Models (SNuBIC)" (project number 463312734).
+* Individual grant no. 528753982.
 
-This project has benefited from funding from the European Research Council through the
+This project has benefited from funding from the [European Research Council](https://erc.europa.eu)
+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
+This project has benefited from funding from [Vetenskapsrådet](https://www.vr.se)
+(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
+This project has benefited from funding from the United States
+[National Science Foundation](https://www.nsf.gov/) (NSF) 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
+This project has benefited from funding from the German
+[Federal Ministry of Education and Research](https://www.bmbf.de) (BMBF)
+through the project grant "Adaptive earth system modeling
 with significantly reduced computation time for exascale supercomputers
 (ADAPTEX)" (funding id: 16ME0668K).
+
+This project has benefited from funding by the
+[Daimler und Benz Stiftung](https://www.daimler-benz-stiftung.de) (Daimler and Benz Foundation)
+through grant no. 32-10/22.
+
+Trixi.jl is supported by [NumFOCUS](https://numfocus.org/) as an Affiliated Project.
diff --git a/docs/literate/src/files/differentiable_programming.jl b/docs/literate/src/files/differentiable_programming.jl
@@ -43,7 +43,7 @@ scatter(real.(λ), imag.(λ), label="central flux")
 # As you can see here, the maximal real part is close to zero.
 
 relative_maximum = maximum(real, λ) / maximum(abs, λ)
-@test 3.0e-10 < relative_maximum < 8.0e-10 #src
+@test 3.0e-10 < relative_maximum < 9.0e-10 #src
 
 # Interestingly, if we add dissipation by switching to the `flux_lax_friedrichs`
 # at the interfaces, the maximal real part of the eigenvalues increases.
@@ -87,7 +87,7 @@ scatter(real.(λ), imag.(λ), label="central flux")
 # Here, the maximal real part is basically zero to machine accuracy.
 
 relative_maximum = maximum(real, λ) / maximum(abs, λ)
-@test 1.0e-17 < relative_maximum < 1.0e-15 #src
+@test 1.0e-17 < relative_maximum < 2.0e-15 #src
 
 # Moreover, the eigenvectors are not as ill-conditioned as in 2D.
 

diff --git a/docs/src/index.md b/docs/src/index.md
@@ -344,29 +344,58 @@ or [create an issue](https://github.com/trixi-framework/Trixi.jl/issues/new).
 
 ## Acknowledgments
 
-![funding-logo](https://user-images.githubusercontent.com/3637659/233821022-84910be7-8649-4999-a0ff-22d5e20f0b90.jpg)
-
-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.
+```@raw html
+<div style="width: 100%; text-align: center; font-size: 0;">
+  <div><!--
+    BMBF     --><img src="https://github.com/trixi-framework/Trixi.jl/assets/3637659/f59af636-3098-4be6-bf80-c6be3f17cbc6" style="height: 120px; width: auto"><!--
+    DFG      --><img src="https://github.com/trixi-framework/Trixi.jl/assets/3637659/e67b9ed3-7699-466a-bdaf-2ba070a29a8e" style="height: 120px; width: auto"><!--
+    SRC      --><img src="https://github.com/trixi-framework/Trixi.jl/assets/3637659/48f9da06-6f7a-4586-b23e-739bee3901c0" style="height: 120px; width: auto"><!--
+    -->
+  </div>
+  <div><!--
+    ERC      --><img src="https://github.com/trixi-framework/Trixi.jl/assets/3637659/9371e7e4-3491-4433-ac5f-b3bfb215f5ca" style="height: 120px; width: auto"><!--
+    NSF      --><img src="https://github.com/trixi-framework/Trixi.jl/assets/3637659/5325103c-ae81-4747-b87c-c6e4a1b1d7a8" style="height: 120px; width: auto"><!--
+    DUBS     --><img src="https://github.com/trixi-framework/Trixi.jl/assets/3637659/bb021e6e-42e6-4fe1-a414-c847402e1937" style="height: 120px; width: auto"><!--
+    -->
+  </div>
+  <div><!--
+    NumFOCUS --><img src="https://github.com/trixi-framework/Trixi.jl/assets/3637659/8496ac9e-b586-475f-adb7-69bcfc415185" style="height: 120px; width: auto"><!--
+    -->
+  </div>
+</div>
+```
 
-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 by the [Deutsche
+Forschungsgemeinschaft](https://www.dfg.de/) (DFG, German Research Foundation)
+through the following grants:
+* Excellence Strategy EXC 2044-390685587, Mathematics Münster: Dynamics-Geometry-Structure.
+* Research unit FOR 5409 "Structure-Preserving Numerical Methods for Bulk- and
+  Interface Coupling of Heterogeneous Models (SNuBIC)" (project number 463312734).
+* Individual grant no. 528753982.
 
-This project has benefited from funding from the European Research Council through the
+This project has benefited from funding from the [European Research Council](https://erc.europa.eu)
+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
+This project has benefited from funding from [Vetenskapsrådet](https://www.vr.se)
+(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
+This project has benefited from funding from the United States
+[National Science Foundation](https://www.nsf.gov/) (NSF) 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
+This project has benefited from funding from the German
+[Federal Ministry of Education and Research](https://www.bmbf.de) (BMBF)
+through the project grant "Adaptive earth system modeling
 with significantly reduced computation time for exascale supercomputers
 (ADAPTEX)" (funding id: 16ME0668K).
+
+This project has benefited from funding by the
+[Daimler und Benz Stiftung](https://www.daimler-benz-stiftung.de) (Daimler and Benz Foundation)
+through grant no. 32-10/22.
+
+Trixi.jl is supported by [NumFOCUS](https://numfocus.org/) as an Affiliated Project.
diff --git a/docs/src/styleguide.md b/docs/src/styleguide.md
@@ -17,11 +17,11 @@ conventions, we apply and enforce automated source code formatting
   * Maximum line length (strictly): **92**.
   * Functions that mutate their *input* are named with a trailing `!`.
   * Functions order their parameters [similar to Julia Base](https://docs.julialang.org/en/v1/manual/style-guide/#Write-functions-with-argument-ordering-similar-to-Julia-Base-1).
-    * The main modified argument comes first. For example, if the right-hand side `du` is modified, 
-      it should come first. If only the `cache` is modified, e.g., in `prolong2interfaces!` 
+    * The main modified argument comes first. For example, if the right-hand side `du` is modified,
+      it should come first. If only the `cache` is modified, e.g., in `prolong2interfaces!`
       and its siblings, put the `cache` first.
     * Otherwise, use the order `mesh, equations, solver, cache`.
-    * If something needs to be specified in more detail for dispatch, put the additional argument before the general one 
+    * If something needs to be specified in more detail for dispatch, put the additional argument before the general one
       that is specified in more detail. For example, we use `have_nonconservative_terms(equations), equations`
       and `dg.mortar, dg`.
   * Prefer `for i in ...` to `for i = ...` for better semantic clarity and greater flexibility.
@@ -55,7 +55,7 @@ julia -e 'using Pkg; Pkg.add("JuliaFormatter")'
 ```
 You can then recursively format the core Julia files in the Trixi.jl repo by executing
 ```shell
-julia -e 'using JuliaFormatter; format(["benchmark", "ext", "src", "utils"])'
+julia -e 'using JuliaFormatter; format(["benchmark", "examples", "ext", "src", "test", "utils"])'
 ```
 from inside the Trixi.jl repository. For convenience, there is also a script you can
 directly run from your terminal shell, which will automatically install JuliaFormatter in a
@@ -67,12 +67,12 @@ You can get more information about using the convenience script by running it wi
 `--help`/`-h` flag.
 
 ### Checking formatting before committing
-It can be convenient to check the formatting of source code automatically before each commit. 
+It can be convenient to check the formatting of source code automatically before each commit.
 We use git-hooks for it and provide a `pre-commit` script in the `utils` folder. The script uses
-[JuliaFormatter.jl](https://github.com/domluna/JuliaFormatter.jl) just like formatting script that 
-runs over the whole Trixi.jl directory. 
-You can copy the `pre-commit`-script into `.git/hooks/pre-commit` and it will check your formatting 
+[JuliaFormatter.jl](https://github.com/domluna/JuliaFormatter.jl) just like formatting script that
+runs over the whole Trixi.jl directory.
+You can copy the `pre-commit`-script into `.git/hooks/pre-commit` and it will check your formatting
 before each commit. If errors are found the commit is aborted and you can add the corrections via
-```shell 
+```shell
 git add -p
 ```
diff --git a/examples/dgmulti_1d/elixir_advection_gauss_sbp.jl b/examples/dgmulti_1d/elixir_advection_gauss_sbp.jl
@@ -23,8 +23,8 @@ dg = DGMulti(polydeg = 3,
 
 cells_per_dimension = (8,)
 mesh = DGMultiMesh(dg, cells_per_dimension,
-                   coordinates_min=(-1.0,), coordinates_max=(1.0,),
-                   periodicity=true)
+                   coordinates_min = (-1.0,), coordinates_max = (1.0,),
+                   periodicity = true)
 
 ###############################################################################
 #  setup the test problem (no source term needed for linear advection)
@@ -49,20 +49,19 @@ ode = semidiscretize(semi, tspan)
 summary_callback = SummaryCallback()
 
 # analyse the solution in regular intervals and prints the results
-analysis_callback = AnalysisCallback(semi, interval=100, uEltype=real(dg))
+analysis_callback = AnalysisCallback(semi, interval = 100, uEltype = real(dg))
 
 # handles the re-calculation of the maximum Δt after each time step
-stepsize_callback = StepsizeCallback(cfl=0.75)
+stepsize_callback = StepsizeCallback(cfl = 0.75)
 
 # collect all callbacks such that they can be passed to the ODE solver
 callbacks = CallbackSet(summary_callback, analysis_callback, stepsize_callback)
 
 ###############################################################################
 # run the simulation
 
-sol = solve(ode, CarpenterKennedy2N54(williamson_condition=false),
-            dt=1.0, save_everystep=false, callback=callbacks);
+sol = solve(ode, CarpenterKennedy2N54(williamson_condition = false),
+            dt = 1.0, save_everystep = false, callback = callbacks);
 
 # Print the timer summary
 summary_callback()
-
diff --git a/examples/dgmulti_1d/elixir_euler_fdsbp_periodic.jl b/examples/dgmulti_1d/elixir_euler_fdsbp_periodic.jl
@@ -2,17 +2,19 @@
 using Trixi, OrdinaryDiffEq
 
 dg = DGMulti(element_type = Line(),
-             approximation_type = periodic_derivative_operator(
-               derivative_order=1, accuracy_order=4, xmin=0.0, xmax=1.0, N=50),
+             approximation_type = periodic_derivative_operator(derivative_order = 1,
+                                                               accuracy_order = 4,
+                                                               xmin = 0.0, xmax = 1.0,
+                                                               N = 50),
              surface_flux = flux_hll,
              volume_integral = VolumeIntegralWeakForm())
 
 equations = CompressibleEulerEquations1D(1.4)
 initial_condition = initial_condition_convergence_test
 source_terms = source_terms_convergence_test
 
-mesh = DGMultiMesh(dg, coordinates_min=(-1.0,),
-                       coordinates_max=( 1.0,))
+mesh = DGMultiMesh(dg, coordinates_min = (-1.0,),
+                   coordinates_max = (1.0,))
 
 semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition, dg,
                                     source_terms = source_terms)
@@ -21,15 +23,16 @@ tspan = (0.0, 0.4)
 ode = semidiscretize(semi, tspan)
 
 summary_callback = SummaryCallback()
-alive_callback = AliveCallback(alive_interval=10)
+alive_callback = AliveCallback(alive_interval = 10)
 analysis_interval = 100
-analysis_callback = AnalysisCallback(semi, interval=analysis_interval, uEltype=real(dg))
-stepsize_callback = StepsizeCallback(cfl=1.0)
-callbacks = CallbackSet(summary_callback, alive_callback, stepsize_callback, analysis_callback)
+analysis_callback = AnalysisCallback(semi, interval = analysis_interval, uEltype = real(dg))
+stepsize_callback = StepsizeCallback(cfl = 1.0)
+callbacks = CallbackSet(summary_callback, alive_callback, stepsize_callback,
+                        analysis_callback)
 
 ###############################################################################
 # run the simulation
 
-sol = solve(ode, CarpenterKennedy2N54(williamson_condition=false),
-            dt = 0.5 * estimate_dt(mesh, dg), save_everystep=false, callback=callbacks);
+sol = solve(ode, CarpenterKennedy2N54(williamson_condition = false),
+            dt = 0.5 * estimate_dt(mesh, dg), save_everystep = false, callback = callbacks);
 summary_callback() # print the timer summary
diff --git a/examples/dgmulti_1d/elixir_euler_flux_diff.jl b/examples/dgmulti_1d/elixir_euler_flux_diff.jl
@@ -13,25 +13,25 @@ source_terms = source_terms_convergence_test
 
 cells_per_dimension = (8,)
 mesh = DGMultiMesh(dg, cells_per_dimension,
-                   coordinates_min=(-1.0,), coordinates_max=(1.0,), periodicity=true)
+                   coordinates_min = (-1.0,), coordinates_max = (1.0,), periodicity = true)
 semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition, dg;
-                                    source_terms=source_terms)
+                                    source_terms = source_terms)
 
 tspan = (0.0, 1.1)
 ode = semidiscretize(semi, tspan)
 
 summary_callback = SummaryCallback()
-alive_callback = AliveCallback(alive_interval=10)
+alive_callback = AliveCallback(alive_interval = 10)
 analysis_interval = 100
-analysis_callback = AnalysisCallback(semi, interval=analysis_interval, uEltype=real(dg))
+analysis_callback = AnalysisCallback(semi, interval = analysis_interval, uEltype = real(dg))
 callbacks = CallbackSet(summary_callback,
                         analysis_callback,
                         alive_callback)
 
 ###############################################################################
 # run the simulation
 
-sol = solve(ode, CarpenterKennedy2N54(williamson_condition=false),
-            dt = 0.5 * estimate_dt(mesh, dg), save_everystep=false, callback=callbacks);
+sol = solve(ode, CarpenterKennedy2N54(williamson_condition = false),
+            dt = 0.5 * estimate_dt(mesh, dg), save_everystep = false, callback = callbacks);
 
 summary_callback() # print the timer summary