Merge branch 'main' into oriented-bbox

Author: LasNikas

.github/workflows/SpellCheck.yml

@@ -10,4 +10,4 @@ jobs:
       - name: Checkout Actions Repository
         uses: actions/checkout@v5
       - name: Check spelling
-        uses: crate-ci/typos@v1.35.7
+        uses: crate-ci/typos@v1.37.0

NEWS.md

@@ -9,8 +9,16 @@ used in the Julia ecosystem. Notable changes will be documented in this file for
 ### Features
 
 - Added an incompressible SPH solver `ImplicitIncompressibleSPHSystem` (#751).
+- Added `SplitIntegrationCallback` to integrate the `TotalLagrangianSPHSystem`s
+  in a `Semidiscretization` separately from the other systems (#794).
 
+### Important Bugfixes
 
+- Fixed `kernel_grad` threshold with single precision and small particle spacing (#913).
+- Fixed error with `UpdateCallback` when `SaveSolutionCallback` comes first in the
+  `CallbackSet` (#924).
+- Fixed error when using shifting techniques without `UpdateCallback` (#925).
+- Updated program flow diagram (#917).
 
 ## Version 0.4
 

Project.toml

@@ -1,7 +1,7 @@
 name = "TrixiParticles"
 uuid = "66699cd8-9c01-4e9d-a059-b96c86d16b3a"
 authors = ["erik.faulhaber <44124897+efaulhaber@users.noreply.github.com>"]
-version = "0.4.1-dev"
+version = "0.4.2-dev"
 
 [deps]
 Adapt = "79e6a3ab-5dfb-504d-930d-738a2a938a0e"

README.md

@@ -28,7 +28,9 @@ It offers intuitive configuration, robust pre- and post-processing, and vendor-a
 
 ## Features
 - Incompressible Navier-Stokes
-  - Methods: Weakly Compressible Smoothed Particle Hydrodynamics (WCSPH), Entropically Damped Artificial Compressibility (EDAC)
+  - Methods: Weakly Compressible Smoothed Particle Hydrodynamics (WCSPH),
+    Entropically Damped Artificial Compressibility (EDAC),
+    Implicit Incompressible SPH (IISPH)
   - Models: Surface Tension, Open Boundaries
 - Solid-body mechanics
   - Methods:  Total Lagrangian SPH (TLSPH), Discrete Element Method (DEM)

docs/Project.toml

@@ -2,6 +2,7 @@
 Asciicast = "2600d445-abca-43b9-92aa-ce144ac0b05b"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 DocumenterCitations = "daee34ce-89f3-4625-b898-19384cb65244"
+DocumenterMermaid = "a078cd44-4d9c-4618-b545-3ab9d77f9177"
 Literate = "98b081ad-f1c9-55d3-8b20-4c87d4299306"
 OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
@@ -10,6 +11,7 @@ Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
 Asciicast = "0.1.3"
 Documenter = "1"
 DocumenterCitations = "1"
+DocumenterMermaid = "0.2"
 Literate = "2"
 OrdinaryDiffEq = "6"
 Plots = "1"

docs/literate/src/tut_packing.jl

@@ -140,7 +140,7 @@ background_pressure = 1.0
 
 # For particle interaction, we select a [smoothing kernel](@ref smoothing_kernel)
 # with a suitable smoothing length. Empirically, a factor of `0.8` times the
-# particle spacing gives good results [neher2025robustefficientpreprocessingtechniques](@cite).
+# particle spacing gives good results [Neher2025](@cite).
 smoothing_kernel = SchoenbergQuinticSplineKernel{2}()
 smoothing_length = 0.8 * particle_spacing
 
@@ -203,7 +203,7 @@ plot(packed_ic)
 plot!(geometry, seriestype=:path, color=:black, label=nothing, linewidth=2)
 
 # We can see that the particles now stay inside the geometry,
-# but their distribution near the surface can still be improved by adding boundary particles [neher2025robustefficientpreprocessingtechniques](@cite).
+# but their distribution near the surface can still be improved by adding boundary particles [Neher2025](@cite).
 # Therefore, we set up a dedicated boundary packing system
 # by setting `is_boundary = true`.
 # For convex geometries, it is useful to slightly compress the

docs/make.jl

@@ -1,4 +1,4 @@
-using Documenter, DocumenterCitations
+using Documenter, DocumenterCitations, DocumenterMermaid
 using TrixiParticles
 using TrixiParticles.TrixiBase
 using TrixiParticles.PointNeighbors

docs/src/overview.md

@@ -17,8 +17,65 @@ During a single time step or an intermediate step of the time integration scheme
 `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)
+```mermaid
+%% Make arrows bend at right angles
+%%{ init : { "flowchart" : { "curve" : "stepAfter" }}}%%
 
+%% TD means vertical layout
+flowchart TD
+    %% --- Define color palette and styles ---
+    classDef start_node fill:#d9ead3,stroke:#333,color:#333
+    classDef time_integration fill:#d9d2e9,stroke:#333,color:#333
+    classDef primary_stage fill:#cfe2f3,stroke:#333,color:#333
+    classDef update fill:#eeeeee,stroke:#333,color:#333
+    classDef updates fill:#fff2cc,stroke:#333,color:#333
+    classDef physics fill:#fce5cd,stroke:#333,color:#333
+
+    A(simulation) --> B[time integration];
+
+    %% Add hidden dummy node to branch the arrow nicely
+    B --- dummy[ ];
+    style dummy width:0;
+    dummy --> C["drift!<br/>(update du/dt)"];
+
+    subgraph kick["<div style='padding: 10px; font-weight: bold;'>kick! (update dv/dt)</div>"]
+        %% Horizontal layout within this subgraph
+        direction LR;
+
+        subgraph updates["<div style='padding: 10px; font-weight: bold;'>update_systems_and_nhs</div>"]
+            %% Vertical layout within this subgraph
+            direction TB;
+
+            H["update_positions!<br/>(moving boundaries and structures)"];
+            I["update_nhs!<br/>(update neighborhood search)"];
+            J["update_quantities!<br/>(recalculate density etc.)"];
+            K["update_pressure!<br/>(recalculate pressure etc.)"];
+            L["update_boundary_interpolation!<br/>(interpolate boundary pressure)"];
+            M["update_final!<br/>(update shifting)"];
+
+            H --> I --> J --> K --> L --> M;
+        end
+
+        F["system_interaction!<br/>(e.g. momentum/continuity equation)"];
+        G["add_source_terms!<br/>(gravity and source terms)"];
+
+        updates --> F --> G;
+    end
+
+    dummy --> kick;
+
+    %% Color the sub-tasks by their function
+    class A start_node;
+    class B time_integration;
+    class C primary_stage;
+    class kick primary_stage;
+    class updates update;
+    class H,I,J,K,L,M updates;
+    class F,G physics;
+
+    %% Style the arrows
+    linkStyle default stroke-width:2px,stroke:#555
+```
 
 ## Structure
 What we refer to as schemes are various models such as Weakly Compressible Smoothed Particle Hydrodynamics (WCSPH)

docs/src/preprocessing/preprocessing.md

@@ -302,7 +302,7 @@ Pages = [joinpath("preprocessing", "geometries", "io.jl")]
 ```
 
 # [Particle Packing](@id particle_packing)
-To obtain a body-fitted and isotropic particle distribution, an initial configuration (see [Sampling of Geometries](@ref sampling_of_geometries)) is first generated. This configuration is then packed using a [`ParticlePackingSystem`](@ref) following the steps introduced in [neher2025robustefficientpreprocessingtechniques](@cite).
+To obtain a body-fitted and isotropic particle distribution, an initial configuration (see [Sampling of Geometries](@ref sampling_of_geometries)) is first generated. This configuration is then packed using a [`ParticlePackingSystem`](@ref) following the steps introduced in [Neher2025](@cite).
 For a hands-on tutorial with complete examples, see the particle packing tutorial.
 The preprocessing pipeline consists of the following steps: