Io simulations

.buildkite/pipeline.yml

@@ -1,3 +1,5 @@
+env:
+
 steps:
   - label: "CUDA Julia {{matrix.version}}"
     matrix:
@@ -7,12 +9,13 @@ steps:
     plugins:
       - JuliaCI/julia#v1:
           version: "{{matrix.version}}"
-    command: |
-      true
+      - JuliaCI/julia-test#v1: ~
+    env:
+      TRIXI_TEST: "CUDA"
     agents:
       queue: "juliagpu"
       cuda: "*"
     if: build.message !~ /\[skip ci\]/
     timeout_in_minutes: 60
     soft_fail:
-      - exit_status: 3
+      - exit_status: 3

.git-blame-ignore-revs

@@ -0,0 +1 @@
+2bc1cc68c4fed509a2a3e71d02b84e0be5c5565b

.github/workflows/Documenter.yml

@@ -33,7 +33,7 @@ jobs:
   build:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
       - uses: julia-actions/setup-julia@v2
         with:
           version: '1.10'

.github/workflows/Downgrade.yml

@@ -68,7 +68,7 @@ jobs:
           # - mpi
           - threaded
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
       - uses: julia-actions/setup-julia@v2
         with:
           version: ${{ matrix.version }}

.github/workflows/FormatCheck.yml

@@ -11,7 +11,7 @@ jobs:
   format-suggestions:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
       - uses: julia-actions/julia-format@v4
         with:
           version: "1.0.60"

.github/workflows/Invalidations.yml

@@ -19,12 +19,12 @@ jobs:
     - uses: julia-actions/setup-julia@v2
       with:
         version: '1'
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
     - uses: julia-actions/julia-buildpkg@v1
     - uses: julia-actions/julia-invalidations@v1
       id: invs_pr
 
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
       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@v4
+        uses: actions/checkout@v5
       - 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@v4
+        uses: actions/checkout@v5
       - name: Check spelling
-        uses: crate-ci/typos@v1.34.0
+        uses: crate-ci/typos@v1.35.7

.github/workflows/benchmark.yml

@@ -15,7 +15,7 @@ jobs:
         arch:
           - x64
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           fetch-depth: 0
       - run: |

.github/workflows/ci.yml

@@ -103,7 +103,7 @@ jobs:
             arch: x64
             trixi_test: threaded
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
       - uses: julia-actions/setup-julia@v2
         with:
           version: ${{ matrix.version }}
@@ -176,8 +176,8 @@ 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@v4
-      - uses: actions/download-artifact@v4
+      - uses: actions/checkout@v5
+      - uses: actions/download-artifact@v5
       - run: ls -R
       # Next, we merge the individual coverage files and upload
       # the combined results to Coveralls.

.github/workflows/downstream.yml

@@ -64,7 +64,7 @@ jobs:
           - TrixiShallowWater.jl
           - TrixiAtmo.jl
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
       - uses: julia-actions/setup-julia@v2
         with:
           version: ${{ matrix.version }}
@@ -76,7 +76,7 @@ jobs:
         # Note: we retrieve the current `main` branch of the downstream package to ensure
         # that compatibility errors we make in Trixi.jl are detected already here
         # See also https://github.com/trixi-framework/Trixi.jl/pull/1707#discussion_r1382938895
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
         with:
           repository: trixi-framework/${{ matrix.package }}
           path: downstream

.mailmap

@@ -0,0 +1,19 @@
+Hendrik Ranocha <[email protected]> <[email protected]>
+Michael Schlottke-Lakemper <[email protected]> <[email protected]>
+Jesse Chan <[email protected]> <[email protected]>
+Gregor Gassner <[email protected]>
+Gregor Gassner <[email protected]> <[email protected]>
+Erik Faulhaber <[email protected]>
+Erik Faulhaber <[email protected]> <[email protected]>
+Erik Faulhaber <[email protected]> <[email protected]>
+Valentin Churavy <[email protected]> <[email protected]>
+Benjamin Bolm <[email protected]>
+Lars Christmann <[email protected]> <[email protected]>
+Felipe Santillan <[email protected]> <loko1@DESKTOP-MP2S0TM>
+Benedict Geihe <[email protected]>
+Benedict Geihe <[email protected]> <[email protected]>
+JuliaOd <[email protected]> <[email protected]>
+Daniel Doehring <[email protected]> <[email protected]>
+Christof Czernik <[email protected]> <[email protected]>
+Felipe Santillan <[email protected]>
+Warisa Roongaraya <[email protected]>

NEWS.md

@@ -5,6 +5,37 @@ Trixi.jl follows the interpretation of
 used in the Julia ecosystem. Notable changes will be documented in this file
 for human readability.
 
+
+## Changes when updating to v0.13 from v0.12.x
+
+#### Changed
+
+- The `polyester` preference got merged with the `native_threading` preference and the `Trixi.set_polyester!` 
+  function got renamed to `Trixi.set_threading_backend!` ([#2476]).
+- Default wave-speed estimate used within `flux_lax_friedrichs` changed from `max_abs_speed_naive` to
+  `max_abs_speed` which is less diffusive.
+  In v0.13, `flux_lax_friedrichs = FluxLaxFriedrichs(max_abs_speed = max_abs_speed)`
+  instead of the previous default 
+  `FluxLaxFriedrichs(max_abs_speed = max_abs_speed_naive)` ([#2458]).
+- The signature of the `VisualizationCallback` constructor changed.
+  In the new version, it is mandatory to pass the semidiscretization `semi` to
+  determine the default plotting type (1D for 1D simulations, 2D for 2D and 3D simulations).
+  This can further be customized via the keyword argument `plot_data_creator`, which had
+  the default value `plot_data_creator = PlotData2D` before the change ([#2468]).
+
+#### Removed
+
+- Deprecations introduced in earlier versions of Trixi.jl have been removed.
+
+
+## Changes in the v0.12 lifecycle
+
+#### Added
+- Initial support for adapting data-structures between different storage arrays was added. This enables future work to support GPU with Trixi ([#2212]).
+
+#### Deprecated
+
+
 ## Changes when updating to v0.12 from v0.11.x
 
 #### Added
@@ -26,10 +57,10 @@ for human readability.
 
 #### Removed
 
-- The shallow-water equation types `ShallowWaterEquations1D`, `ShallowWaterEquations2D`, and 
-  `ShallowWaterEquationsQuasi1D` have been removed from Trixi.jl and are now available via 
-  [TrixiShallowWater.jl](https://github.com/trixi-framework/TrixiShallowWater.jl/). 
-  This also affects the related functions `hydrostatic_reconstruction_audusse_etal`, 
+- The shallow-water equation types `ShallowWaterEquations1D`, `ShallowWaterEquations2D`, and
+  `ShallowWaterEquationsQuasi1D` have been removed from Trixi.jl and are now available via
+  [TrixiShallowWater.jl](https://github.com/trixi-framework/TrixiShallowWater.jl/).
+  This also affects the related functions `hydrostatic_reconstruction_audusse_etal`,
   `flux_nonconservative_audusse_etal`, and `FluxHydrostaticReconstruction`. ([#2379])
 - The additional `ìnitial_cache` entries in the caches of `SemidiscretizationHyperbolic`
   and `SemidiscretizationHyperbolicParabolic`, and the corresponding keyword arguments of
@@ -39,7 +70,7 @@ for human readability.
 
 #### Added
 
-- Added symmetry plane/reflective wall velocity+stress boundary conditions for the compressible Navier-Stokes equations in 2D and 3D. 
+- Added symmetry plane/reflective wall velocity+stress boundary conditions for the compressible Navier-Stokes equations in 2D and 3D.
   Currently available only for the `P4estMesh` mesh type, `GradientVariablesPrimitive`, and `Adiabatic` heat boundary condition ([#2416]).
 - Added `LaplaceDiffusionEntropyVariables1D`, `LaplaceDiffusionEntropyVariables2D`, and `LaplaceDiffusionEntropyVariables3D`. These add scalar diffusion to each
   equation of a system, but apply diffusion in terms of the entropy variables, which symmetrizes the viscous formulation and ensures semi-discrete entropy dissipation ([#2406]).
@@ -52,8 +83,8 @@ for human readability.
 
 #### Deprecated
 
-- The (2D) aerodynamic coefficients 
-  `DragCoefficientPressure, LiftCoefficientPressure, DragCoefficientShearStress, LiftCoefficientShearStress` have been renamed to 
+- The (2D) aerodynamic coefficients
+  `DragCoefficientPressure, LiftCoefficientPressure, DragCoefficientShearStress, LiftCoefficientShearStress` have been renamed to
   `DragCoefficientPressure2D, LiftCoefficientPressure2D, DragCoefficientShearStress2D, LiftCoefficientShearStress2D`. ([#2375])
 
 ## Changes when updating to v0.11 from v0.10.x