Merge branch 'main' into PERK_p2_Single_fixed_time_step

trixi-framework · Jul 8, 2024 · 9013eac · 9013eac
2 parents fe3133e + b592f3c
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diff --git a/.github/workflows/SpellCheck.yml b/.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
diff --git a/.zenodo.json b/.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"
         },

diff --git a/AUTHORS.md b/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),
@@ -38,8 +38,10 @@ are listed in alphabetical order:
 * Julia Odenthal
 * Sigrun Ortleb
 * Hendrik Ranocha
+* Warisa Roongaraya
 * Andrés M. Rueda-Ramírez
 * Felipe Santillan
 * Michael Schlottke-Lakemper
 * Toskan Theine
 * Andrew Winters
+* Huiyu Xie
diff --git a/CODE_OF_CONDUCT.md b/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).

diff --git a/NEWS.md b/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

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 = "0.7.16-pre"
+version = "0.8.4-DEV"
 
 [deps]
 CodeTracking = "da1fd8a2-8d9e-5ec2-8556-3022fb5608a2"
@@ -104,7 +104,7 @@ 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"
 

diff --git a/README.md b/README.md
@@ -26,16 +26,16 @@ 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)
+  10th July 2024, 11:00–11:30, 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/JBKVGF/),<br/>
+  10th July 2024, 15:30–16:00, 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)
+  12th July 2024, 14:00–17:00, Function (4.1)
 
 The last talk is part of the 
-[Julia for High-Performance Computing](https://pretalx.com/juliacon2024/talk/JBKVGF/)
+[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 ♥️
@@ -259,8 +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)

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, 0.6, 0.7"
+Trixi = "0.4, 0.5, 0.6, 0.7, 0.8"
diff --git a/docs/Project.toml b/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"
diff --git a/docs/literate/src/files/first_steps/create_first_setup.jl b/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

diff --git a/docs/literate/src/files/hohqmesh_tutorial.jl b/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

diff --git a/docs/make.jl b/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(

diff --git a/docs/src/index.md b/docs/src/index.md
@@ -323,8 +323,8 @@ In addition, you can also refer to Trixi.jl directly as
 
 ## [Authors](@id authors-index-md)
 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) and [Andrew Winters](https://liu.se/en/employee/andwi94)

diff --git a/docs/src/restart.md b/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)
 ```
 

diff --git a/docs/src/styleguide.md b/docs/src/styleguide.md
@@ -51,7 +51,7 @@ PRs that verify that running JuliaFormatter.jl again will not change the source
 To format your contributions before created a PR (or, at least, before requesting a review
 of your PR), you need to install JuliaFormatter.jl first by running
 ```shell
-julia -e 'using Pkg; Pkg.add("JuliaFormatter")'
+julia -e 'using Pkg; Pkg.add(PackageSpec(name = "JuliaFormatter", version="1.0.45"))'
 ```
 You can then recursively format the core Julia files in the Trixi.jl repo by executing
 ```shell

diff --git a/docs/src/visualization.md b/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

diff --git a/examples/p4est_2d_dgsem/elixir_advection_restart.jl b/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))
 

diff --git a/examples/p4est_2d_dgsem/elixir_advection_restart_amr.jl b/examples/p4est_2d_dgsem/elixir_advection_restart_amr.jl
@@ -0,0 +1,54 @@
+
+using OrdinaryDiffEq
+using Trixi
+
+###############################################################################
+# create a restart file
+
+elixir_file = "elixir_advection_extended.jl"
+restart_file = "restart_000000021.h5"
+
+trixi_include(@__MODULE__, joinpath(@__DIR__, elixir_file))
+
+###############################################################################
+# adapt the parameters that have changed compared to "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_file)
+mesh = load_mesh(restart_filename)
+
+semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition, solver,
+                                    boundary_conditions = boundary_conditions)
+
+tspan = (load_time(restart_filename), 2.0)
+dt = load_dt(restart_filename)
+ode = semidiscretize(semi, tspan, restart_filename);
+
+# Do not overwrite the initial snapshot written by elixir_advection_extended.jl.
+save_solution.condition.save_initial_solution = false
+
+# Add AMR callback
+amr_controller = ControllerThreeLevel(semi, IndicatorMax(semi, variable = first),
+                                      base_level = 0,
+                                      med_level = 0, med_threshold = 0.8,
+                                      max_level = 1, max_threshold = 1.2)
+amr_callback = AMRCallback(semi, amr_controller,
+                           interval = 5,
+                           adapt_initial_condition = true,
+                           adapt_initial_condition_only_refine = true)
+callbacks_ext = CallbackSet(amr_callback, callbacks.discrete_callbacks...)
+
+integrator = init(ode, CarpenterKennedy2N54(williamson_condition = false),
+                  dt = dt, # solve needs some value here but it will be overwritten by the stepsize_callback
+                  save_everystep = false, callback = callbacks_ext, maxiters = 100_000);
+
+# Get the last time index and work with that.
+load_timestep!(integrator, restart_filename)
+
+###############################################################################
+# run the simulation
+
+sol = solve!(integrator)
+summary_callback() # print the timer summary
diff --git a/examples/p4est_2d_dgsem/elixir_euler_NACA0012airfoil_mach085.jl b/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))

diff --git a/examples/p4est_2d_dgsem/elixir_euler_subsonic_cylinder.jl b/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))
 

diff --git a/examples/p4est_2d_dgsem/elixir_navierstokes_NACA0012airfoil_mach08.jl b/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),

diff --git a/examples/p4est_3d_dgsem/elixir_advection_restart.jl b/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,

diff --git a/examples/structured_2d_dgsem/elixir_advection_restart.jl b/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))