Merge branch 'main' into update-callback

.github/workflows/SpellCheck.yml

@@ -10,4 +10,4 @@ jobs:
       - name: Checkout Actions Repository
         uses: actions/checkout@v4
       - name: Check spelling
-        uses: crate-ci/typos@v1.18.2
+        uses: crate-ci/typos@v1.19.0

SECURITY.md

@@ -0,0 +1,30 @@
+# Security Policy
+
+The Trixi.jl development team takes security issues seriously. We appreciate
+all efforts to responsibly disclose any security issues and will make every
+effort to acknowledge contributions.
+
+
+## Supported Versions
+
+The current stable release following the interpretation of
+[semantic versioning (SemVer)](https://julialang.github.io/Pkg.jl/dev/compatibility/#Version-specifier-format-1)
+used in the Julia ecosystem is supported with security updates.
+
+
+## Reporting a Vulnerability
+
+To report a security issue, please use the GitHub Security Advisory
+["Report a Vulnerability"](https://github.com/trixi-framework/TrixiParticles.jl/security/advisories/new)
+tab.
+
+We will send a response indicating the next steps in handling your report.
+After the initial reply to your report, we will keep you informed of the
+progress towards a fix and full announcement, and may ask for additional
+information or guidance.
+
+Please report security bugs in third-party modules directly to the person
+or team maintaining the module.
+
+Public notifications of vulnerabilities will be shared in community channels
+such as Slack.

docs/make.jl

@@ -92,16 +92,19 @@ DocMeta.setdocmeta!(TrixiParticles, :DocTestSetup, :(using TrixiParticles); recu
 makedocs(sitename="TrixiParticles.jl",
          # Run doctests and check docs for the following modules
          modules=[TrixiParticles],
+         format=Documenter.HTML(),
          # Explicitly specify documentation structure
          pages=[
              "Home" => "index.md",
              "News" => "news.md",
              "Installation" => "install.md",
              "Getting started" => "getting_started.md",
+             "Development" => "development.md",
              "Tutorial" => "tutorial.md",
              "Examples" => "examples.md",
              "Visualization" => "visualization.md",
              "Components" => [
+                 "Overview" => "overview.md",
                  "General" => [
                      "Semidiscretization" => joinpath("general", "semidiscretization.md"),
                      "Initial Condition and Setups" => joinpath("general",
@@ -132,5 +135,4 @@ makedocs(sitename="TrixiParticles.jl",
          ])
 
 deploydocs(repo="github.com/trixi-framework/TrixiParticles.jl",
-           devbranch="main",
-           push_preview=true)
+           devbranch="main", push_preview=true)

docs/src/development.md

@@ -0,0 +1,23 @@
+# [Development](@id development)
+
+
+## Preview of the documentation
+
+To generate the Documentation, first instantiate the `docs` environment
+by executing the following command from the TrixiParticles.jl root directory:
+```bash
+julia --project=docs -e "using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()"
+```
+This command only has to be run once. After that, maintain the `docs` environment
+as described under [Installation](@ref installation-issues).
+
+With an instantiated `docs` environment, generate the docs with the following command (again from the TrixiParticles.jl root directory):
+```bash
+julia --project=docs --color=yes docs/make.jl
+```
+You can then open the generated files in `docs/build` with your webbrowser.
+Alternatively, run
+```bash
+python3 -m http.server -d docs/build
+```
+and open `localhost:8000` in your webbrowser.

docs/src/examples.md

@@ -1,14 +1,68 @@
 # Examples
 
-
 ## Fluid
 
+### Accelerated Tank 2D (`fluid/accelerated_tank_2d.jl`)
+```@raw html
+<img src="https://github.com/trixi-framework/TrixiParticles.jl/assets/10238714/4c4c537a-8585-4456-9a1b-8b5adbf68533" width="60%"/>
+```
 
-## Structure Mechanics
-
+### Dam Break 2D (`fluid/dam_break_2d.jl`)
+```@raw html
+<img src="https://github.com/trixi-framework/TrixiParticles.jl/assets/10238714/683e9363-5705-49cc-9a5c-3b47d73ea4b8" width="60%"/>
+```
+
+### Dam Break 3D (`fluid/dam_break_3d.jl`)
+```@raw html
+<img src="https://github.com/trixi-framework/TrixiParticles.jl/assets/10238714/76a2b235-1b49-465f-a207-76859410b783" width="60%"/>
+```
+
+### Falling Water Column (`fluid/falling_water_column_2d.jl`)
+```@raw html
+<img src="https://github.com/trixi-framework/TrixiParticles.jl/assets/10238714/06a522f0-424f-49d3-afd0-29593373aa29" width="60%"/>
+```
+
+### Hydrostatic Water Column (`fluid/hydrostatic_water_column_*.jl`)
+```@raw html
+<img src="https://github.com/trixi-framework/TrixiParticles.jl/assets/10238714/fac6c41f-7af8-4936-9dd5-b6ff2b9f6ff4" width="60%"/>
+```
 
+### Moving Wall (`fluid/moving_wall_2d.jl`)
+```@raw html
+<img src="https://github.com/trixi-framework/TrixiParticles.jl/assets/10238714/c10faddf-0400-47c9-b225-f5d286a8ecb8" width="60%"/>
+```
+
+### Oscillating Drop (`fluid/oscillating_drop_2d.jl`)
+```@raw html
+<img src="https://github.com/trixi-framework/TrixiParticles.jl/assets/10238714/1dfa9dcf-7fc1-4221-ad83-a54c5d9ab9fb" width="60%"/>
+```
+
+### Periodic Channel (`fluid/periodic_channel_2d.jl`)
+```@raw html
+<img src="https://github.com/trixi-framework/TrixiParticles.jl/assets/10238714/f9a542bf-956b-4647-843b-94cbb085a4fa" width="60%"/>
+```
+
 ## Fluid Structure Interaction
 
+### Dam Break with Elastic Plate (`fsi/dam_break_plate_2d.jl`)
+```@raw html
+<img src="https://github.com/trixi-framework/TrixiParticles.jl/assets/10238714/ada0d554-e0ba-44ed-923d-2b77ef252258" width="60%"/>
+```
+
+### Falling Sphere 2D (`fsi/falling_sphere_2d.jl`)
+```@raw html
+<img src="https://github.com/trixi-framework/TrixiParticles.jl/assets/10238714/217c80b5-3472-41c9-8003-7163641dd452" width="60%"/>
+```
+
+### Falling Spheres 2D (`fsi/falling_spheres_2d.jl`)
+```@raw html
+<img src="https://github.com/trixi-framework/TrixiParticles.jl/assets/10238714/b3964f68-2782-43e6-b6ff-be96f9f224ae" width="60%"/>
+```
+
+## Structure Mechanics
 
-## Postprocessing
-
+### Oscillating Beam (`solid/oscillating_beam_2d.jl`)
+```@raw html
+<img src="https://github.com/trixi-framework/TrixiParticles.jl/assets/10238714/e05ace63-e330-441a-a391-eda3d2764074" width="60%"/>
+```
+

docs/src/index.md

@@ -12,13 +12,36 @@ TrixiParticles.jl is a numerical simulation framework designed for particle-base
   - VTK
 
 ## Examples
-
+```@raw html
+<table align="center" border="0">
+  <tr>
+    <td align="center">
+      <img src="https://github.com/trixi-framework/TrixiParticles.jl/assets/10238714/683e9363-5705-49cc-9a5c-3b47d73ea4b8" style="width: 80% !important;"/><br><figcaption>2D Dam Break</figcaption>
+    </td>
+    <td align="center">
+      <img src="https://github.com/trixi-framework/TrixiParticles.jl/assets/10238714/c10faddf-0400-47c9-b225-f5d286a8ecb8" style="width: 80% !important;"/><br><figcaption>Moving Wall</figcaption>
+    </td>
+  </tr>
+  <tr>
+    <td align="center">
+      <img src="https://github.com/trixi-framework/TrixiParticles.jl/assets/10238714/e05ace63-e330-441a-a391-eda3d2764074" style="width: 80% !important;"/><br><figcaption>Oscillating Beam</figcaption>
+    </td>
+    <td align="center">
+      <img src="https://github.com/trixi-framework/TrixiParticles.jl/assets/10238714/ada0d554-e0ba-44ed-923d-2b77ef252258" style="width: 80% !important;"/><br><figcaption>Dam Break with Elastic Plate</figcaption>
+    </td>
+  </tr>
+</table>
+```
 
 ## Quickstart
 1. [Installation](@ref installation)
 2. [Getting started](@ref getting_started)
 
+If you have any questions concerning **TrixiParticles.jl** you can join our community [on Slack](https://join.slack.com/t/trixi-framework/shared_invite/zt-sgkc6ppw-6OXJqZAD5SPjBYqLd8MU~g) or open an issue with your question.
 
 ## Start with development
+To get started with development have a look at these pages:
+
 1. [Installation](@ref installation)
-2. [Contributing](@ref)
+2. [Development](@ref development)
+3. [Contributing](@ref)

docs/src/install.md

@@ -45,7 +45,7 @@ and always have a reproducible environment at hand to share with others.
 - [PythonPlot.jl](https://github.com/JuliaPy/PythonPlot.jl) -- Plotting library that can be used instead of Plots.jl
 - [ParaView](https://www.paraview.org/) -- Software that can be used for visualization of results
 
-## Common issues
+## [Common issues](@id installation-issues)
 
 If you followed the [installation instructions for developers](@ref for-developers) and you
 run into any problems with packages when pulling the latest version of TrixiParticles.jl,

docs/src/overview.md

@@ -0,0 +1,23 @@
+# Overview
+The following page gives a rough overview of important parts of the code.
+
+## Program flow
+
+To initiate a simulation, the goal is to solve an ordinary differential equation, for example,
+by employing the time integration schemes provided by OrdinaryDiffEq.jl. These schemes are then 
+utilized to integrate ``\mathrm{d}u/\mathrm{d}t`` and ``\mathrm{d}v/\mathrm{d}t``, where ``u``
+represents the particles' positions and ``v`` their properties such as velocity and density.
+During a single time step or an intermediate step of the time integration scheme, the functions
+`drift!` and `kick!` are invoked, followed by the functions depicted in this diagram
+(with key parts highlighted in orange/yellow).
+
+![Main Program Flow](https://github.com/trixi-framework/TrixiParticles.jl/assets/10238714/d7c6eedd-7173-4879-b62e-3e6d4bc5091f)
+
+
+## Structure
+What we refer to as schemes are various models such as Weakly Compressible Smoothed Particle Hydrodynamics (WCSPH)
+or Total Lagrangian Smoothed Particle Hydrodynamics (TLSPH). These schemes are categorized based on the applicable
+physical regimes, namely fluid, solid, gas, and others. Each scheme comprises at least two files: a `system.jl` file
+and an `rhs.jl` file. The `system.jl` file provides the data structure holding the particles of this scheme and some
+routines, particularly those for allocation and the main update routines, excluding system interactions.
+The interactions between particles of this scheme (and with particles of other schemes) are handled in the `rhs.jl` file.

examples/fluid/periodic_channel_2d.jl

@@ -42,10 +42,15 @@ fluid_system = WeaklyCompressibleSPHSystem(tank.fluid, fluid_density_calculator,
 # ==========================================================================================
 # ==== Boundary
 boundary_density_calculator = AdamiPressureExtrapolation()
+viscosity_wall = nothing
+# Activate to switch to no-slip walls
+#viscosity_wall = ViscosityAdami(nu=0.0025 * smoothing_length * sound_speed / 8)
+
 boundary_model = BoundaryModelDummyParticles(tank.boundary.density, tank.boundary.mass,
                                              state_equation=state_equation,
                                              boundary_density_calculator,
-                                             smoothing_kernel, smoothing_length)
+                                             smoothing_kernel, smoothing_length,
+                                             viscosity=viscosity_wall)
 
 boundary_system = BoundarySPHSystem(tank.boundary, boundary_model)
 

examples/fsi/dam_break_2d.jl → examples/fsi/dam_break_plate_2d.jl

@@ -14,7 +14,7 @@ fluid_particle_spacing = 0.01
 n_particles_x = 5
 
 # Change spacing ratio to 3 and boundary layers to 1 when using Monaghan-Kajtar boundary model
-boundary_layers = 3
+boundary_layers = 4
 spacing_ratio = 1
 
 # ==========================================================================================
@@ -29,7 +29,7 @@ tank_size = 4 .* initial_fluid_size
 fluid_density = 1000.0
 sound_speed = 20 * sqrt(gravity * initial_fluid_size[2])
 state_equation = StateEquationCole(; sound_speed, reference_density=fluid_density,
-                                   exponent=7)
+                                   exponent=1)
 
 tank = RectangularTank(fluid_particle_spacing, initial_fluid_size, tank_size, fluid_density,
                        n_layers=boundary_layers, spacing_ratio=spacing_ratio,
@@ -65,8 +65,8 @@ solid = union(plate, fixed_particles)
 
 # ==========================================================================================
 # ==== Fluid
-smoothing_length = 1.2 * fluid_particle_spacing
-smoothing_kernel = SchoenbergCubicSplineKernel{2}()
+smoothing_length = 3.5 * fluid_particle_spacing
+smoothing_kernel = WendlandC2Kernel{2}()
 
 fluid_density_calculator = ContinuityDensity()
 viscosity = ArtificialViscosityMonaghan(alpha=0.02, beta=0.0)

examples/fsi/falling_sphere_2d.jl

@@ -4,4 +4,4 @@ trixi_include(@__MODULE__,
               joinpath(examples_dir(), "fsi", "falling_spheres_2d.jl"),
               solid_system_2=nothing, fluid_particle_spacing=0.02,
               initial_fluid_size=(1.0, 0.9), tank_size=(1.0, 1.0),
-              tspan=(0.0, 2.0), abstol=1e-6, reltol=1e-3)
+              tspan=(0.0, 1.0), abstol=1e-6, reltol=1e-3)

examples/fsi/falling_sphere_3d.jl

@@ -11,4 +11,4 @@ trixi_include(@__MODULE__,
               sphere_type=RoundSphere(),
               output_directory="out", prefix="",
               write_meta_data=false, # Files with meta data can't be read by meshio
-              tspan=(0.0, 2.0), abstol=1e-6, reltol=1e-3)
+              tspan=(0.0, 1.0), abstol=1e-6, reltol=1e-3)

examples/fsi/falling_spheres_2d.jl

@@ -13,7 +13,7 @@ spacing_ratio = 1
 # ==========================================================================================
 # ==== Experiment Setup
 gravity = 9.81
-tspan = (0.0, 2.0)
+tspan = (0.0, 1.0)
 
 # Boundary geometry and initial fluid particle positions
 initial_fluid_size = (2.0, 0.9)

src/TrixiParticles.jl

@@ -61,7 +61,7 @@ export GridNeighborhoodSearch, TrivialNeighborhoodSearch
 export examples_dir, validation_dir, trixi_include
 export trixi2vtk
 export RectangularTank, RectangularShape, SphereShape
-export VoxelSphere, RoundSphere, reset_wall!
+export VoxelSphere, RoundSphere, reset_wall!, extrude_geometry
 export SourceTermDamping
 export ShepardKernelCorrection, KernelCorrection, AkinciFreeSurfaceCorrection,
        GradientCorrection, BlendedGradientCorrection, MixedKernelGradientCorrection

src/general/file_system.jl

@@ -13,10 +13,19 @@ function system_names(systems)
 end
 
 function get_git_hash()
+    pkg_directory = pkgdir(@__MODULE__)
+    git_directory = joinpath(pkg_directory, ".git")
+
+    # Check if the .git directory exists
+    if !isdir(git_directory)
+        return "UnknownVersion"
+    end
+
     try
-        return string(readchomp(Cmd(`git describe --tags --always --first-parent --dirty`,
-                                    dir=pkgdir(@__MODULE__))))
+        git_cmd = Cmd(`git describe --tags --always --first-parent --dirty`,
+                      dir=pkg_directory)
+        return string(readchomp(git_cmd))
     catch e
-        return "Git is not installed or not accessible"
+        return "UnknownVersion"
     end
 end