Merge branch 'main' into particle-refinement

.github/workflows/Documenter.yml

@@ -8,10 +8,12 @@ on:
     paths-ignore:
       - '.github/workflows/ci.yml'
       - '.github/workflows/CompatHelper.yml'
+      - '.github/workflows/TagBot.yml'
   pull_request:
     paths-ignore:
       - '.github/workflows/ci.yml'
       - '.github/workflows/CompatHelper.yml'
+      - '.github/workflows/TagBot.yml'
   workflow_dispatch:
 
 concurrency:
@@ -28,11 +30,11 @@ jobs:
       - name: Check out project
         uses: actions/checkout@v4
       - name: Set up Julia
-        uses: julia-actions/setup-julia@v1
+        uses: julia-actions/setup-julia@v2
         with:
           version: '1'
           show-versioninfo: true
-      - uses: julia-actions/cache@v1
+      - uses: julia-actions/cache@v2
       - name: Build package
         uses: julia-actions/julia-buildpkg@v1
       - name: Install dependencies

.github/workflows/FormatCheck.yml

@@ -15,11 +15,11 @@ jobs:
       - name: Check out project
         uses: actions/checkout@v4
       - name: Set up Julia
-        uses: julia-actions/setup-julia@v1
+        uses: julia-actions/setup-julia@v2
         with:
           version: '1'
       - run: julia -e 'using InteractiveUtils; versioninfo(verbose=true)'
-      - uses: julia-actions/cache@v1
+      - uses: julia-actions/cache@v2
       - name: Install JuliaFormatter and format
         # This will use the latest version by default but you can set the version like so:
         #

.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@v1.21.0

.github/workflows/ci.yml

@@ -61,10 +61,10 @@ jobs:
       - name: Check out project
         uses: actions/checkout@v4
       - name: Set up Julia
-        uses: julia-actions/setup-julia@v1
+        uses: julia-actions/setup-julia@v2
         with:
           version: ${{ matrix.version }}
-      - uses: julia-actions/cache@v1
+      - uses: julia-actions/cache@v2
       - name: Build package
         uses: julia-actions/julia-buildpkg@v1
       - name: Run unit tests

.typos.toml

@@ -2,3 +2,5 @@
 ba = "ba"
 Shepard = "Shepard"
 shepard = "shepard"
+Strack = "Strack"
+Lok = "Lok"

.zenodo.json

@@ -20,7 +20,7 @@
             "orcid": "0000-0001-6083-7038"
         },
         {
-            "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"
         },

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),
 [Sven Berger](mailto:[email protected]),
 or any other of the principal developers responsible for enforcement listed in
 [AUTHORS.md](AUTHORS.md).
@@ -128,4 +128,4 @@ enforcement ladder](https://github.com/mozilla/diversity).
 
 For answers to common questions about this code of conduct, see the FAQ at
 https://www.contributor-covenant.org/faq. Translations are available at
-https://www.contributor-covenant.org/translations.
+https://www.contributor-covenant.org/translations.

NEWS.md

@@ -1,11 +1,10 @@
 # Changelog
 
 TrixiParticles.jl follows the interpretation of [semantic versioning (semver)](https://julialang.github.io/Pkg.jl/dev/compatibility/#Version-specifier-format-1)
-used in the Julia ecosystem. Notable changes will be documented in this file for human readability. 
-We aim at 3 to 4 month between major release versions and about 2 weeks between minor versions. 
+used in the Julia ecosystem. Notable changes will be documented in this file for human readability.
+We aim at 3 to 4 month between major release versions and about 2 weeks between minor versions.
 
-
-## Version 0.1.x
+## Version 0.2.x
 
 ### Highlights
 
@@ -15,16 +14,32 @@ We aim at 3 to 4 month between major release versions and about 2 weeks between
 
 ### Deprecated
 
+## Version 0.1.3
 
-## Pre Initial Release (v0.1.0)
-This section summarizes the initial features that TrixiParticles.jl was released with.
+### Added
+Open boundaries using the method of characteristics based on the work of Lastiwka et al., "Permeable and non-reflecting boundary conditions in SPH" (2009) were added for WCSPH and EDAC.
+
+## Version 0.1.2
+
+### Added
+A surface tension and adhesion model based on the work by Akinci et al., "Versatile Surface Tension and Adhesion for SPH Fluids" (2013) was added to WCSPH.
+
+## Version 0.1.1
 
 ### Highlights
-#### EDAC
+
+#### Discrete Element Method
+A basic implementation of the discrete element method was added.
+
+# Pre Initial Release (v0.1.0)
+This section summarizes the initial features that TrixiParticles.jl was released with.
+
+## Highlights
+### EDAC
 An implementation of EDAC (Entropically Damped Artificial Compressibility) was added,
 which allows for more stable simulations compared to basic WCSPH and reduces spurious pressure oscillations.
 
-#### WCSPH
+### WCSPH
 An implementation of WCSPH (Weakly Compressible Smoothed Particle Hydrodynamics), which is the classical SPH approach.
 
 Features:
@@ -36,5 +51,5 @@ Features:
 - Density diffusion based on the models by Molteni & Colagrossi (2009), Ferrari et al. (2009) and Antuono et al. (2010).
 
 
-#### TLSPH
+### TLSPH
 An implementation of TLSPH (Total Lagrangian Smoothed Particle Hydrodynamics) for solid bodies enabling FSI (Fluid Structure Interactions).

Project.toml

@@ -1,48 +1,52 @@
 name = "TrixiParticles"
 uuid = "66699cd8-9c01-4e9d-a059-b96c86d16b3a"
 authors = ["erik.faulhaber <[email protected]>"]
-version = "0.1.0"
+version = "0.1.4-dev"
 
 [deps]
+Adapt = "79e6a3ab-5dfb-504d-930d-738a2a938a0e"
 CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
 DiffEqCallbacks = "459566f4-90b8-5000-8ac3-15dfb0a30def"
 FastPow = "c0e83750-1142-43a8-81cf-6c956b72b4d1"
 ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
+GPUArrays = "0c68f7d7-f131-5f86-a1c3-88cf8149b2d7"
 JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
+KernelAbstractions = "63c18a36-062a-441e-b654-da1e3ab1ce7c"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
-Morton = "2a6d852e-3fac-5a38-885c-fe708af2d09e"
 MuladdMacro = "46d2c3a1-f734-5fdb-9937-b9b9aeba4221"
+PointNeighbors = "1c4d5385-0a27-49de-8e2c-43b175c8985c"
 Polyester = "f517fe37-dbe3-4b94-8317-1923a5111588"
 Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
 RecipesBase = "3cdcf5f2-1ef4-517c-9805-6587b60abb01"
 Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
 SciMLBase = "0bca4576-84f4-4d90-8ffe-ffa030f20462"
 StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
 StrideArrays = "d1fa6d79-ef01-42a6-86c9-f7c551f8593b"
-ThreadingUtilities = "8290d209-cae3-49c0-8002-c8c24d57dab5"
 TimerOutputs = "a759f4b9-e2f1-59dc-863e-4aeb61b1ea8f"
 TrixiBase = "9a0f1c46-06d5-4909-a5a3-ce25d3fa3284"
 WriteVTK = "64499a7a-5c06-52f2-abe2-ccb03c286192"
 
 [compat]
+Adapt = "3, 4"
 CSV = "0.10"
 DataFrames = "1.6"
 DiffEqCallbacks = "2.25, 3"
 FastPow = "0.1"
 ForwardDiff = "0.10"
+GPUArrays = "9, 10"
 JSON = "0.21"
-Morton = "0.1"
+KernelAbstractions = "0.9"
 MuladdMacro = "0.2"
+PointNeighbors = "0.2.3"
 Polyester = "0.7.5"
 RecipesBase = "1"
 Reexport = "1"
 SciMLBase = "1, 2"
 StaticArrays = "1"
 StrideArrays = "0.1"
-ThreadingUtilities = "0.5"
 TimerOutputs = "0.5"
-TrixiBase = "0.1"
+TrixiBase = "0.1.3"
 WriteVTK = "1"
 julia = "1.9"

README.md

@@ -17,8 +17,9 @@ Its features include:
 ## Features
 - Incompressible Navier-Stokes
   - Methods: Weakly Compressible Smoothed Particle Hydrodynamics (WCSPH), Entropically Damped Artificial Compressibility (EDAC)
+  - Models: Surface Tension, Open Boundaries
 - Solid-body mechanics
-  - Methods:  Total Lagrangian SPH (TLSPH)
+  - Methods:  Total Lagrangian SPH (TLSPH), Discrete Element Method (DEM)
 - Fluid-Structure Interaction
 - Output formats:
   - VTK
@@ -128,7 +129,7 @@ with the help of TrixiParticles.jl, please cite it as
 ## Authors
 Erik Faulhaber (University of Cologne) and Niklas Neher (HLRS) implemented the foundations
 for TrixiParticles.jl and are principal developers along with Sven Berger (hereon).
-The project was started by Michael Schlottke-Lakemper (RWTH Aachen University/HLRS)
+The project was started by Michael Schlottke-Lakemper (University of Augsburg)
 and Gregor Gassner (University of Cologne), who provide scientific direction and technical advice.
 The full list of contributors can be found in [AUTHORS.md](AUTHORS.md).
 

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/Project.toml

@@ -2,7 +2,6 @@
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
 TrixiBase = "9a0f1c46-06d5-4909-a5a3-ce25d3fa3284"
-TrixiParticles = "66699cd8-9c01-4e9d-a059-b96c86d16b3a"
 
 [compat]
 Documenter = "1"

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",
@@ -113,6 +116,8 @@ makedocs(sitename="TrixiParticles.jl",
                      "Util" => joinpath("general", "util.md"),
                  ],
                  "Systems" => [
+                     "Discrete Element Method (Solid)" => joinpath("systems",
+                                                                   "dem.md"),
                      "Weakly Compressible SPH (Fluid)" => joinpath("systems",
                                                                    "weakly_compressible_sph.md"),
                      "Entropically Damped Artificial Compressibility for SPH (Fluid)" => joinpath("systems",
@@ -132,5 +137,4 @@ 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 +1,68 @@
+# [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.
+
+
+## Release management
+
+To create a new release for TrixiParticles.jl, perform the following steps:
+1) Make sure that all PRs and changes that you want to go into the release are merged to
+   `main` and that the latest commit on `main` has passed all CI tests.
+2) Determine the currently released version of TrixiParticles.jl, e.g., on the
+   [release page](https://github.com/trixi-framework/TrixiParticles.jl/releases). For this manual,
+   we will assume that the latest release was `v0.2.3`.
+3) Decide on the next version number. We follow [semantic versioning](https://semver.org/),
+   thus each version is of the form `vX.Y.Z` where `X` is the major version, `Y` the minor
+   version, and `Z` the patch version. In this manual, we assume that the major version is
+   always `0`, thus the decision process on the new version is as follows:
+   * If the new release contains *breaking changes* (i.e., user code might not work as
+     before without modifications), increase the *minor* version by one and set the
+     *patch* version to zero. In our example, the new version should thus be `v0.3.0`.
+   * If the new release only contains minor modifications and/or bug fixes, the *minor*
+     version is kept as-is and the *patch* version is increased by one. In our example, the
+     new version should thus be `v0.2.4`.
+4) Edit the `version` string in the
+   [`Project.toml`](https://github.com/trixi-framework/TrixiParticles.jl/blob/main/Project.toml)
+   and set it to the new version. Push/merge this change to `main`.
+5) Go to GitHub and add a comment to the commit that you would like to become the new
+   release (typically this will be the commit where you just updated the version). You can
+   comment on a commit by going to the
+   [commit overview](https://github.com/trixi-framework/TrixiParticles.jl/commits/main/) and clicking
+   on the title of the commit. The comment should contain the following text:
+   ```
+   @JuliaRegistrator register
+   ```
+6) Wait for the magic to happen! Specifically, JuliaRegistrator will create a new PR to the
+   Julia registry with the new release information. After a grace period of ~15 minutes,
+   this PR will be merged automatically. A short while after,
+   [TagBot](https://github.com/trixi-framework/TrixiParticles.jl/blob/main/.github/workflows/TagBot.yml)
+   will create a new release of TrixiParticles.jl in our GitHub repository.
+7) Once the new release has been created, the new version can be obtained through the Julia
+   package manager as usual.
+8) To make sure people do not mistake the latest state of `main` as the latest release, we
+   set the version in the `Project.toml` to a *development* version. The development version
+   should be the latest released version, with the patch version incremented by one, and the
+   `-dev` suffix added. For example, if you just released `v0.3.0`, the new development
+   version should be `v0.3.1-dev`. If you just released `v0.2.4`, the new development
+   version should be `v0.2.5-dev`.
+