Merge branch 'main' into twolayer_swe

.github/workflows/CacheNotebooks.yml

@@ -11,7 +11,7 @@ jobs:
     steps:
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
       - name: Checkout caching branch
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           ref: tutorial_notebooks
 

.github/workflows/DocPreviewCleanup.yml

@@ -12,7 +12,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout gh-pages branch
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           ref: gh-pages
 

.github/workflows/Documenter.yml

@@ -33,7 +33,7 @@ jobs:
   build:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: julia-actions/setup-julia@v1
         with:
           version: '1.9'

.github/workflows/FormatCheck.yml

@@ -20,7 +20,7 @@ jobs:
         with:
           version: ${{ matrix.julia-version }}
 
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Install JuliaFormatter and format
         # This will use the latest version by default but you can set the version like so:
         #
@@ -30,7 +30,7 @@ jobs:
         #       format(".")
         run: |
           julia  -e 'using Pkg; Pkg.add(PackageSpec(name = "JuliaFormatter"))'
-          julia  -e 'using JuliaFormatter; format(["benchmark", "ext", "src", "utils"])'
+          julia  -e 'using JuliaFormatter; format(["benchmark", "examples", "ext", "src", "test", "utils"])'
       - name: Format check
         run: |
           julia -e '

.github/workflows/Invalidations.yml

@@ -19,12 +19,12 @@ jobs:
     - uses: julia-actions/setup-julia@v1
       with:
         version: '1'
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - uses: julia-actions/julia-buildpkg@v1
     - uses: julia-actions/julia-invalidations@v1
       id: invs_pr
 
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         ref: ${{ github.event.repository.default_branch }}
     - uses: julia-actions/julia-buildpkg@v1

.github/workflows/ReviewChecklist.yml

@@ -12,7 +12,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: Add review checklist
         uses: trixi-framework/add-pr-review-checklist@v1
         with:

.github/workflows/SpellCheck.yml

@@ -8,6 +8,6 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout Actions Repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: Check spelling
-        uses: crate-ci/[email protected].5
+        uses: crate-ci/[email protected].21

.github/workflows/benchmark.yml

@@ -15,7 +15,7 @@ jobs:
         arch:
           - x64
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
       - run: |

.github/workflows/ci.yml

@@ -101,7 +101,7 @@ jobs:
             arch: x64
             trixi_test: threaded
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: julia-actions/setup-julia@v1
         with:
           version: ${{ matrix.version }}
@@ -175,7 +175,7 @@ jobs:
       # Instead, we use the more tedious approach described above.
       # At first, we check out the repository and download all artifacts
       # (and list files for debugging).
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: actions/download-artifact@v3
       - run: ls -R
       # Next, we merge the individual coverage files and upload

.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

@@ -12,7 +12,9 @@ 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
+- Implementation of the polytropic Euler equations in 2D
 - Subcell positivity limiting support for conservative variables in 2D for `TreeMesh`
+- AMR for hyperbolic-parabolic equations on 2D/3D `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 = "0.5.40-pre"
+version = "0.5.48-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"
@@ -71,7 +71,7 @@ PrecompileTools = "1.1"
 RecipesBase = "1.1"
 Reexport = "1.0"
 Requires = "1.1"
-SciMLBase = "1.90"
+SciMLBase = "1.90, 2"
 Setfield = "0.8, 1"
 SimpleUnPack = "1.1"
 StartUpDG = "0.17"

README.md

@@ -7,6 +7,7 @@
 [![Build Status](https://github.com/trixi-framework/Trixi.jl/workflows/CI/badge.svg)](https://github.com/trixi-framework/Trixi.jl/actions?query=workflow%3ACI)
 [![Codecov](https://codecov.io/gh/trixi-framework/Trixi.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/trixi-framework/Trixi.jl)
 [![Coveralls](https://coveralls.io/repos/github/trixi-framework/Trixi.jl/badge.svg?branch=main)](https://coveralls.io/github/trixi-framework/Trixi.jl?branch=main)
+[![Aqua QA](https://raw.githubusercontent.com/JuliaTesting/Aqua.jl/master/badge.svg)](https://github.com/JuliaTesting/Aqua.jl)
 [![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)
 [![Downloads](https://shields.io/endpoint?url=https://pkgs.genieframework.com/api/v1/badge/Trixi)](https://pkgs.genieframework.com?packages=Trixi)
@@ -17,16 +18,6 @@
   <img width="300px" src="https://trixi-framework.github.io/assets/logo.png">
 </p>
 
-***
-**Trixi.jl at JuliaCon 2023**<br/>
-At this year's JuliaCon, we will be present with an online contribution that involves Trixi.jl:
-
-* [Scaling Trixi.jl to more than 10,000 cores using MPI](https://pretalx.com/juliacon2023/talk/PC8PZ8/),
-  27th July 2023, 10:30–11:30 (US/Eastern), 32-G449 (Kiva)
-
-We are looking forward to seeing you there ♥️
-***
-
 **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
@@ -247,7 +238,7 @@ 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).
@@ -265,31 +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](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 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
+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.

docs/Project.toml

@@ -13,7 +13,7 @@ Trixi2Vtk = "bc1476a1-1ca6-4cc3-950b-c312b255ff95"
 
 [compat]
 CairoMakie = "0.6, 0.7, 0.8, 0.9, 0.10"
-Documenter = "0.27"
+Documenter = "1"
 ForwardDiff = "0.10"
 HOHQMesh = "0.1, 0.2"
 LaTeXStrings = "1.2"

docs/literate/make.jl

@@ -51,12 +51,25 @@ function create_tutorials(files)
     # Run tests on all tutorial files
     @testset "TrixiTutorials" begin
         for (i, (title, filename)) in enumerate(files)
+            # Evaluate each tutorial in its own module to avoid leaking of
+            # function/variable names, polluting the namespace of later tutorials
+            # by stuff defined in earlier tutorials.
             if filename isa Vector # Several files of one topic
                 for j in eachindex(filename)
-                    @testset "$(filename[j][2][2])" begin include(joinpath(repo_src, filename[j][2][1], filename[j][2][2])) end
+                    mod = gensym(filename[j][2][2])
+                    @testset "$(filename[j][2][2])" begin
+                        @eval module $mod
+                            include(joinpath($repo_src, $(filename[j][2][1]), $(filename[j][2][2])))
+                        end
+                    end
                 end
             else # Single files
-                @testset "$title" begin include(joinpath(repo_src, filename)) end
+                mod = gensym(title)
+                @testset "$title" begin
+                    @eval module $mod
+                        include(joinpath($repo_src, $filename))
+                    end
+                end
             end
         end
     end

docs/literate/src/files/DGMulti_1.jl

@@ -194,3 +194,15 @@ plot(pd["rho"])
 plot!(getmesh(pd))
 
 # For more information, please have a look in the [StartUpDG.jl documentation](https://jlchan.github.io/StartUpDG.jl/stable/).
+
+
+# ## Package versions
+
+# These results were obtained using the following versions.
+
+using InteractiveUtils
+versioninfo()
+
+using Pkg
+Pkg.status(["Trixi", "StartUpDG", "OrdinaryDiffEq", "Plots"],
+           mode=PKGMODE_MANIFEST)

docs/literate/src/files/DGMulti_2.jl

@@ -38,3 +38,15 @@ D = couple_continuously(legendre_derivative_operator(xmin=0.0, xmax=1.0, N=4),
 
 # For more information and other SBP operators, see the documentations of [StartUpDG.jl](https://jlchan.github.io/StartUpDG.jl/dev/)
 # and [SummationByPartsOperators.jl](https://ranocha.de/SummationByPartsOperators.jl/stable/).
+
+
+# ## Package versions
+
+# These results were obtained using the following versions.
+
+using InteractiveUtils
+versioninfo()
+
+using Pkg
+Pkg.status(["Trixi", "StartUpDG", "SummationByPartsOperators"],
+           mode=PKGMODE_MANIFEST)

docs/literate/src/files/DGSEM_FluxDiff.jl

@@ -236,3 +236,15 @@ plot(sol)
 # [`flux_chandrashekar`](@ref), [`flux_kennedy_gruber`](@ref).
 # As surface flux you can use all volume fluxes and additionally for instance [`flux_lax_friedrichs`](@ref),
 # [`flux_hll`](@ref), [`flux_hllc`](@ref).
+
+
+# ## Package versions
+
+# These results were obtained using the following versions.
+
+using InteractiveUtils
+versioninfo()
+
+using Pkg
+Pkg.status(["Trixi", "OrdinaryDiffEq", "Plots"],
+           mode=PKGMODE_MANIFEST)

docs/literate/src/files/adaptive_mesh_refinement.jl

@@ -202,3 +202,15 @@ plot!(getmesh(pd))
 # Source: Trixi.jl's YouTube channel [`Trixi Framework`](https://www.youtube.com/channel/UCpd92vU2HjjTPup-AIN0pkg)
 
 # For more information, please have a look at the respective links.
+
+
+# ## Package versions
+
+# These results were obtained using the following versions.
+
+using InteractiveUtils
+versioninfo()
+
+using Pkg
+Pkg.status(["Trixi", "OrdinaryDiffEq", "Plots"],
+           mode=PKGMODE_MANIFEST)

docs/literate/src/files/adding_new_parabolic_terms.jl

@@ -158,3 +158,15 @@ sol = solve(ode, RDPK3SpFSAL49(); abstol=time_int_tol, reltol=time_int_tol,
 using Plots
 plot(sol)
 
+
+# ## Package versions
+
+# These results were obtained using the following versions.
+
+using InteractiveUtils
+versioninfo()
+
+using Pkg
+Pkg.status(["Trixi", "OrdinaryDiffEq", "Plots"],
+           mode=PKGMODE_MANIFEST)
+

docs/literate/src/files/adding_new_scalar_equations.jl

@@ -211,3 +211,15 @@ semi = remake(semi, solver=DGSEM(3, flux_godunov, VolumeIntegralFluxDifferencing
 ode = semidiscretize(semi, (0.0, 0.5))
 sol = solve(ode, SSPRK43(); ode_default_options()...)
 plot(sol)
+
+
+# ## Package versions
+
+# These results were obtained using the following versions.
+
+using InteractiveUtils
+versioninfo()
+
+using Pkg
+Pkg.status(["Trixi", "OrdinaryDiffEq", "Plots"],
+           mode=PKGMODE_MANIFEST)