Merge branch 'main' into Maxwell1D

.github/workflows/SpellCheck.yml

@@ -10,4 +10,4 @@ jobs:
       - name: Checkout Actions Repository
         uses: actions/checkout@v4
       - name: Check spelling
-        uses: crate-ci/typos@v1.21.0
+        uses: crate-ci/typos@v1.22.9

AUTHORS.md

@@ -38,6 +38,7 @@ are listed in alphabetical order:
 * Julia Odenthal
 * Sigrun Ortleb
 * Hendrik Ranocha
+* Warisa Roongaraya
 * Andrés M. Rueda-Ramírez
 * Felipe Santillan
 * Michael Schlottke-Lakemper

NEWS.md

@@ -4,6 +4,20 @@ 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 v0.8 from v0.7.x
+
+#### Added
+
+#### Changed
+
+- The specification of boundary names on which `AnalysisSurfaceIntegral`s are computed (such as drag and lift coefficients) has changed from `Symbol` and `Vector{Symbol}` to `NTuple{Symbol}`.
+  Thus, for one boundary the syntax changes from `:boundary` to `(:boundary,)` and for `Vector`s `[:boundary1, :boundary2]` to `(:boundary1, :boundary2)` ([#1959]).
+- The names of output files like the one created from the `SaveSolutionCallback` have changed from `%06d` to `%09d` to allow longer-running simulations ([#1996]).
+
+#### Deprecated
+
+#### Removed
+
 ## Changes in the v0.7 lifecycle
 
 #### Added

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 = "0.7.16-pre"
+version = "0.8.2-DEV"
 
 [deps]
 CodeTracking = "da1fd8a2-8d9e-5ec2-8556-3022fb5608a2"

docs/Project.toml

@@ -25,5 +25,5 @@ Measurements = "2.5"
 OrdinaryDiffEq = "6.49.1"
 Plots = "1.9"
 Test = "1"
-Trixi2Vtk = "0.3"
+Trixi2Vtk = "0.3.16"
 TrixiBase = "0.1.1"

docs/literate/src/files/first_steps/create_first_setup.jl

@@ -260,28 +260,28 @@ plot!(getmesh(pd))
 # import Pkg
 # Pkg.add(["Trixi2Vtk"])
 # ```
-# Now we load the Trixi2Vtk.jl package and convert the file `out/solution_000032.h5` with
+# Now we load the Trixi2Vtk.jl package and convert the file `out/solution_000000032.h5` with
 # the final solution using the [`trixi2vtk`](@ref) function saving the resulting file in the
 # `out` folder.
 
 using Trixi2Vtk
-trixi2vtk(joinpath("out", "solution_000032.h5"), output_directory="out")
+trixi2vtk(joinpath("out", "solution_000000032.h5"), output_directory="out")
 
-# Now two files `solution_000032.vtu` and `solution_000032_celldata.vtu` have been generated in the
+# Now two files `solution_000000032.vtu` and `solution_000000032_celldata.vtu` have been generated in the
 # `out` folder. The first one contains all the information for visualizing the solution, the
 # second one contains all the cell-based or discretization-based information.
 
 # Now let's visualize the solution from the generated files in ParaView. Follow this short
 # instruction to get the visualization.
 # - Download, install and open [ParaView](https://www.paraview.org/download/).
-# - Press `Ctrl+O` and select the generated files `solution_000032.vtu` and
-#   `solution_000032_celldata.vtu` from the `out` folder.
+# - Press `Ctrl+O` and select the generated files `solution_000000032.vtu` and
+#   `solution_000000032_celldata.vtu` from the `out` folder.
 # - In the upper-left corner in the Pipeline Browser window, left-click on the eye-icon near
-#   `solution_000032.vtu`.
+#   `solution_000000032.vtu`.
 # - In the lower-left corner in the Properties window, change the Coloring from Solid Color to
 #   scalar. This already generates the visualization of the final solution.
 # - Now let's add the mesh to the visualization. In the upper-left corner in the
-#   Pipeline Browser window, left-click on the eye-icon near `solution_000032_celldata.vtu`.
+#   Pipeline Browser window, left-click on the eye-icon near `solution_000000032_celldata.vtu`.
 # - In the lower-left corner in the Properties window, change the Representation from Surface
 #   to Wireframe. Then a white grid should appear on the visualization.
 # Now, if you followed the instructions exactly, you should get a similar image as shown in the

docs/literate/src/files/hohqmesh_tutorial.jl

@@ -54,7 +54,7 @@ end #hide #md
 
 using Trixi2Vtk
 redirect_stdio(stdout=devnull, stderr=devnull) do # code that prints annoying stuff we don't want to see here #hide #md
-trixi2vtk("out/solution_000180.h5", output_directory="out")
+trixi2vtk("out/solution_000000180.h5", output_directory="out")
 end #hide #md
 
 # Note this step takes about 15-30 seconds as the package `Trixi2Vtk` must be precompiled and executed for the first time
@@ -64,7 +64,7 @@ end #hide #md
 # visualization nodes. For instance, if we want to use 12 uniformly spaced nodes for visualization we can execute
 
 redirect_stdio(stdout=devnull, stderr=devnull) do # code that prints annoying stuff we don't want to see here #hide #md
-trixi2vtk("out/solution_000180.h5", output_directory="out", nvisnodes=12)
+trixi2vtk("out/solution_000000180.h5", output_directory="out", nvisnodes=12)
 end #hide #md
 
 # By default `trixi2vtk` sets `nvisnodes` to be the same as the number of nodes specified in

docs/make.jl

@@ -102,11 +102,21 @@ tutorials = create_tutorials(files)
 
 # Create changelog
 Changelog.generate(
-    Changelog.Documenter(),                    # output type
-    joinpath(@__DIR__, "..", "NEWS.md"),       # input file
-    joinpath(@__DIR__, "src", "changelog.md"); # output file
-    repo = "trixi-framework/Trixi.jl",         # default repository for links
+    Changelog.Documenter(),                        # output type
+    joinpath(@__DIR__, "..", "NEWS.md"),           # input file
+    joinpath(@__DIR__, "src", "changelog_tmp.md"); # output file
+    repo = "trixi-framework/Trixi.jl",             # default repository for links
+    branch = "main",                               # default branch for links
 )
+# Fix edit URL of changelog
+open(joinpath(@__DIR__, "src", "changelog.md"), "w") do io
+    for line in eachline(joinpath(@__DIR__, "src", "changelog_tmp.md"))
+        if startswith(line, "EditURL")
+            line = "EditURL = \"https://github.com/trixi-framework/Trixi.jl/blob/main/NEWS.md\""
+        end
+        println(io, line)
+    end
+end
 
 # Make documentation
 makedocs(

docs/src/restart.md

@@ -30,7 +30,7 @@ conditionals like `if restart` with a boolean variable `restart` that is user de
 
 First we need to define from which file we want to restart, e.g.
 ```julia
-restart_file = "restart_000021.h5"
+restart_file = "restart_000000021.h5"
 restart_filename = joinpath("out", restart_file)
 ```
 

docs/src/visualization.md

@@ -415,15 +415,15 @@ julia> using Trixi2Vtk
 ```
 To process an HDF5 file generated by Trixi.jl, execute
 ```julia
-julia> trixi2vtk(joinpath("out", "solution_000000.h5"), output_directory="out")
+julia> trixi2vtk(joinpath("out", "solution_000000000.h5"), output_directory="out")
 ```
 This will create two unstructured VTK files in the `out` subdirectory that can
-be opened with ParaView or VisIt: `solution_000000.vtu` contains the
-discontinuous Galerkin solution data while `solution_000000_celldata.vtu` holds
+be opened with ParaView or VisIt: `solution_000000000.vtu` contains the
+discontinuous Galerkin solution data while `solution_000000000_celldata.vtu` holds
 any cell-based values such as the current AMR indicator or the cell refinement
 level.
 
-!["solution_000000_scalar_mesh"](https://github.com/trixi-framework/Trixi2Vtk.jl/raw/main/docs/src/assets/solution_000000_scalar_mesh.png)
+!["solution_000000000_scalar_mesh"](https://github.com/trixi-framework/Trixi2Vtk.jl/raw/main/docs/src/assets/solution_000000_scalar_mesh.png)
 
 This allows you to generate VTK files for solution, restart and mesh files. By
 default, Trixi2Vtk generates `.vtu` (unstructured VTK) files for both
@@ -440,7 +440,7 @@ publication-quality images, but increases the file size.
 If you want to convert multiple solution/restart files at once, you can just supply
 multiple input files as the positional arguments to `trixi2vtk`, e.g.,
 ```julia
-julia> trixi2vtk("out/solution_000000.h5", "out/solution_000040.h5")
+julia> trixi2vtk("out/solution_000000000.h5", "out/solution_000000040.h5")
 ```
 You may also use file globbing to select a range of files based on filename patterns, e.g.,
 ```julia
@@ -450,7 +450,7 @@ to convert all solution files in the `out/` directory or
 ```julia
 julia> trixi2vtk("out/restart_00[0-9]000.h5")
 ```
-to convert every one-thousandth restart file (`out/restart_000000.h5`,
+to convert every one-thousandth restart file (`out/restart_000000000.h5`,
 `out/restart_001000.h5` etc.).
 
 When multiple solution/restart files are provided, Trixi2Vtk will also generate a

examples/p4est_2d_dgsem/elixir_advection_restart.jl

@@ -6,7 +6,7 @@ using Trixi
 # create a restart file
 
 elixir_file = "elixir_advection_extended.jl"
-restart_file = "restart_000021.h5"
+restart_file = "restart_000000021.h5"
 
 trixi_include(@__MODULE__, joinpath(@__DIR__, elixir_file))
 

examples/p4est_2d_dgsem/elixir_advection_restart_amr.jl

@@ -6,7 +6,7 @@ using Trixi
 # create a restart file
 
 elixir_file = "elixir_advection_extended.jl"
-restart_file = "restart_000021.h5"
+restart_file = "restart_000000021.h5"
 
 trixi_include(@__MODULE__, joinpath(@__DIR__, elixir_file))
 

examples/p4est_2d_dgsem/elixir_euler_NACA0012airfoil_mach085.jl

@@ -84,7 +84,7 @@ analysis_interval = 2000
 
 l_inf = 1.0 # Length of airfoil
 
-force_boundary_names = [:AirfoilBottom, :AirfoilTop]
+force_boundary_names = (:AirfoilBottom, :AirfoilTop)
 drag_coefficient = AnalysisSurfaceIntegral(semi, force_boundary_names,
                                            DragCoefficientPressure(aoa(), rho_inf(),
                                                                    u_inf(equations), l_inf))

examples/p4est_2d_dgsem/elixir_euler_subsonic_cylinder.jl

@@ -89,11 +89,11 @@ rho_inf = 1.4
 u_inf = 0.38
 l_inf = 1.0 # Diameter of circle
 
-drag_coefficient = AnalysisSurfaceIntegral(semi, :x_neg,
+drag_coefficient = AnalysisSurfaceIntegral(semi, (:x_neg,),
                                            DragCoefficientPressure(aoa, rho_inf, u_inf,
                                                                    l_inf))
 
-lift_coefficient = AnalysisSurfaceIntegral(semi, :x_neg,
+lift_coefficient = AnalysisSurfaceIntegral(semi, (:x_neg,),
                                            LiftCoefficientPressure(aoa, rho_inf, u_inf,
                                                                    l_inf))
 

examples/p4est_2d_dgsem/elixir_navierstokes_NACA0012airfoil_mach08.jl

@@ -119,7 +119,7 @@ summary_callback = SummaryCallback()
 
 analysis_interval = 2000
 
-force_boundary_names = [:AirfoilBottom, :AirfoilTop]
+force_boundary_names = (:AirfoilBottom, :AirfoilTop)
 drag_coefficient = AnalysisSurfaceIntegral(semi, force_boundary_names,
                                            DragCoefficientPressure(aoa(), rho_inf(),
                                                                    u_inf(equations),

examples/p4est_3d_dgsem/elixir_advection_restart.jl

@@ -14,7 +14,7 @@ trixi_include(@__MODULE__, joinpath(@__DIR__, "elixir_advection_basic.jl"),
 # Note: If you get a restart file from somewhere else, you need to provide
 # appropriate setups in the elixir loading a restart file
 
-restart_filename = joinpath("out", "restart_000010.h5")
+restart_filename = joinpath("out", "restart_000000010.h5")
 mesh = load_mesh(restart_filename)
 
 semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition_convergence_test,

examples/structured_2d_dgsem/elixir_advection_restart.jl

@@ -6,7 +6,7 @@ using Trixi
 # create a restart file
 
 elixir_file = "elixir_advection_extended.jl"
-restart_file = "restart_000021.h5"
+restart_file = "restart_000000021.h5"
 
 trixi_include(@__MODULE__, joinpath(@__DIR__, elixir_file))
 

examples/structured_3d_dgsem/elixir_advection_restart.jl

@@ -14,7 +14,7 @@ trixi_include(@__MODULE__, joinpath(@__DIR__, "elixir_advection_basic.jl"),
 # Note: If you get a restart file from somewhere else, you need to provide
 # appropriate setups in the elixir loading a restart file
 
-restart_filename = joinpath("out", "restart_000010.h5")
+restart_filename = joinpath("out", "restart_000000010.h5")
 mesh = load_mesh(restart_filename)
 
 semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition_convergence_test,

examples/tree_2d_dgsem/elixir_advection_restart.jl

@@ -15,7 +15,7 @@ trixi_include(@__MODULE__, joinpath(@__DIR__, "elixir_advection_extended.jl"), a
 # Note: If you get a restart file from somewhere else, you need to provide
 # appropriate setups in the elixir loading a restart file
 
-restart_filename = joinpath("out", "restart_000040.h5")
+restart_filename = joinpath("out", "restart_000000040.h5")
 mesh = load_mesh(restart_filename)
 
 semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition, solver)

examples/tree_2d_dgsem/elixir_advection_restart_amr.jl

@@ -15,7 +15,7 @@ trixi_include(@__MODULE__, joinpath(@__DIR__, "elixir_advection_extended.jl"), a
 # Note: If you get a restart file from somewhere else, you need to provide
 # appropriate setups in the elixir loading a restart file
 
-restart_filename = joinpath("out", "restart_000040.h5")
+restart_filename = joinpath("out", "restart_000000040.h5")
 mesh = load_mesh(restart_filename)
 
 semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition, solver)

examples/tree_3d_dgsem/elixir_advection_restart.jl

@@ -13,7 +13,7 @@ trixi_include(@__MODULE__, joinpath(@__DIR__, "elixir_advection_extended.jl"))
 # Note: If you get a restart file from somewhere else, you need to provide
 # appropriate setups in the elixir loading a restart file
 
-restart_filename = joinpath("out", "restart_000019.h5")
+restart_filename = joinpath("out", "restart_000000019.h5")
 mesh = load_mesh(restart_filename)
 
 semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition, solver)

examples/unstructured_2d_dgsem/elixir_euler_restart.jl

@@ -13,7 +13,7 @@ trixi_include(@__MODULE__, joinpath(@__DIR__, "elixir_euler_basic.jl"))
 # Note: If you get a restart file from somewhere else, you need to provide
 # appropriate setups in the elixir loading a restart file
 
-restart_filename = joinpath("out", "restart_000050.h5")
+restart_filename = joinpath("out", "restart_000000050.h5")
 mesh = load_mesh(restart_filename)
 
 semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition, solver,

src/callbacks_step/analysis.jl

@@ -657,6 +657,15 @@ include("analysis_dg2d_parallel.jl")
 include("analysis_dg3d.jl")
 include("analysis_dg3d_parallel.jl")
 
+# This version of `analyze` is used for [`AnalysisSurfaceIntegral`](@ref) which requires
+# `semi` to be passed along to retrieve the current boundary indices, which are non-static 
+# in the case of AMR.
+function analyze(quantity::AnalysisSurfaceIntegral, du, u, t,
+                 semi::AbstractSemidiscretization)
+    mesh, equations, solver, cache = mesh_equations_solver_cache(semi)
+    analyze(quantity, du, u, t, mesh, equations, solver, cache, semi)
+end
+
 # Special analyze for `SemidiscretizationHyperbolicParabolic` such that
 # precomputed gradients are available. Required for `enstrophy` (see above) and viscous forces.
 # Note that this needs to be included after `analysis_surface_integral_2d.jl` to
@@ -669,6 +678,6 @@ function analyze(quantity::AnalysisSurfaceIntegral{Variable},
     mesh, equations, solver, cache = mesh_equations_solver_cache(semi)
     equations_parabolic = semi.equations_parabolic
     cache_parabolic = semi.cache_parabolic
-    analyze(quantity, du, u, t, mesh, equations, equations_parabolic, solver, cache,
+    analyze(quantity, du, u, t, mesh, equations, equations_parabolic, solver, cache, semi,
             cache_parabolic)
 end

src/callbacks_step/analysis_surface_integral_2d.jl

@@ -21,30 +21,18 @@ drag coefficient [`DragCoefficientPressure`](@ref) of e.g. an airfoil with the b
 name `:Airfoil` in 2D.
 
 - `semi::Semidiscretization`: Passed in to retrieve boundary condition information
-- `boundary_symbol_or_boundary_symbols::Symbol|Vector{Symbol}`: Name(s) of the boundary/boundaries
+- `boundary_symbols::NTuple{NBoundaries, Symbol}`: Name(s) of the boundary/boundaries
   where the quantity of interest is computed
 - `variable::Variable`: Quantity of interest, like lift or drag
 """
-struct AnalysisSurfaceIntegral{Variable}
-    indices::Vector{Int} # Indices in `boundary_condition_indices` where quantity of interest is computed
+struct AnalysisSurfaceIntegral{Variable, NBoundaries}
     variable::Variable # Quantity of interest, like lift or drag
+    boundary_symbols::NTuple{NBoundaries, Symbol} # Name(s) of the boundary/boundaries
 
-    function AnalysisSurfaceIntegral(semi, boundary_symbol, variable)
-        @unpack boundary_symbol_indices = semi.boundary_conditions
-        indices = boundary_symbol_indices[boundary_symbol]
-
-        return new{typeof(variable)}(indices, variable)
-    end
-
-    function AnalysisSurfaceIntegral(semi, boundary_symbols::Vector{Symbol}, variable)
-        @unpack boundary_symbol_indices = semi.boundary_conditions
-        indices = Vector{Int}()
-        for name in boundary_symbols
-            append!(indices, boundary_symbol_indices[name])
-        end
-        sort!(indices)
-
-        return new{typeof(variable)}(indices, variable)
+    function AnalysisSurfaceIntegral(semi,
+                                     boundary_symbols::NTuple{NBoundaries, Symbol},
+                                     variable) where {NBoundaries}
+        return new{typeof(variable), NBoundaries}(variable, boundary_symbols)
     end
 end
 
@@ -255,14 +243,26 @@ function (drag_coefficient::DragCoefficientShearStress)(u, normal_direction, x,
            (0.5 * rhoinf * uinf^2 * linf)
 end
 
+function get_boundary_indices(boundary_symbols, boundary_symbol_indices)
+    indices = Int[]
+    for name in boundary_symbols
+        append!(indices, boundary_symbol_indices[name])
+    end
+    sort!(indices) # Try to achieve some data locality by sorting
+
+    return indices
+end
+
 function analyze(surface_variable::AnalysisSurfaceIntegral, du, u, t,
                  mesh::P4estMesh{2},
-                 equations, dg::DGSEM, cache)
+                 equations, dg::DGSEM, cache, semi)
     @unpack boundaries = cache
     @unpack surface_flux_values, node_coordinates, contravariant_vectors = cache.elements
     @unpack weights = dg.basis
 
-    @unpack indices, variable = surface_variable
+    @unpack variable, boundary_symbols = surface_variable
+    @unpack boundary_symbol_indices = semi.boundary_conditions
+    indices = get_boundary_indices(boundary_symbols, boundary_symbol_indices)
 
     surface_integral = zero(eltype(u))
     index_range = eachnode(dg)
@@ -308,13 +308,15 @@ end
 function analyze(surface_variable::AnalysisSurfaceIntegral{Variable},
                  du, u, t, mesh::P4estMesh{2},
                  equations, equations_parabolic,
-                 dg::DGSEM, cache,
+                 dg::DGSEM, cache, semi,
                  cache_parabolic) where {Variable <: VariableViscous}
     @unpack boundaries = cache
     @unpack surface_flux_values, node_coordinates, contravariant_vectors = cache.elements
     @unpack weights = dg.basis
 
-    @unpack indices, variable = surface_variable
+    @unpack variable, boundary_symbols = surface_variable
+    @unpack boundary_symbol_indices = semi.boundary_conditions
+    indices = get_boundary_indices(boundary_symbols, boundary_symbol_indices)
 
     # Additions for parabolic
     @unpack viscous_container = cache_parabolic