Merge branch 'refactor_update' into more_semi_refactor

Author: svchb

.buildkite/pipeline.yml

@@ -2,7 +2,7 @@ steps:
   - label: "CUDA"
     plugins:
       - JuliaCI/julia#v1:
-          version: "1.11"
+          version: "1.12"
     agents:
       queue: "juliagpu"
       cuda: "*"
@@ -16,7 +16,7 @@ steps:
   - label: "AMDGPU"
     plugins:
       - JuliaCI/julia#v1:
-          version: "1.11"
+          version: "1.12"
     agents:
       queue: "juliagpu"
       rocm: "*"
@@ -30,7 +30,7 @@ steps:
   - label: "Metal"
     plugins:
       - JuliaCI/julia#v1:
-          version: "1.11"
+          version: "1.12"
     agents:
       queue: "juliaecosystem"
       os: "macos"

.github/workflows/Documenter.yml

@@ -37,7 +37,7 @@ jobs:
         with:
           version: '1'
           show-versioninfo: true
-      - uses: julia-actions/cache@v2
+      - uses: julia-actions/cache@v3
       - name: Build package
         uses: julia-actions/julia-buildpkg@v1
       - name: Install dependencies

.github/workflows/FormatCheck.yml

@@ -19,7 +19,7 @@ jobs:
         with:
           version: '1'
       - run: julia -e 'using InteractiveUtils; versioninfo(verbose=true)'
-      - uses: julia-actions/cache@v2
+      - uses: julia-actions/cache@v3
       - 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@v6
       - name: Check spelling
-        uses: crate-ci/typos@v1.41.0
+        uses: crate-ci/typos@v1.44.0

.github/workflows/ci.yml

@@ -44,6 +44,7 @@ jobs:
         version:
           - '1.10'
           - '1.11'
+          - '1.12'
         os:
           - ubuntu-latest
         include:
@@ -53,9 +54,9 @@ jobs:
             os: windows-latest
           - version: '1.10'
             os: macos-14
-          - version: '1.11'
+          - version: '1.12'
             os: windows-latest
-          - version: '1.11'
+          - version: '1.12'
             os: macos-14
 
     steps:
@@ -70,7 +71,7 @@ jobs:
       - name: Display Julia version
         run: julia -e 'using InteractiveUtils; versioninfo(verbose=true)'
 
-      - uses: julia-actions/cache@v2
+      - uses: julia-actions/cache@v3
 
       - name: Build package
         uses: julia-actions/julia-buildpkg@v1
@@ -94,7 +95,7 @@ jobs:
       - name: Upload unit coverage report to Codecov
         # Only run coverage in one Job (Ubuntu and latest Julia version)
         if: matrix.os == 'ubuntu-latest' && matrix.version == '1.11'
-        uses: codecov/codecov-action@v5
+        uses: codecov/codecov-action@v6
         with:
           files: lcov.info
           fail_ci_if_error: true
@@ -121,7 +122,7 @@ jobs:
       - name: Upload total coverage report to Codecov
         # Only run coverage in one Job (Ubuntu and latest Julia version)
         if: matrix.os == 'ubuntu-latest' && matrix.version == '1.11'
-        uses: codecov/codecov-action@v5
+        uses: codecov/codecov-action@v6
         with:
           files: lcov.info
           fail_ci_if_error: true

NEWS.md

@@ -6,10 +6,30 @@ used in the Julia ecosystem. Notable changes will be documented in this file for
 
 ## Version 0.4.4
 
+### API Changes
+
+- Custom quantities called in the `PostprocessCallback` are now passed CPU arrays when
+  the simulation is run on a GPU (#1065).
+
 ### Features
 
-- Added `StateEquationAdaptiveCole` an adaptive sound speed version of the Cole state equation (#875)
+- Added `StateEquationAdaptiveCole` an adaptive sound speed version of the Cole state equation (#875).
+- Added `RigidBodySystem` that supports rigid body dynamics for FSI (#1076).
+- Added `RigidContactModel` that supports rigid-wall and rigid-rigid collisions (#1090, #1091).
+- Added a specialized neighborhood search for TLSPH self-interaction (#1016).
+- Added CFL condition for TLSPH and split integration (#1030).
+- Added new validation case hydrostatic water column (#724).
+- Added Carreau–Yasuda non-Newtonian viscosity model (#1010).
 
+### Important Bugfixes
+
+- Fixed the periodic array of cylinders example file (#975).
+- A `StepsizeCallback` can now be used with open boundaries (#1074).
+
+### Documentation
+
+- Added a new tutorial for rigid body dynamics (#1095).
+- Better overview page for tutorials (#1093).
 
 ## Version 0.4.3
 
@@ -34,7 +54,7 @@ used in the Julia ecosystem. Notable changes will be documented in this file for
 
 - Added GPU and FP32 support for DEM (#979).
 
-  
+
 ### Performance
 - Improved GPU performance with shifting up to a factor of 10x (#974, #993).
 
@@ -360,5 +380,3 @@ Features:
 #### TLSPH
 
 An implementation of TLSPH (Total Lagrangian Smoothed Particle Hydrodynamics) for solid bodies enabling FSI (Fluid Structure Interactions).
-
-

Project.toml

@@ -1,9 +1,10 @@
 name = "TrixiParticles"
 uuid = "66699cd8-9c01-4e9d-a059-b96c86d16b3a"
-version = "0.4.4-dev"
+version = "0.4.5-dev"
 authors = ["erik.faulhaber <44124897+efaulhaber@users.noreply.github.com>"]
 
 [deps]
+Accessors = "7d9f7c33-5ae7-4f3b-8dc6-eff91059b697"
 Adapt = "79e6a3ab-5dfb-504d-930d-738a2a938a0e"
 CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
@@ -17,7 +18,6 @@ GPUArraysCore = "46192b85-c4d5-4398-a991-12ede77f4527"
 JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
 KernelAbstractions = "63c18a36-062a-441e-b654-da1e3ab1ce7c"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
-MuladdMacro = "46d2c3a1-f734-5fdb-9937-b9b9aeba4221"
 PointNeighbors = "1c4d5385-0a27-49de-8e2c-43b175c8985c"
 Polyester = "f517fe37-dbe3-4b94-8317-1923a5111588"
 Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
@@ -36,13 +36,17 @@ WriteVTK = "64499a7a-5c06-52f2-abe2-ccb03c286192"
 [weakdeps]
 OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
 OrdinaryDiffEqCore = "bbf590c4-e513-4bbe-9b18-05decba2e5d8"
+CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba"
 
 [extensions]
 TrixiParticlesOrdinaryDiffEqExt = ["OrdinaryDiffEq", "OrdinaryDiffEqCore"]
+TrixiParticlesCUDAExt = "CUDA"
 
 [compat]
+Accessors = "0.1.43"
 Adapt = "4"
 CSV = "0.10"
+CUDA = "5.9.1"
 DataFrames = "1.6"
 DelimitedFiles = "1"
 DiffEqCallbacks = "4"
@@ -52,9 +56,8 @@ ForwardDiff = "1"
 GPUArraysCore = "0.2"
 JSON = "1"
 KernelAbstractions = "0.9"
-MuladdMacro = "0.2"
 OrdinaryDiffEq = "6.91"
-OrdinaryDiffEqCore = "2"
+OrdinaryDiffEqCore = "2, 3"
 PointNeighbors = "0.6.5"
 Polyester = "0.7.10"
 ReadVTK = "0.2"

README.md

@@ -33,7 +33,7 @@ It offers intuitive configuration, robust pre- and post-processing, and vendor-a
     Implicit Incompressible SPH (IISPH)
   - Models: Surface Tension, Open Boundaries
 - Solid-body mechanics
-  - Methods:  Total Lagrangian SPH (TLSPH), Discrete Element Method (DEM)
+  - Methods:  Total Lagrangian SPH (TLSPH), Discrete Element Method (DEM), Rigid Body Dynamics (RBD)
 - Fluid-Structure Interaction
 - Particle sampling of complex geometries from `.stl` and `.asc` files.
 - Output formats:
@@ -178,7 +178,9 @@ or [create an issue](https://github.com/trixi-framework/TrixiParticles.jl/issues
 ## Acknowledgments
 <p align="center">
   <img align="middle" src="https://github.com/trixi-framework/TrixiParticles.jl/assets/44124897/05132bf1-180f-4228-b30a-37dfb6e36ed5" width=20%/>&nbsp;&nbsp;&nbsp;
-  <img align="middle" src="https://github.com/trixi-framework/TrixiParticles.jl/assets/44124897/ae2a91d1-7c10-4e0f-8b92-6ed1c43ddc28" width=20%/>&nbsp;&nbsp;&nbsp;
+  <img align="middle" src="https://github.com/user-attachments/assets/480ceabe-b44c-4dc2-a4ce-d99ba49767f4" width=20%/>&nbsp;&nbsp;&nbsp;
+  <img align="middle" src="https://github.com/user-attachments/assets/80e897bd-c3fc-4bfc-aafb-a6d5810e0206" width=20%/>&nbsp;&nbsp;&nbsp;
 </p>
 
-The project has benefited from funding from [hereon](https://www.hereon.de/) and [HiRSE](https://www.helmholtz-hirse.de/).
+The project has benefited from funding from [hereon](https://www.hereon.de/), [HiRSE](https://www.helmholtz-hirse.de/), and through [ScienceServe](https://www.helmholtz.de/en/research/current-calls-for-applications/article/scienceserve-boosting-research-software-at-helmholtz/) for the MATRIX project.
+

docs/literate/src/tut_custom_kernel.jl

@@ -60,29 +60,30 @@ struct MyGaussianKernel <: TrixiParticles.AbstractSmoothingKernel{2} end
 
 # By looking at the implementation of existing kernels in TrixiParticles.jl,
 # we can see that a kernel implementation requires three functions.
-# `TrixiParticles.kernel`, which is the kernel function itself,
-# `TrixiParticles.kernel_deriv`, which is the derivative of the kernel function,
-# and `TrixiParticles.compact_support`, which defines the compact support of the
-# kernel in relation to the smoothing length.
+# `TrixiParticles.kernel_unsafe`, which is the kernel function itself,
+# `TrixiParticles.kernel_deriv_div_r_unsafe`, which is the derivative of the
+# kernel divided by ``r``, and `TrixiParticles.compact_support`, which defines
+# the compact support of the kernel in relation to the smoothing length.
 # The latter is relevant for determining the search radius of the neighborhood search.
-function TrixiParticles.kernel(kernel::MyGaussianKernel, r, h)
+#
+# We implement `kernel_deriv_div_r_unsafe` instead of `kernel_deriv` directly since
+# this avoids an extra division in the hot loop and is robust near ``r=0``.
+# The public function `TrixiParticles.kernel_deriv` is defined automatically by
+# TrixiParticles from this method (and multiplies by ``r`` again when needed).
+# In the unsafe functions, we do not check the compact support; this is handled in the
+# safe wrappers `TrixiParticles.kernel` and `TrixiParticles.kernel_deriv` based on the
+# compact support defined in `TrixiParticles.compact_support`.
+function TrixiParticles.kernel_unsafe(kernel::MyGaussianKernel, r::Real, h)
     q = r / h
 
-    if q < 2
-        return 1 / (pi * h^2) * exp(-q^2)
-    end
-
-    return 0.0
+    return 1 / (pi * h^2) * exp(-q^2)
 end
 
-function TrixiParticles.kernel_deriv(kernel::MyGaussianKernel, r, h)
+function TrixiParticles.kernel_deriv_div_r_unsafe(kernel::MyGaussianKernel, r::Real, h)
     q = r / h
 
-    if q < 2
-        return 1 / (pi * h^2) * (-2 * q) * exp(-q^2) / h
-    end
-
-    return 0.0
+    kernel_deriv = 1 / (pi * h^2) * (-2 * q) * exp(-q^2) / h
+    return kernel_deriv / r
 end
 
 TrixiParticles.compact_support(::MyGaussianKernel, h) = 2 * h

docs/literate/src/tut_packing.jl

@@ -125,8 +125,8 @@ plot!(geometry, linestyle=:dash, label=nothing, showaxis=false, color=:black,
 # ## Particle packing
 
 # In the following, we will essentially follow the same steps described in the fluid tutorials.
-# That means we will generate systems that are then passed to the [`Semidiscretization`](@ref Semidiscretization).
-# The difference from a typical physical simulation is that we use [`ParticlePackingSystem`](@ref ParticlePackingSystem),
+# That means we will generate systems that are then passed to the [`Semidiscretization`](@ref).
+# The difference from a typical physical simulation is that we use [`ParticlePackingSystem`](@ref),
 # which does not represent any physical law. Instead, we only use the simulation framework to time-integrate
 # the packing process.