Merge branch 'subcell-limiting' into subcell-limiting-renaming-MCL

bennibolm · Nov 14, 2023 · e470849 · e470849
2 parents d45bcbf + bc5d5e4
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diff --git a/.github/workflows/downstream.yml b/.github/workflows/downstream.yml
@@ -0,0 +1,94 @@
+# Note: this file is inspired by the downstream testing facilities in the SciML ecosystem
+# x-ref: https://github.com/SciML/SciMLBase.jl/blob/ffe68aebedee5915190623cb08160d7ef1fbcce0/.github/workflows/Downstream.yml
+
+name: Downstream
+on:
+  push:
+    branches:
+      - main
+    paths-ignore:
+      - 'AUTHORS.md'
+      - 'CITATION.bib'
+      - 'CONTRIBUTING.md'
+      - 'LICENSE.md'
+      - 'NEWS.md'
+      - 'README.md'
+      - '.zenodo.json'
+      - '.github/workflows/benchmark.yml'
+      - '.github/workflows/CompatHelper.yml'
+      - '.github/workflows/TagBot.yml'
+      - 'benchmark/**'
+      # - 'docs/**'
+      - 'utils/**'
+  pull_request:
+    paths-ignore:
+      - 'AUTHORS.md'
+      - 'CITATION.bib'
+      - 'CONTRIBUTING.md'
+      - 'LICENSE.md'
+      - 'NEWS.md'
+      - 'README.md'
+      - '.zenodo.json'
+      - '.github/workflows/benchmark.yml'
+      - '.github/workflows/CompatHelper.yml'
+      - '.github/workflows/TagBot.yml'
+      - 'benchmark/**'
+      # - 'docs/**'
+      - 'utils/**'
+  workflow_dispatch:
+
+# Cancel redundant CI tests automatically
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  test:
+    if: "!contains(github.event.head_commit.message, 'skip ci')"
+    # We could also include the Julia version as in
+    # name: ${{ matrix.trixi_test }} - ${{ matrix.os }} - Julia ${{ matrix.version }} - ${{ matrix.arch }} - ${{ github.event_name }}
+    # to be more specific. However, that requires us updating the required CI tests whenever we update Julia.
+    name: ${{ matrix.package }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        version:
+          - '1.9'
+        os:
+          - ubuntu-latest
+        arch:
+          - x64
+        package:
+          - Trixi2Vtk.jl
+          - TrixiShallowWater.jl
+    steps:
+      - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: ${{ matrix.version }}
+          arch: ${{ matrix.arch }}
+      - run: julia -e 'using InteractiveUtils; versioninfo(verbose=true)'
+      - uses: julia-actions/cache@v1
+      - uses: julia-actions/julia-buildpkg@v1
+      - name: Retrieve downstream package
+        # Note: we retrieve the current `main` branch of the downstream package to ensure
+        # that compatibility errors we make in Trixi.jl are detected already here
+        # See also https://github.com/trixi-framework/Trixi.jl/pull/1707#discussion_r1382938895
+        uses: actions/checkout@v4
+        with:
+          repository: trixi-framework/${{ matrix.package }}
+          path: downstream
+      - name: Load upstream package into downstream environment
+        shell: julia --color=yes --project=downstream {0}
+        run: |
+          using Pkg
+          Pkg.develop(PackageSpec(path="."))
+          Pkg.update()
+      - name: Run downstream tests (without coverage)
+        shell: julia --color=yes --project=downstream {0}
+        run: |
+          using Pkg
+          Pkg.test(coverage=false)
+        env:
+          TRIXI_TEST: upstream
diff --git a/NEWS.md b/NEWS.md
@@ -4,6 +4,30 @@ Trixi.jl follows the interpretation of [semantic versioning (semver)](https://ju
 used in the Julia ecosystem. Notable changes will be documented in this file
 for human readability.
 
+## Changes when updating to v0.6 from v0.5.x
+
+#### Added
+
+#### Changed
+
+- The wave speed estimates for `flux_hll`, `FluxHLL()` are now consistent across equations.
+  In particular, the functions `min_max_speed_naive`, `min_max_speed_einfeldt` are now 
+  conceptually identical across equations.
+  Users, who have been using `flux_hll` for MHD have now to use `flux_hlle` in order to use the
+  Einfeldt wave speed estimate.
+- Parabolic diffusion terms are now officially supported and not marked as experimental
+  anymore.
+
+#### Deprecated
+
+#### Removed
+
+- The neural network-based shock indicators have been migrated to a new repository
+  [TrixiSmartShockFinder.jl](https://github.com/trixi-framework/TrixiSmartShockFinder.jl).
+  To continue using the indicators, you will need to use both Trixi.jl and
+  TrixiSmartShockFinder.jl, as explained in the latter packages' `README.md`.
+
+
 ## Changes in the v0.5 lifecycle
 
 #### Added
@@ -13,8 +37,11 @@ for human readability.
 - 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`
+- Implementation of the quasi-1D shallow water equations
+- Subcell (positivity and local min/max) limiting support for conservative variables
+  in 2D for `TreeMesh`
 - AMR for hyperbolic-parabolic equations on 2D/3D `TreeMesh`
+- Added `GradientVariables` type parameter to `AbstractEquationsParabolic`
 
 #### Changed
 
@@ -31,6 +58,9 @@ for human readability.
 
 #### Removed
 
+- Migrate neural network-based shock indicators to a new repository
+  [TrixiSmartShockFinder.jl](https://github.com/trixi-framework/TrixiSmartShockFinder.jl).
+
 
 ## Changes when updating to v0.5 from v0.4.x
 

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 = "0.5.48-pre"
+version = "0.6.1-pre"
 
 [deps]
 CodeTracking = "da1fd8a2-8d9e-5ec2-8556-3022fb5608a2"
@@ -58,6 +58,7 @@ FillArrays = "0.13.2, 1"
 ForwardDiff = "0.10.18"
 HDF5 = "0.14, 0.15, 0.16, 0.17"
 IfElse = "0.1"
+LinearAlgebra = "1"
 LinearMaps = "2.7, 3.0"
 LoopVectorization = "0.12.118"
 MPI = "0.20"
@@ -68,12 +69,14 @@ OffsetArrays = "1.3"
 P4est = "0.4"
 Polyester = "0.7.5"
 PrecompileTools = "1.1"
+Printf = "1"
 RecipesBase = "1.1"
 Reexport = "1.0"
 Requires = "1.1"
 SciMLBase = "1.90, 2"
 Setfield = "0.8, 1"
 SimpleUnPack = "1.1"
+SparseArrays = "1"
 StartUpDG = "0.17"
 Static = "0.3, 0.4, 0.5, 0.6, 0.7, 0.8"
 StaticArrayInterface = "1.4"

diff --git a/README.md b/README.md
@@ -18,7 +18,7 @@
   <img width="300px" src="https://trixi-framework.github.io/assets/logo.png">
 </p>
 
-**Trixi.jl** is a numerical simulation framework for hyperbolic conservation
+**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
 having an extensible design with a fast implementation, Trixi.jl is
@@ -46,6 +46,7 @@ installation and postprocessing procedures. Its features include:
 * Periodic and weakly-enforced boundary conditions
 * Multiple governing equations:
   * Compressible Euler equations
+  * Compressible Navier-Stokes equations
   * Magnetohydrodynamics (MHD) equations
   * Multi-component compressible Euler and MHD equations
   * Linearized Euler and acoustic perturbation equations
@@ -56,6 +57,7 @@ installation and postprocessing procedures. Its features include:
 * Multi-physics simulations
   * [Self-gravitating gas dynamics](https://github.com/trixi-framework/paper-self-gravitating-gas-dynamics)
 * Shared-memory parallelization via multithreading
+* Multi-node parallelization via MPI
 * Visualization and postprocessing of the results
   * In-situ and a posteriori visualization with [Plots.jl](https://github.com/JuliaPlots/Plots.jl)
   * Interactive visualization with [Makie.jl](https://makie.juliaplots.org/)

diff --git a/benchmark/Project.toml b/benchmark/Project.toml
@@ -8,4 +8,4 @@ Trixi = "a7f1ee26-1774-49b1-8366-f1abc58fbfcb"
 BenchmarkTools = "0.5, 0.7, 1.0"
 OrdinaryDiffEq = "5.65, 6"
 PkgBenchmark = "0.2.10"
-Trixi = "0.4, 0.5"
+Trixi = "0.4, 0.5, 0.6"
diff --git a/docs/Project.toml b/docs/Project.toml
@@ -21,4 +21,5 @@ Literate = "2.9"
 Measurements = "2.5"
 OrdinaryDiffEq = "6.49.1"
 Plots = "1.9"
+Test = "1"
 Trixi2Vtk = "0.3"
diff --git a/docs/literate/src/files/DGMulti_1.jl b/docs/literate/src/files/DGMulti_1.jl
@@ -168,7 +168,7 @@ meshIO = StartUpDG.triangulate_domain(StartUpDG.RectangularDomainWithHole());
 
 # The pre-defined Triangulate geometry in StartUpDG has integer boundary tags. With [`DGMultiMesh`](@ref)
 # we assign boundary faces based on these integer boundary tags and create a mesh compatible with Trixi.jl.
-mesh = DGMultiMesh(meshIO, dg, Dict(:outer_boundary=>1, :inner_boundary=>2))
+mesh = DGMultiMesh(dg, meshIO, Dict(:outer_boundary=>1, :inner_boundary=>2))
 #-
 boundary_condition_convergence_test = BoundaryConditionDirichlet(initial_condition)
 boundary_conditions = (; :outer_boundary => boundary_condition_convergence_test,

diff --git a/docs/literate/src/files/adding_new_parabolic_terms.jl b/docs/literate/src/files/adding_new_parabolic_terms.jl
@@ -18,8 +18,15 @@ equations_hyperbolic = LinearScalarAdvectionEquation2D(advection_velocity);
 # `ConstantAnisotropicDiffusion2D` has a field for `equations_hyperbolic`. It is useful to have
 # information about the hyperbolic system available to the parabolic part so that we can reuse
 # functions defined for hyperbolic equations (such as `varnames`).
-
-struct ConstantAnisotropicDiffusion2D{E, T} <: Trixi.AbstractEquationsParabolic{2, 1}
+#
+# The abstract type `Trixi.AbstractEquationsParabolic` has three parameters: `NDIMS` (the spatial dimension,
+# e.g., 1D, 2D, or 3D), `NVARS` (the number of variables), and `GradientVariable`, which we set as
+# `GradientVariablesConservative`. This indicates that the gradient should be taken with respect to the
+# conservative variables (e.g., the same variables used in `equations_hyperbolic`). Users can also take
+# the gradient with respect to a different set of variables; see, for example, the implementation of
+# [`CompressibleNavierStokesDiffusion2D`](@ref), which can utilize either "primitive" or "entropy" variables.
+
+struct ConstantAnisotropicDiffusion2D{E, T} <: Trixi.AbstractEquationsParabolic{2, 1, GradientVariablesConservative}
   diffusivity::T
   equations_hyperbolic::E
 end

diff --git a/docs/src/index.md b/docs/src/index.md
@@ -12,7 +12,7 @@
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3996439.svg)](https://doi.org/10.5281/zenodo.3996439)
 
 [**Trixi.jl**](https://github.com/trixi-framework/Trixi.jl)
-is a numerical simulation framework for hyperbolic conservation
+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
 having an extensible design with a fast implementation, Trixi.jl is
@@ -40,6 +40,7 @@ installation and postprocessing procedures. Its features include:
 * Periodic and weakly-enforced boundary conditions
 * Multiple governing equations:
   * Compressible Euler equations
+  * Compressible Navier-Stokes equations
   * Magnetohydrodynamics (MHD) equations
   * Multi-component compressible Euler and MHD equations
   * Linearized Euler and acoustic perturbation equations
@@ -50,6 +51,7 @@ installation and postprocessing procedures. Its features include:
 * Multi-physics simulations
   * [Self-gravitating gas dynamics](https://github.com/trixi-framework/paper-self-gravitating-gas-dynamics)
 * Shared-memory parallelization via multithreading
+* Multi-node parallelization via MPI
 * Visualization and postprocessing of the results
   * In-situ and a posteriori visualization with [Plots.jl](https://github.com/JuliaPlots/Plots.jl)
   * Interactive visualization with [Makie.jl](https://makie.juliaplots.org/)

diff --git a/docs/src/overview.md b/docs/src/overview.md
@@ -60,10 +60,9 @@ different features on different mesh types.
 | Flux differencing                                            |          ✅         |             ✅            |               ✅              |          ✅          |               ✅            | [`VolumeIntegralFluxDifferencing`](@ref)
 | Shock capturing                                              |          ✅         |             ✅            |               ✅              |          ✅          |               ❌            | [`VolumeIntegralShockCapturingHG`](@ref)
 | Nonconservative equations                                    |          ✅         |             ✅            |               ✅              |          ✅          |               ✅            | e.g., GLM MHD or shallow water equations
-| Parabolic termsᵇ                                             |          ✅         |             ✅            |               ❌              |          ✅          |               ✅            | e.g., [`CompressibleNavierStokesDiffusion2D`](@ref)
+| Parabolic terms                                              |          ✅         |             ✅            |               ❌              |          ✅          |               ✅            | e.g., [`CompressibleNavierStokesDiffusion2D`](@ref)
 
 ᵃ: quad = quadrilateral, hex = hexahedron
-ᵇ: Parabolic terms do not currently support adaptivity. 
 
 ## Time integration methods
 

diff --git a/examples/p4est_2d_dgsem/elixir_mhd_alfven_wave.jl b/examples/p4est_2d_dgsem/elixir_mhd_alfven_wave.jl
@@ -12,7 +12,9 @@ initial_condition = initial_condition_convergence_test
 
 # Get the DG approximation space
 volume_flux = (flux_central, flux_nonconservative_powell)
-solver = DGSEM(polydeg = 4, surface_flux = (flux_hll, flux_nonconservative_powell),
+solver = DGSEM(polydeg = 4,
+               surface_flux = (flux_hlle,
+                               flux_nonconservative_powell),
                volume_integral = VolumeIntegralFluxDifferencing(volume_flux))
 
 coordinates_min = (0.0, 0.0)

diff --git a/examples/p4est_2d_dgsem/elixir_navierstokes_convergence.jl b/examples/p4est_2d_dgsem/elixir_navierstokes_convergence.jl
@@ -161,6 +161,7 @@ end
            v1_yy * v1 * mu_ -
            v2_xy * v1 * mu_ -
            v1_y * v1_y * mu_ -
+           v2_x * v1_y * mu_ -
            4.0 / 3.0 * v2_yy * v2 * mu_ +
            2.0 / 3.0 * v1_xy * v2 * mu_ -
            4.0 / 3.0 * v2_y * v2_y * mu_ +

diff --git a/examples/p4est_3d_dgsem/elixir_mhd_alfven_wave_nonconforming.jl b/examples/p4est_3d_dgsem/elixir_mhd_alfven_wave_nonconforming.jl
@@ -10,7 +10,9 @@ equations = IdealGlmMhdEquations3D(5 / 3)
 initial_condition = initial_condition_convergence_test
 
 volume_flux = (flux_hindenlang_gassner, flux_nonconservative_powell)
-solver = DGSEM(polydeg = 3, surface_flux = (flux_hll, flux_nonconservative_powell),
+solver = DGSEM(polydeg = 3,
+               surface_flux = (flux_hlle,
+                               flux_nonconservative_powell),
                volume_integral = VolumeIntegralFluxDifferencing(volume_flux))
 
 coordinates_min = (-1.0, -1.0, -1.0)

diff --git a/examples/structured_2d_dgsem/elixir_euler_convergence_wavingflag_IDP.jl b/examples/structured_2d_dgsem/elixir_euler_convergence_wavingflag_IDP.jl
@@ -14,8 +14,8 @@ volume_flux = flux_ranocha
 polydeg = 3
 basis = LobattoLegendreBasis(polydeg)
 limiter_idp = SubcellLimiterIDP(equations, basis;
-                                positivity_variables_cons = [1],
-                                positivity_variables_nonlinear = (pressure,),
+                                positivity_variables_cons = ["rho"],
+                                positivity_variables_nonlinear = [pressure],
                                 positivity_correction_factor = 0.1,
                                 spec_entropy = false,
                                 max_iterations_newton = 10,

diff --git a/examples/structured_2d_dgsem/elixir_euler_double_mach.jl b/examples/structured_2d_dgsem/elixir_euler_double_mach.jl
@@ -22,7 +22,7 @@ polydeg = 4
 basis = LobattoLegendreBasis(polydeg)
 
 limiter_idp = SubcellLimiterIDP(equations, basis;
-                                local_minmax_variables_cons = [1],
+                                local_minmax_variables_cons = ["rho"],
                                 spec_entropy = true,
                                 positivity_correction_factor = 0.1,
                                 max_iterations_newton = 100,

diff --git a/examples/structured_2d_dgsem/elixir_euler_free_stream_sc_subcell.jl b/examples/structured_2d_dgsem/elixir_euler_free_stream_sc_subcell.jl
@@ -14,8 +14,8 @@ volume_flux = flux_ranocha
 polydeg = 3
 basis = LobattoLegendreBasis(polydeg)
 limiter_idp = SubcellLimiterIDP(equations, basis;
-                                positivity_variables_cons = [1],
-                                positivity_variables_nonlinear = (pressure,),
+                                positivity_variables_cons = ["rho"],
+                                positivity_variables_nonlinear = [pressure],
                                 positivity_correction_factor = 0.1,
                                 spec_entropy = false,
                                 smoothness_indicator = false,

diff --git a/examples/structured_2d_dgsem/elixir_euler_shock_upstream_sc_subcell.jl b/examples/structured_2d_dgsem/elixir_euler_shock_upstream_sc_subcell.jl
@@ -37,7 +37,7 @@ polydeg = 5
 basis = LobattoLegendreBasis(polydeg)
 
 limiter_idp = SubcellLimiterIDP(equations, basis;
-                                local_minmax_variables_cons = [1],
+                                local_minmax_variables_cons = ["rho"],
                                 spec_entropy = true,
                                 max_iterations_newton = 100,
                                 bar_states = true)

diff --git a/examples/structured_2d_dgsem/elixir_euler_source_terms_sc_subcell.jl b/examples/structured_2d_dgsem/elixir_euler_source_terms_sc_subcell.jl
@@ -16,7 +16,7 @@ volume_flux = flux_ranocha
 polydeg = 3
 basis = LobattoLegendreBasis(polydeg)
 limiter_idp = SubcellLimiterIDP(equations, basis;
-                                local_minmax_variables_cons = [1],
+                                local_minmax_variables_cons = ["rho"],
                                 spec_entropy = true,
                                 bar_states = false)
 volume_integral = VolumeIntegralSubcellLimiting(limiter_idp;

diff --git a/examples/structured_3d_dgsem/elixir_mhd_alfven_wave.jl b/examples/structured_3d_dgsem/elixir_mhd_alfven_wave.jl
@@ -10,7 +10,9 @@ equations = IdealGlmMhdEquations3D(5 / 3)
 initial_condition = initial_condition_convergence_test
 
 volume_flux = (flux_central, flux_nonconservative_powell)
-solver = DGSEM(polydeg = 5, surface_flux = (flux_hll, flux_nonconservative_powell),
+solver = DGSEM(polydeg = 5,
+               surface_flux = (flux_hlle,
+                               flux_nonconservative_powell),
                volume_integral = VolumeIntegralFluxDifferencing(volume_flux))
 
 # Create the mesh

diff --git a/examples/t8code_2d_dgsem/elixir_mhd_alfven_wave.jl b/examples/t8code_2d_dgsem/elixir_mhd_alfven_wave.jl
@@ -11,7 +11,7 @@ initial_condition = initial_condition_convergence_test
 
 # Get the DG approximation space
 volume_flux = (flux_central, flux_nonconservative_powell)
-solver = DGSEM(polydeg = 4, surface_flux = (flux_hll, flux_nonconservative_powell),
+solver = DGSEM(polydeg = 4, surface_flux = (flux_hlle, flux_nonconservative_powell),
                volume_integral = VolumeIntegralFluxDifferencing(volume_flux))
 
 coordinates_min = (0.0, 0.0)