Merge branch 'main' into particle-refinement-prototype

trixi-framework · Nov 14, 2024 · 364dd0f · 364dd0f
2 parents 0974472 + 4b7f515
commit 364dd0f
Show file tree

Hide file tree

Showing 36 changed files with 198 additions and 194 deletions.
diff --git a/.github/workflows/FormatCheck.yml b/.github/workflows/FormatCheck.yml
@@ -25,7 +25,7 @@ jobs:
         #
         # julia  -e 'using Pkg; Pkg.add(PackageSpec(name = "JuliaFormatter", version = "0.13.0"))'
         run: |
-          julia  -e 'using Pkg; Pkg.add(PackageSpec(name = "JuliaFormatter", version="1.0.45"))'
+          julia  -e 'using Pkg; Pkg.add(PackageSpec(name = "JuliaFormatter", version="1.0.62"))'
           julia  -e 'using JuliaFormatter; format(".")'
       - name: Format check
         run: |

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@v1.25.0
+        uses: crate-ci/typos@v1.26.8
diff --git a/README.md b/README.md
@@ -78,7 +78,7 @@ git clone [email protected]:trixi-framework/TrixiParticles.jl.git
 cd TrixiParticles.jl
 mkdir run
 julia --project=run -e 'using Pkg; Pkg.develop(PackageSpec(path="."))' # Add TrixiParticles.jl to `run` project
-julia --project=run -e 'using Pkg; Pkg.add("OrdinaryDiffEq", "Plots")' # Add additional packages
+julia --project=run -e 'using Pkg; Pkg.add(["OrdinaryDiffEq", "Plots"])' # Add additional packages
 ```
 
 If you installed TrixiParticles.jl this way, you always have to start Julia with the

diff --git a/docs/make.jl b/docs/make.jl
@@ -115,7 +115,7 @@ makedocs(sitename="TrixiParticles.jl",
              "Examples" => "examples.md",
              "Visualization" => "visualization.md",
              "Preprocessing" => [
-                 "Sampling of Geometries" => joinpath("preprocessing", "preprocessing.md"),
+                 "Sampling of Geometries" => joinpath("preprocessing", "preprocessing.md")
              ],
              "Components" => [
                  "Overview" => "overview.md",
@@ -127,7 +127,7 @@ makedocs(sitename="TrixiParticles.jl",
                      "Density Calculators" => joinpath("general", "density_calculators.md"),
                      "Smoothing Kernels" => joinpath("general", "smoothing_kernels.md"),
                      "Neighborhood Search" => joinpath("general", "neighborhood_search.md"),
-                     "Util" => joinpath("general", "util.md"),
+                     "Util" => joinpath("general", "util.md")
                  ],
                  "Systems" => [
                      "Discrete Element Method (Solid)" => joinpath("systems",
@@ -138,18 +138,18 @@ makedocs(sitename="TrixiParticles.jl",
                                                                                                   "entropically_damped_sph.md"),
                      "Total Lagrangian SPH (Elastic Structure)" => joinpath("systems",
                                                                             "total_lagrangian_sph.md"),
-                     "Boundary" => joinpath("systems", "boundary.md"),
+                     "Boundary" => joinpath("systems", "boundary.md")
                  ],
                  "Time Integration" => "time_integration.md",
                  "Callbacks" => "callbacks.md",
                  "TrixiBase.jl API Reference" => "reference-trixibase.md",
-                 "PointNeighbors.jl API Reference" => "reference-pointneighbors.md",
+                 "PointNeighbors.jl API Reference" => "reference-pointneighbors.md"
              ],
              "Authors" => "authors.md",
              "Contributing" => "contributing.md",
              "Code of Conduct" => "code_of_conduct.md",
              "License" => "license.md",
-             "References" => "references.md",
+             "References" => "references.md"
          ])
 
 deploydocs(repo="github.com/trixi-framework/TrixiParticles.jl",

diff --git a/docs/src/install.md b/docs/src/install.md
@@ -25,7 +25,7 @@ git clone [email protected]:trixi-framework/TrixiParticles.jl.git
 cd TrixiParticles.jl
 mkdir run
 julia --project=run -e 'using Pkg; Pkg.develop(PackageSpec(path="."))' # Add TrixiParticles.jl to `run` project
-julia --project=run -e 'using Pkg; Pkg.add("OrdinaryDiffEq", "Plots")' # Add additional packages
+julia --project=run -e 'using Pkg; Pkg.add(["OrdinaryDiffEq", "Plots"])' # Add additional packages
 ```
 
 If you installed TrixiParticles.jl this way, you always have to start Julia with the

diff --git a/docs/src/visualization.md b/docs/src/visualization.md
@@ -16,11 +16,15 @@ Follow these steps to view the exported VTK files in ParaView:
 5. Hold the left mouse button to move the solution around.
 
 You will now see the following:
-![image](https://github.com/svchb/TrixiParticles.jl/assets/10238714/45c90fd2-984b-4eee-b130-e691cefb33ab)
+![image](https://github.com/user-attachments/assets/383d323a-3020-4232-9dc3-682b0afe8653)
+
+It is useful to make the particles larger.
+For this, **first** make sure you have "fluid_1.pvd" highlighted in the "Pipeline Browser" then in the "Properties" window in the bottom left change "Point Size" to a larger value.
+![image](https://github.com/user-attachments/assets/6e975d2c-82ed-4d53-936b-bb0beafaf515)
 
 To now view the result variables **first** make sure you have "fluid_1.pvd" highlighted in the "Pipeline Browser" then select them in the variable selection combo box (see picture below).
 Let's, for example, pick "density". To now view the time progression of the result hit the "play button" (see picture below).
-![image](https://github.com/svchb/TrixiParticles.jl/assets/10238714/7565a13f-9532-4a69-9f81-e79505400b1c)
+![image](https://github.com/user-attachments/assets/10dcf7eb-5808-4d4d-9db8-4beb25b5e51a)
 
 ## API
 

diff --git a/examples/n_body/n_body_benchmark_trixi.jl b/examples/n_body/n_body_benchmark_trixi.jl
@@ -62,7 +62,7 @@ velocity = [0.0 1.66007664274403694e-3 -2.76742510726862411e-3 2.964601375647616
 
 masses = [
     1.0, 9.54791938424326609e-4, 2.85885980666130812e-4, 4.36624404335156298e-5,
-    5.15138902046611451e-5,
+    5.15138902046611451e-5
 ] * SOLAR_MASS
 
 # Offset sun momentum

diff --git a/examples/n_body/n_body_solar_system.jl b/examples/n_body/n_body_solar_system.jl
@@ -20,7 +20,7 @@ velocity = [-1.4663 -1.5205e+04 -3.4770e+04 2.9288e+04 2.4533e+04 -1.0724e+03 8.
             4.8370 2.5180e+04 -316.8994 -172.5873 -1.9295e+03 -4.8696e+03 -1.3824e+03 2.4527e+03 1.9082e+03]
 
 masses = [
-    1.99e30, 3.30e23, 4.87e24, 5.97e24, 6.42e23, 1.90e27, 5.68e26, 8.68e25, 1.02e26,
+    1.99e30, 3.30e23, 4.87e24, 5.97e24, 6.42e23, 1.90e27, 5.68e26, 8.68e25, 1.02e26
 ]
 
 initial_condition = InitialCondition(; coordinates, velocity, density=1.0, mass=masses)

diff --git a/examples/postprocessing/interpolation_point_line.jl b/examples/postprocessing/interpolation_point_line.jl
@@ -27,7 +27,7 @@ println(interpolate_point([
                               [position_x, 0.1],
                               [position_x, 0.0],
                               [position_x, -0.01],
-                              [position_x, -0.05],
+                              [position_x, -0.05]
                           ], semi, fluid_system, sol))
 
 # It is also possible to interpolate along a line

diff --git a/src/callbacks/density_reinit.jl b/src/callbacks/density_reinit.jl
@@ -31,7 +31,7 @@ function Base.show(io::IO, ::MIME"text/plain",
         callback = cb.affect!
         setup = [
             "interval" => callback.interval,
-            "reinit_initial_solution" => callback.reinit_initial_solution,
+            "reinit_initial_solution" => callback.reinit_initial_solution
         ]
         summary_box(io, "DensityReinitializationCallback", setup)
     end

diff --git a/src/callbacks/info.jl b/src/callbacks/info.jl
@@ -19,7 +19,7 @@ function Base.show(io::IO, ::MIME"text/plain", cb::DiscreteCallback{<:Any, <:Inf
         callback = cb.affect!
 
         setup = [
-            "interval" => callback.interval,
+            "interval" => callback.interval
         ]
         summary_box(io, "InfoCallback", setup)
     end

diff --git a/src/callbacks/post_process.jl b/src/callbacks/post_process.jl
@@ -156,7 +156,7 @@ function Base.show(io::IO, ::MIME"text/plain",
             "output directory" => callback.output_directory,
             "append timestamp" => callback.append_timestamp ? "yes" : "no",
             "write json file" => callback.write_csv ? "yes" : "no",
-            "write csv file" => callback.write_json ? "yes" : "no",
+            "write csv file" => callback.write_json ? "yes" : "no"
         ]
 
         for (i, key) in enumerate(keys(callback.func))
@@ -193,7 +193,7 @@ function Base.show(io::IO, ::MIME"text/plain",
             "output directory" => callback.output_directory,
             "append timestamp" => callback.append_timestamp ? "yes" : "no",
             "write json file" => callback.write_csv ? "yes" : "no",
-            "write csv file" => callback.write_json ? "yes" : "no",
+            "write csv file" => callback.write_json ? "yes" : "no"
         ]
 
         for (i, key) in enumerate(keys(callback.func))

diff --git a/src/callbacks/solution_saving.jl b/src/callbacks/solution_saving.jl
@@ -251,7 +251,7 @@ function Base.show(io::IO, ::MIME"text/plain",
             "save final solution" => solution_saving.save_final_solution ? "yes" :
                                      "no",
             "output directory" => abspath(solution_saving.output_directory),
-            "prefix" => solution_saving.prefix,
+            "prefix" => solution_saving.prefix
         ]
         summary_box(io, "SolutionSavingCallback", setup)
     end
@@ -275,7 +275,7 @@ function Base.show(io::IO, ::MIME"text/plain",
             "save final solution" => solution_saving.save_final_solution ? "yes" :
                                      "no",
             "output directory" => abspath(solution_saving.output_directory),
-            "prefix" => solution_saving.prefix,
+            "prefix" => solution_saving.prefix
         ]
         summary_box(io, "SolutionSavingCallback", setup)
     end
@@ -300,7 +300,7 @@ function Base.show(io::IO, ::MIME"text/plain",
             "save final solution" => solution_saving.save_final_solution ? "yes" :
                                      "no",
             "output directory" => abspath(solution_saving.output_directory),
-            "prefix" => solution_saving.prefix,
+            "prefix" => solution_saving.prefix
         ]
         summary_box(io, "SolutionSavingCallback", setup)
     end

diff --git a/src/callbacks/stepsize.jl b/src/callbacks/stepsize.jl
@@ -94,7 +94,7 @@ function Base.show(io::IO, ::MIME"text/plain",
 
         setup = [
             "is constant" => string(is_constant(stepsize_callback)),
-            "CFL number" => stepsize_callback.cfl_number,
+            "CFL number" => stepsize_callback.cfl_number
         ]
         summary_box(io, "StepsizeCallback", setup)
     end

diff --git a/src/callbacks/update.jl b/src/callbacks/update.jl
@@ -116,7 +116,7 @@ function Base.show(io::IO, ::MIME"text/plain",
     else
         update_cb = cb.affect!
         setup = [
-            "interval" => update_cb.interval,
+            "interval" => update_cb.interval
         ]
         summary_box(io, "UpdateCallback", setup)
     end
@@ -132,7 +132,7 @@ function Base.show(io::IO, ::MIME"text/plain",
     else
         update_cb = cb.affect!.affect!
         setup = [
-            "dt" => update_cb.interval,
+            "dt" => update_cb.interval
         ]
         summary_box(io, "UpdateCallback", setup)
     end

diff --git a/test/examples/dam_break_2d_corrections.jl b/test/examples/dam_break_2d_corrections.jl
@@ -15,7 +15,7 @@
         "gradient_summation_correction" => GradientCorrection(),
         "mixed_kernel_gradient_summation_correction" => MixedKernelGradientCorrection(),
         "gradient_continuity_correction" => GradientCorrection(),
-        "mixed_kernel_gradient_continuity_correction" => MixedKernelGradientCorrection(),
+        "mixed_kernel_gradient_continuity_correction" => MixedKernelGradientCorrection()
     )
 
     smoothing_length_dict = Dict(
@@ -29,7 +29,7 @@
         "gradient_summation_correction" => 3.5 * particle_spacing,
         "mixed_kernel_gradient_summation_correction" => 3.5 * particle_spacing,
         "gradient_continuity_correction" => 4.5 * particle_spacing,
-        "mixed_kernel_gradient_continuity_correction" => 4.0 * particle_spacing,
+        "mixed_kernel_gradient_continuity_correction" => 4.0 * particle_spacing
     )
 
     density_calculator_dict = Dict(
@@ -43,7 +43,7 @@
         "gradient_summation_correction" => SummationDensity(),
         "gradient_continuity_correction" => ContinuityDensity(),
         "mixed_kernel_gradient_summation_correction" => SummationDensity(),
-        "mixed_kernel_gradient_continuity_correction" => ContinuityDensity(),
+        "mixed_kernel_gradient_continuity_correction" => ContinuityDensity()
     )
 
     smoothing_kernel_dict = Dict(
@@ -57,7 +57,7 @@
         "gradient_summation_correction" => WendlandC6Kernel{2}(),
         "gradient_continuity_correction" => WendlandC6Kernel{2}(),
         "mixed_kernel_gradient_summation_correction" => WendlandC6Kernel{2}(),
-        "mixed_kernel_gradient_continuity_correction" => WendlandC6Kernel{2}(),
+        "mixed_kernel_gradient_continuity_correction" => WendlandC6Kernel{2}()
     )
 
     @testset "continuity_reinit" begin

diff --git a/test/examples/examples.jl b/test/examples/examples.jl
@@ -73,7 +73,7 @@
                                                                                          viscosity=ViscosityMorris(nu=0.0015),
                                                                                          density_calculator=ContinuityDensity(),
                                                                                          acceleration=(0.0,
-                                                                                                       -gravity)),),
+                                                                                                       -gravity)),)
             )
 
             for (test_description, kwargs) in hydrostatic_water_column_tests
@@ -157,7 +157,7 @@
                                                 correction=AkinciFreeSurfaceCorrection(fluid_density),
                                                 density_diffusion=nothing,
                                                 adhesion_coefficient=0.05,
-                                                sound_speed=100.0),
+                                                sound_speed=100.0)
             )
 
             for (test_description, kwargs) in dam_break_tests
@@ -170,7 +170,7 @@
                                                             "dam_break_2d.jl");
                                                    tspan=(0, 0.1), kwargs...) [
                         r"┌ Info: The desired tank length in y-direction .*\n",
-                        r"└ New tank length in y-direction.*\n",
+                        r"└ New tank length in y-direction.*\n"
                     ]
 
                     @test sol.retcode == ReturnCode.Success
@@ -185,7 +185,7 @@
                                                     "dam_break_oil_film_2d.jl"),
                                            tspan=(0.0, 0.05)) [
                 r"┌ Info: The desired tank length in y-direction .*\n",
-                r"└ New tank length in y-direction.*\n",
+                r"└ New tank length in y-direction.*\n"
             ]
             @test sol.retcode == ReturnCode.Success
             @test count_rhs_allocations(sol, semi) == 0
@@ -286,7 +286,7 @@
                 r"┌ Info: The desired tank length in y-direction .*\n",
                 r"└ New tank length in y-direction.*\n",
                 r"┌ Info: The desired tank length in z-direction .*\n",
-                r"└ New tank length in z-direction.*\n",
+                r"└ New tank length in z-direction.*\n"
             ]
             @test sol.retcode == ReturnCode.Success
             @test count_rhs_allocations(sol, semi) == 0
@@ -375,7 +375,7 @@
             @test_nowarn_mod trixi_include(@__MODULE__,
                                            joinpath(examples_dir(), "n_body",
                                                     "n_body_benchmark_trixi.jl")) [
-                r"WARNING: Method definition interact!.*\n",
+                r"WARNING: Method definition interact!.*\n"
             ]
         end
 
@@ -402,7 +402,7 @@
                 r"WARNING: using deprecated binding PlotUtils.*\n",
                 r"WARNING: Makie.* is deprecated.*\n",
                 r"  likely near none:1\n",
-                r", use .* instead.\n",
+                r", use .* instead.\n"
             ]
             @test sol.retcode == ReturnCode.Success
         end