Merge branch 'main' into msl/structuredmesh-view

.github/review-checklist.md

@@ -19,7 +19,7 @@ This checklist is meant to assist creators of PRs (to let them know what reviewe
 - [ ] 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`.
+- [ ] If the PR introduces a significant change or new feature, it is documented in `NEWS.md` with its PR number.
 
 #### Testing
 - [ ] The PR passes all tests.
@@ -35,4 +35,4 @@ This checklist is meant to assist creators of PRs (to let them know what reviewe
 - [ ] 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.*
+*Created with :heart: by the Trixi.jl community.*

.github/workflows/Documenter.yml

@@ -38,7 +38,7 @@ jobs:
         with:
           version: '1.10'
           show-versioninfo: true
-      - uses: julia-actions/cache@v1
+      - uses: julia-actions/cache@v2
       - uses: julia-actions/julia-buildpkg@v1
         env:
           PYTHON: ""

.github/workflows/Downgrade.yml

@@ -69,10 +69,10 @@ jobs:
           version: ${{ matrix.version }}
           arch: ${{ matrix.arch }}
       - run: julia -e 'using InteractiveUtils; versioninfo(verbose=true)'
-      - uses: julia-actions/cache@v1
+      - uses: julia-actions/cache@v2
       - uses: julia-actions/julia-downgrade-compat@v1
         with:
-          skip: LinearAlgebra,Printf,SparseArrays,UUIDs,DiffEqBase
+          skip: LinearAlgebra,Printf,SparseArrays,UUIDs,DiffEqBase,DelimitedFiles
           projects: ., test
       - uses: julia-actions/julia-buildpkg@v1
         env:

.github/workflows/ci.yml

@@ -112,7 +112,7 @@ jobs:
           version: ${{ matrix.version }}
           arch: ${{ matrix.arch }}
       - run: julia -e 'using InteractiveUtils; versioninfo(verbose=true)'
-      - uses: julia-actions/cache@v1
+      - uses: julia-actions/cache@v2
       - uses: julia-actions/julia-buildpkg@v1
         env:
           PYTHON: ""

.github/workflows/downstream.yml

@@ -69,7 +69,7 @@ jobs:
           version: ${{ matrix.version }}
           arch: ${{ matrix.arch }}
       - run: julia -e 'using InteractiveUtils; versioninfo(verbose=true)'
-      - uses: julia-actions/cache@v1
+      - uses: julia-actions/cache@v2
       - uses: julia-actions/julia-buildpkg@v1
       - name: Retrieve downstream package
         # Note: we retrieve the current `main` branch of the downstream package to ensure

.zenodo.json

@@ -5,7 +5,7 @@
     "upload_type": "software",
     "creators": [
         {
-            "affiliation": "Applied and Computational Mathematics, RWTH Aachen University, Germany",
+            "affiliation": "High-Performance Scientific Computing, University of Augsburg, Germany",
             "name": "Schlottke-Lakemper, Michael",
             "orcid": "0000-0002-3195-2536"
         },

AUTHORS.md

@@ -7,8 +7,8 @@ provided substantial additions or modifications. Together, these two groups form
 "The Trixi.jl Authors" as mentioned in the [LICENSE.md](LICENSE.md) file.
 
 ## Principal Developers
-* [Michael Schlottke-Lakemper](https://lakemper.eu),
-  RWTH Aachen University/High-Performance Computing Center Stuttgart (HLRS), Germany
+* [Michael Schlottke-Lakemper](https://www.uni-augsburg.de/fakultaet/mntf/math/prof/hpsc),
+  University of Augsburg, Germany
 * [Gregor Gassner](https://www.mi.uni-koeln.de/NumSim/gregor-gassner),
   University of Cologne, Germany
 * [Hendrik Ranocha](https://ranocha.de),
@@ -43,3 +43,4 @@ are listed in alphabetical order:
 * Michael Schlottke-Lakemper
 * Toskan Theine
 * Andrew Winters
+* Huiyu Xie

CODE_OF_CONDUCT.md

@@ -60,7 +60,7 @@ representative at an online or offline event.
 
 Instances of abusive, harassing, or otherwise unacceptable behavior may be
 reported to
-[Michael Schlottke-Lakemper](mailto:m.schlottke-lakemper@acom.rwth-aachen.de),
+[Michael Schlottke-Lakemper](mailto:michael.schlottke-lakemper@uni-a.de),
 [Hendrik Ranocha](mailto:[email protected]),
 or any other of the principal developers responsible for enforcement listed in
 [AUTHORS.md](AUTHORS.md).

NEWS.md

@@ -7,11 +7,14 @@ for human readability.
 ## Changes in the v0.7 lifecycle
 
 #### Added
-- Implementation of `TimeSeriesCallback` for curvilinear meshes on `UnstructuredMesh2D` and extension
-  to 1D and 3D on `TreeMesh`.
-- Implementation of 1D Linearized Euler Equations.
-- New analysis callback for 2D `P4estMesh` to compute integrated quantities along a boundary surface, e.g., pressure lift and drag coefficients.
-- Optional tuple parameter for `GlmSpeedCallback` called `semi_indices` to specify for which semidiscretization of a `SemidiscretizationCoupled` we need to update the GLM speed.
+- Implementation of `TimeSeriesCallback` for curvilinear meshes on `UnstructuredMesh2D` and extension to 1D and 3D on `TreeMesh` ([#1855], [#1873]).
+- Implementation of 1D Linearized Euler Equations ([#1867]).
+- New analysis callback for 2D `P4estMesh` to compute integrated quantities along a boundary surface, e.g., pressure lift and drag coefficients ([#1812]).
+- Optional tuple parameter for `GlmSpeedCallback` called `semi_indices` to specify for which semidiscretization of a `SemidiscretizationCoupled` we need to update the GLM speed ([#1835]).
+- Subcell local one-sided limiting support for nonlinear variables in 2D for `TreeMesh` ([#1792]).
+- New time integrator `PairedExplicitRK2`, implementing the second-order paired explicit Runge-Kutta
+  method with [Convex.jl](https://github.com/jump-dev/Convex.jl) and [ECOS.jl](https://github.com/jump-dev/ECOS.jl) ([#1908])
+- Add subcell limiting support for `StructuredMesh` ([#1946]).
 
 ## Changes when updating to v0.7 from v0.6.x
 
@@ -189,9 +192,8 @@ for human readability.
 #### Added
 
 - Experimental support for artificial neural network-based indicators for shock capturing and
-  adaptive mesh refinement ([#632](https://github.com/trixi-framework/Trixi.jl/pull/632))
-- Experimental support for direct-hybrid aeroacoustics simulations
-  ([#712](https://github.com/trixi-framework/Trixi.jl/pull/712))
+  adaptive mesh refinement ([#632])
+- Experimental support for direct-hybrid aeroacoustics simulations ([#712])
 - Implementation of shallow water equations in 2D
 - Experimental support for interactive visualization with [Makie.jl](https://makie.juliaplots.org/)
 
@@ -227,7 +229,7 @@ for human readability.
   - acoustic perturbation equations
   - Lattice-Boltzmann equations
 - Composable `FluxPlusDissipation` and `FluxLaxFriedrichs()`, `FluxHLL()` with adaptable
-  wave speed estimates were added in [#493](https://github.com/trixi-framework/Trixi.jl/pull/493)
+  wave speed estimates were added in [#493]
 - New structured, curvilinear, conforming mesh type `StructuredMesh`
 - New unstructured, curvilinear, conforming mesh type `UnstructuredMesh2D` in 2D
 - New unstructured, curvilinear, adaptive (non-conforming) mesh type `P4estMesh` in 2D and 3D
@@ -240,13 +242,13 @@ for human readability.
 - `flux_lax_friedrichs(u_ll, u_rr, orientation, equations::LatticeBoltzmannEquations2D)` and
   `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
+  in [#493]. This is considered a bugfix
   (released in Trixi.jl v0.3.22).
 - The required Julia version is updated to v1.6.
 
 #### Deprecated
 
-- `calcflux` → `flux` ([#463](https://github.com/trixi-framework/Trixi.jl/pull/463))
+- `calcflux` → `flux` ([#463])
 - `flux_upwind` → `flux_godunov`
 - `flux_hindenlang` → `flux_hindenlang_gassner`
 - Providing the keyword argument `solution_variables` of `SaveSolutionCallback`
@@ -258,6 +260,6 @@ for human readability.
   only a single two-point numerical flux for nonconservative is deprecated. The new
   interface is described in a tutorial. Now, a tuple of two numerical fluxes of the
   form `(conservative_flux, nonconservative_flux)` needs to be passed for
-  nonconservative equations, see [#657](https://github.com/trixi-framework/Trixi.jl/pull/657).
+  nonconservative equations, see [#657].
 
 #### Removed

Project.toml

@@ -1,12 +1,13 @@
 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 = "0.7.11-pre"
+version = "0.7.17-pre"
 
 [deps]
 CodeTracking = "da1fd8a2-8d9e-5ec2-8556-3022fb5608a2"
 ConstructionBase = "187b0558-2788-49d3-abe0-74a17ed4e7c9"
 DataStructures = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
+DelimitedFiles = "8bb1440f-4735-579b-a4ab-409b98df4dab"
 DiffEqBase = "2b5f629d-d688-5b77-993f-72d75c75574e"
 DiffEqCallbacks = "459566f4-90b8-5000-8ac3-15dfb0a30def"
 Downloads = "f43a241f-c20a-4ad4-852c-f6b1247861c6"
@@ -50,17 +51,23 @@ UUIDs = "cf7118a7-6976-5b1a-9a39-7adc72f591a4"
 
 [weakdeps]
 Makie = "ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a"
+Convex = "f65535da-76fb-5f13-bab9-19810c17039a"
+ECOS = "e2685f51-7e38-5353-a97d-a921fd2c8199"
 
 [extensions]
 TrixiMakieExt = "Makie"
+TrixiConvexECOSExt = ["Convex", "ECOS"]
 
 [compat]
 CodeTracking = "1.0.5"
 ConstructionBase = "1.3"
+Convex = "0.16"
 DataStructures = "0.18.15"
+DelimitedFiles = "1"
 DiffEqBase = "6 - 6.143"
 DiffEqCallbacks = "2.25"
 Downloads = "1.6"
+ECOS = "1.1.2"
 EllipsisNotation = "1.0"
 FillArrays = "0.13.2, 1"
 ForwardDiff = "0.10.24"
@@ -92,14 +99,16 @@ StaticArrays = "1.5"
 StrideArrays = "0.1.26"
 StructArrays = "0.6.11"
 SummationByPartsOperators = "0.5.41"
-T8code = "0.4.3, 0.5"
+T8code = "0.5"
 TimerOutputs = "0.5.7"
 Triangulate = "2.2"
 TriplotBase = "0.1"
 TriplotRecipes = "0.1"
-TrixiBase = "0.1.1"
+TrixiBase = "0.1.3"
 UUIDs = "1.6"
 julia = "1.8"
 
 [extras]
 Makie = "ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a"
+Convex = "f65535da-76fb-5f13-bab9-19810c17039a"
+ECOS = "e2685f51-7e38-5353-a97d-a921fd2c8199"

README.md

@@ -19,6 +19,28 @@
   <img width="300px" src="https://trixi-framework.github.io/assets/logo.png">
 </p>
 
+***
+**Trixi.jl at JuliaCon 2024**<br/>
+At this year's JuliaCon in Eindhoven, Netherlands, we will be present with several contributions
+from the Trixi Framework ecosystem:
+
+* [**Julia for Particle-Based Multiphysics with TrixiParticles.jl**](https://pretalx.com/juliacon2024/talk/TPFF8L/),<br/>
+  [*Erik Faulhaber*](https://github.com/efaulhaber/), [*Niklas Neher*](https://github.com/lasnikas/),
+  10th July 2024, 11:30am–12:00pm, Function (4.1)
+* [**Towards Aerodynamic Simulations in Julia with Trixi.jl**](https://pretalx.com/juliacon2024/talk/XH8KBG/),<br/>
+  [*Daniel Doehring*](https://github.com/danieldoehring/),
+  10th July 2024, 15:00pm–15:30pm, While Loop (4.2)
+* [**libtrixi: serving legacy codes in earth system modeling with fresh Julia CFD**](https://pretalx.com/juliacon2024/talk/SXC7LA/),<br/>
+  [*Benedict Geihe*](https://github.com/benegee/),
+  12th July 2024, 14:00pm–17:00pm, Function (4.1)
+
+The last talk is part of the 
+[Julia for High-Performance Computing](https://juliacon.org/2024/minisymposia/hpc/)
+minisymposium, which this year is hosted by our own [*Hendrik Ranocha*](https://github.com/ranocha/).
+
+We are looking forward to seeing you there ♥️
+***
+
 **Trixi.jl** is a numerical simulation framework for 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
@@ -237,8 +259,8 @@ In addition, you can also refer to Trixi.jl directly as
 
 ## Authors
 Trixi.jl was initiated by [Michael
-Schlottke-Lakemper](https://lakemper.eu)
-(RWTH Aachen University/High-Performance Computing Center Stuttgart (HLRS), Germany) and
+Schlottke-Lakemper](https://www.uni-augsburg.de/fakultaet/mntf/math/prof/hpsc)
+(University of Augsburg, Germany) and
 [Gregor Gassner](https://www.mi.uni-koeln.de/NumSim/gregor-gassner)
 (University of Cologne, Germany). Together with [Hendrik Ranocha](https://ranocha.de)
 (Johannes Gutenberg University Mainz, Germany), [Andrew Winters](https://liu.se/en/employee/andwi94)

docs/.gitignore

@@ -1,3 +1,4 @@
+src/changelog.md
 src/code_of_conduct.md
 src/contributing.md
 

docs/Project.toml

@@ -1,5 +1,6 @@
 [deps]
 CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
+Changelog = "5217a498-cd5d-4ec6-b8c2-9b85a09b6e3e"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
 HOHQMesh = "e4f4c7b8-17cb-445a-93c5-f69190ed6c8c"
@@ -14,6 +15,7 @@ TrixiBase = "9a0f1c46-06d5-4909-a5a3-ce25d3fa3284"
 
 [compat]
 CairoMakie = "0.6, 0.7, 0.8, 0.9, 0.10, 0.11"
+Changelog = "1.1"
 Documenter = "1"
 ForwardDiff = "0.10"
 HOHQMesh = "0.1, 0.2"

docs/literate/src/files/hohqmesh_tutorial.jl

@@ -35,6 +35,7 @@
 # There is a default example for this mesh type that can be executed by
 
 using Trixi
+rm("out", force = true, recursive = true) #hide #md
 redirect_stdio(stdout=devnull, stderr=devnull) do # code that prints annoying stuff we don't want to see here #hide #md
 trixi_include(default_example_unstructured())
 end #hide #md

docs/literate/src/files/index.jl

@@ -56,6 +56,18 @@
 # explained and added to an exemplary simulation of the Sedov blast wave with the 2D compressible Euler
 # equations.
 
+#src Note to developers: Use "{ index }" (but without spaces, see next line) to enable automatic indexing
+# ### [{index} Subcell limiting with the IDP Limiter](@ref subcell_shock_capturing)
+#-
+# Trixi.jl features a subcell-wise limiting strategy utilizing an Invariant Domain-Preserving (IDP)
+# approach. This IDP approach computes a blending factor that balances the high-order
+# discontinuous Galerkin (DG) method with a low-order subcell finite volume (FV) method for each
+# node within an element. This localized approach minimizes the application of dissipation,
+# resulting in less limiting compared to the element-wise strategy. Additionally, the framework
+# supports both local bounds, which are primarily used for shock capturing, and global bounds.
+# The application of global bounds ensures the minimal necessary limiting to meet physical
+# admissibility conditions, such as ensuring the non-negativity of variables.
+
 #src Note to developers: Use "{ index }" (but without spaces, see next line) to enable automatic indexing
 # ### [{index} Non-periodic boundary conditions](@ref non_periodic_boundaries)
 #-