Merge branch 'main' into sc/mhd-treemesh-3d

trixi-framework · Oct 2, 2023 · ec0390b · ec0390b
2 parents 41749dd + 9e41775
commit ec0390b
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diff --git a/.github/workflows/CacheNotebooks.yml b/.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
 

diff --git a/.github/workflows/DocPreviewCleanup.yml b/.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
 

diff --git a/.github/workflows/Documenter.yml b/.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'

diff --git a/.github/workflows/FormatCheck.yml b/.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:
         #

diff --git a/.github/workflows/Invalidations.yml b/.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

diff --git a/.github/workflows/ReviewChecklist.yml b/.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:

diff --git a/.github/workflows/SpellCheck.yml b/.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].9
+        uses: crate-ci/[email protected].15
diff --git a/.github/workflows/benchmark.yml b/.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: |

diff --git a/.github/workflows/ci.yml b/.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

diff --git a/Project.toml b/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 = "0.5.44-pre"
+version = "0.5.45-pre"
 
 [deps]
 CodeTracking = "da1fd8a2-8d9e-5ec2-8556-3022fb5608a2"
@@ -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"

diff --git a/README.md b/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)

diff --git a/docs/src/index.md b/docs/src/index.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)
 

diff --git a/docs/src/overview.md b/docs/src/overview.md
@@ -55,14 +55,15 @@ different features on different mesh types.
 | Element type                                                 | line, square, cube |     line, quadᵃ, hexᵃ    |             quadᵃ            |     quadᵃ, hexᵃ     |    simplex, quadᵃ, hexᵃ    |
 | Adaptive mesh refinement                                     |          ✅         |             ❌            |               ❌              |          ✅          |               ❌            | [`AMRCallback`](@ref)
 | Solver type                                                  |   [`DGSEM`](@ref)  |      [`DGSEM`](@ref)     |        [`DGSEM`](@ref)       |   [`DGSEM`](@ref)   |       [`DGMulti`](@ref)    |
-| Domain                                                       |      hypercube     |     mapped hypercube     |           arbitrary          |      arbitrary      |       arbitraryᵇ   |
+| Domain                                                       |      hypercube     |     mapped hypercube     |           arbitrary          |      arbitrary      |       arbitrary    |
 | Weak form                                                    |          ✅         |             ✅            |               ✅              |          ✅          |               ✅            | [`VolumeIntegralWeakForm`](@ref)
 | Flux differencing                                            |          ✅         |             ✅            |               ✅              |          ✅          |               ✅            | [`VolumeIntegralFluxDifferencing`](@ref)
 | Shock capturing                                              |          ✅         |             ✅            |               ✅              |          ✅          |               ❌            | [`VolumeIntegralShockCapturingHG`](@ref)
 | Nonconservative equations                                    |          ✅         |             ✅            |               ✅              |          ✅          |               ✅            | e.g., GLM MHD or shallow water equations
+| Parabolic termsᵇ                                             |          ✅         |             ✅            |               ❌              |          ✅          |               ✅            | e.g., [`CompressibleNavierStokesDiffusion2D`](@ref)
 
 ᵃ: quad = quadrilateral, hex = hexahedron
-ᵇ: curved meshes supported for `SBP` and `GaussSBP` approximation types for `VolumeIntegralFluxDifferencing` solvers on quadrilateral and hexahedral `DGMultiMesh`es (non-conservative terms not yet supported)
+ᵇ: Parabolic terms do not currently support adaptivity. 
 
 ## Time integration methods
 

diff --git a/src/equations/compressible_navier_stokes_1d.jl b/src/equations/compressible_navier_stokes_1d.jl
@@ -1,3 +1,10 @@
+# By default, Julia/LLVM does not use fused multiply-add operations (FMAs).
+# Since these FMAs can increase the performance of many numerical algorithms,
+# we need to opt-in explicitly.
+# See https://ranocha.de/blog/Optimizing_EC_Trixi for further details.
+@muladd begin
+#! format: noindent
+
 @doc raw"""
     CompressibleNavierStokesDiffusion1D(equations; mu, Pr,
                                         gradient_variables=GradientVariablesPrimitive())
@@ -77,7 +84,8 @@ w_2 = \frac{\rho v1}{p},\, w_3 = -\frac{\rho}{p}
     This code is experimental and may be changed or removed in any future release.
 """
 struct CompressibleNavierStokesDiffusion1D{GradientVariables, RealT <: Real,
-                                           E <: AbstractCompressibleEulerEquations{1}} <:
+                                           E <: AbstractCompressibleEulerEquations{1}
+                                           } <:
        AbstractCompressibleNavierStokesDiffusion{1, 3}
     # TODO: parabolic
     # 1) For now save gamma and inv(gamma-1) again, but could potentially reuse them from the Euler equations
@@ -109,7 +117,8 @@ function CompressibleNavierStokesDiffusion1D(equations::CompressibleEulerEquatio
     CompressibleNavierStokesDiffusion1D{typeof(gradient_variables), typeof(gamma),
                                         typeof(equations)}(gamma, inv_gamma_minus_one,
                                                            μ, Pr, kappa,
-                                                           equations, gradient_variables)
+                                                           equations,
+                                                           gradient_variables)
 end
 
 # TODO: parabolic
@@ -263,7 +272,8 @@ end
                                                                                       u_inner,
                                                                                       orientation::Integer,
                                                                                       direction,
-                                                                                      x, t,
+                                                                                      x,
+                                                                                      t,
                                                                                       operator_type::Gradient,
                                                                                       equations::CompressibleNavierStokesDiffusion1D{
                                                                                                                                      GradientVariablesPrimitive
@@ -278,7 +288,8 @@ end
                                                                                       u_inner,
                                                                                       orientation::Integer,
                                                                                       direction,
-                                                                                      x, t,
+                                                                                      x,
+                                                                                      t,
                                                                                       operator_type::Divergence,
                                                                                       equations::CompressibleNavierStokesDiffusion1D{
                                                                                                                                      GradientVariablesPrimitive
@@ -299,7 +310,8 @@ end
                                                                                        u_inner,
                                                                                        orientation::Integer,
                                                                                        direction,
-                                                                                       x, t,
+                                                                                       x,
+                                                                                       t,
                                                                                        operator_type::Gradient,
                                                                                        equations::CompressibleNavierStokesDiffusion1D{
                                                                                                                                       GradientVariablesPrimitive
@@ -316,7 +328,8 @@ end
                                                                                        u_inner,
                                                                                        orientation::Integer,
                                                                                        direction,
-                                                                                       x, t,
+                                                                                       x,
+                                                                                       t,
                                                                                        operator_type::Divergence,
                                                                                        equations::CompressibleNavierStokesDiffusion1D{
                                                                                                                                       GradientVariablesPrimitive
@@ -337,7 +350,8 @@ end
                                                                                       w_inner,
                                                                                       orientation::Integer,
                                                                                       direction,
-                                                                                      x, t,
+                                                                                      x,
+                                                                                      t,
                                                                                       operator_type::Gradient,
                                                                                       equations::CompressibleNavierStokesDiffusion1D{
                                                                                                                                      GradientVariablesEntropy
@@ -354,7 +368,8 @@ end
                                                                                       w_inner,
                                                                                       orientation::Integer,
                                                                                       direction,
-                                                                                      x, t,
+                                                                                      x,
+                                                                                      t,
                                                                                       operator_type::Divergence,
                                                                                       equations::CompressibleNavierStokesDiffusion1D{
                                                                                                                                      GradientVariablesEntropy
@@ -374,7 +389,8 @@ end
                                                                                        w_inner,
                                                                                        orientation::Integer,
                                                                                        direction,
-                                                                                       x, t,
+                                                                                       x,
+                                                                                       t,
                                                                                        operator_type::Gradient,
                                                                                        equations::CompressibleNavierStokesDiffusion1D{
                                                                                                                                       GradientVariablesEntropy
@@ -394,10 +410,12 @@ end
                                                                                        w_inner,
                                                                                        orientation::Integer,
                                                                                        direction,
-                                                                                       x, t,
+                                                                                       x,
+                                                                                       t,
                                                                                        operator_type::Divergence,
                                                                                        equations::CompressibleNavierStokesDiffusion1D{
                                                                                                                                       GradientVariablesEntropy
                                                                                                                                       })
     return SVector(flux_inner[1], flux_inner[2], flux_inner[3])
 end
+end # @muladd
diff --git a/src/meshes/tree_mesh.jl b/src/meshes/tree_mesh.jl
@@ -199,6 +199,7 @@ function Base.show(io::IO, ::MIME"text/plain",
             "length" => mesh.tree.length_level_0,
             "periodicity" => mesh.tree.periodicity,
             "current #cells" => mesh.tree.length,
+            "#leaf-cells" => count_leaf_cells(mesh.tree),
             "maximum #cells" => mesh.tree.capacity,
         ]
         summary_box(io, "TreeMesh{" * string(NDIMS) * ", " * string(TreeType) * "}",

diff --git a/src/solvers/dgsem_unstructured/dg_2d.jl b/src/solvers/dgsem_unstructured/dg_2d.jl
@@ -357,9 +357,9 @@ function calc_boundary_flux_by_type!(cache, t, BCs::Tuple{}, BC_indices::Tuple{}
     nothing
 end
 
-function calc_boundary_flux!(cache, t, boundary_condition, boundary_indexing,
+function calc_boundary_flux!(cache, t, boundary_condition::BC, boundary_indexing,
                              mesh::UnstructuredMesh2D, equations,
-                             surface_integral, dg::DG)
+                             surface_integral, dg::DG) where {BC}
     @unpack surface_flux_values = cache.elements
     @unpack element_id, element_side_id = cache.boundaries
 

diff --git a/test/Project.toml b/test/Project.toml
@@ -1,14 +1,5 @@
-[compat]
-BSON = "0.3.3"
-CairoMakie = "0.6, 0.7, 0.8, 0.9, 0.10"
-Flux = "0.13 - 0.13.12" # TODO: Return to "0.13" once https://github.com/FluxML/Flux.jl/issues/2204 is resolved
-ForwardDiff = "0.10"
-MPI = "0.20"
-OrdinaryDiffEq = "6.49.1"
-Plots = "1.16"
-StableRNGs = "1.0.0"
-
 [deps]
+Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"
 BSON = "fbb218c0-5317-5bc6-957e-2ee96dd4b1f0"
 CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
 Downloads = "f43a241f-c20a-4ad4-852c-f6b1247861c6"
@@ -23,6 +14,16 @@ Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 StableRNGs = "860ef19b-820b-49d6-a774-d7a799459cd3"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
+[compat]
+Aqua = "0.7"
+BSON = "0.3.3"
+CairoMakie = "0.6, 0.7, 0.8, 0.9, 0.10"
+Flux = "0.13.15, 0.14"
+ForwardDiff = "0.10"
+MPI = "0.20"
+OrdinaryDiffEq = "6.49.1"
+Plots = "1.16"
+
 [preferences.OrdinaryDiffEq]
 PrecompileAutoSpecialize = false
 PrecompileAutoSwitch = false

diff --git a/test/runtests.jl b/test/runtests.jl
@@ -109,6 +109,7 @@ const TRIXI_NTHREADS = clamp(Sys.CPU_THREADS, 2, 3)
 
     @time if TRIXI_TEST == "all" || TRIXI_TEST == "misc_part2"
         include("test_special_elixirs.jl")
+        include("test_aqua.jl")
     end
 
     @time if TRIXI_TEST == "all" || TRIXI_TEST == "performance_specializations_part1"
-Original file line number
+Diff line change
@@ Expand Up / @@ -15,7 +15,7 @@ jobs: @@
             arch:
               - x64
         steps:
-          - uses: actions/checkout@v3
+          - uses: actions/checkout@v4
             with:
               fetch-depth: 0
           - run: |
@@ Expand Down @@