trixi-framework · LasNikas · Aug 6, 2024 · Jul 20, 2023 · Jul 22, 2023 · Jul 24, 2023
diff --git a/.gitignore b/.gitignore
@@ -20,4 +20,9 @@ run
 *.vtu
 *.pvd
 *.mp4
-*.csv
+
+# ParaView states
+*.pvsm
+
+# FreeCAD models
+*.FCStd
diff --git a/NEWS.md b/NEWS.md
@@ -9,12 +9,16 @@ We aim at 3 to 4 month between major release versions and about 2 weeks between
 ### Highlights
 
 ### Added
+Particle sampling for complex geometries from `.stl` and `.asc` files.
 
 ### Removed
 
 ### Deprecated
 
-## Version 0.2.0
+## Version 0.2.1
+
+### Highlights
+Particle sampling for complex geometries from `.stl` and `.asc` files.
 
 ### Removed
 - Use of the internal neighborhood search has been removed and replaced with PointNeighbors.jl.

diff --git a/Project.toml b/Project.toml
@@ -8,8 +8,10 @@ Adapt = "79e6a3ab-5dfb-504d-930d-738a2a938a0e"
 CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
+DelimitedFiles = "8bb1440f-4735-579b-a4ab-409b98df4dab"
 DiffEqCallbacks = "459566f4-90b8-5000-8ac3-15dfb0a30def"
 FastPow = "c0e83750-1142-43a8-81cf-6c956b72b4d1"
+FileIO = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549"
 ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
 GPUArraysCore = "46192b85-c4d5-4398-a991-12ede77f4527"
 JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"

diff --git a/README.md b/README.md
@@ -21,6 +21,8 @@ Its features include:
 - Solid-body mechanics
   - Methods:  Total Lagrangian SPH (TLSPH), Discrete Element Method (DEM)
 - Fluid-Structure Interaction
+- Preprocess complex shapes
+  - support for STL geometries
 - Output formats:
   - VTK
 

diff --git a/docs/make.jl b/docs/make.jl
@@ -104,6 +104,9 @@ makedocs(sitename="TrixiParticles.jl",
              "Tutorial" => "tutorial.md",
              "Examples" => "examples.md",
              "Visualization" => "visualization.md",
+             "preprocessing" => [
+                 "Sample Geometries" => joinpath("preprocessing", "preprocessing.md"),
+             ],
              "Components" => [
                  "Overview" => "overview.md",
                  "General" => [

diff --git a/docs/src/preprocessing/preprocessing.md b/docs/src/preprocessing/preprocessing.md
@@ -0,0 +1,27 @@
+
+TODO
+
+
+```@autodocs
+Modules = [TrixiParticles]
+Pages = [joinpath("preprocessing", "point_in_poly", "winding_number_horman.jl")]
+```
+
+```@autodocs
+Modules = [TrixiParticles]
+Pages = [joinpath("preprocessing", "point_in_poly", "winding_number_jacobson.jl")]
+```
+
+```@autodocs
+Modules = [TrixiParticles]
+Pages = [joinpath("preprocessing", "geometries", "io.jl")]
+```
+
+
+### [References](@id references_complex_shape)
+- Alec Jacobson, Ladislav Kavan, and Olga Sorkine-Hornung "Robust inside-outside segmentation using generalized winding numbers".
+  In: ACM Transactions on Graphics, 32.4 (2013), pages 1--12.
+  [doi: 10.1145/2461912.2461916](https://igl.ethz.ch/projects/winding-number/robust-inside-outside-segmentation-using-generalized-winding-numbers-siggraph-2013-jacobson-et-al.pdf)
+- Kai Horman, Alexander Agathos "The point in polygon problem for arbitrary polygons".
+  In: Computational Geometry, 20.3 (2001), pages 131--144.
+  [doi: 10.1016/s0925-7721(01)00012-8](https://doi.org/10.1016/S0925-7721(01)00012-8)
diff --git a/examples/preprocessing/complex_shape_2d.jl b/examples/preprocessing/complex_shape_2d.jl
@@ -0,0 +1,28 @@
+using TrixiParticles
+using Plots
+
+particle_spacing = 0.05
+
+filename = "inverted_open_curve"
+file = joinpath("examples", "preprocessing", "data", filename * ".asc")
+
+geometry = load_geometry(file)
+
+trixi2vtk(geometry)
+
+point_in_geometry_algorithm = WindingNumberJacobson(; geometry,
+                                                    winding_number_factor=0.4,
+                                                    hierarchical_winding=true)
+
+# Returns `InitialCondition`
+shape_sampled = ComplexShape(geometry; particle_spacing, density=1.0,
+                             store_winding_number=true,
+                             point_in_geometry_algorithm)
+
+trixi2vtk(shape_sampled.initial_condition)
+
+# Plot the winding number field
+plot(InitialCondition(; coordinates=shape_sampled.grid, density=1.0, particle_spacing),
+     zcolor=shape_sampled.winding_numbers)
+
+# trixi2vtk(shape_sampled.grid, w=shape_sampled.winding_numbers)
diff --git a/examples/preprocessing/complex_shape_3d.jl b/examples/preprocessing/complex_shape_3d.jl
@@ -0,0 +1,18 @@
+using TrixiParticles
+
+particle_spacing = 0.05
+
+filename = "sphere"
+file = joinpath("examples", "preprocessing", "data", filename * ".stl")
+
+geometry = load_geometry(file)
+
+point_in_geometry_algorithm = WindingNumberJacobson(; geometry,
+                                                    # winding_number_factor=0.4,
+                                                    hierarchical_winding=true)
+
+# Returns `InitialCondition`
+shape_sampled = ComplexShape(geometry; particle_spacing, density=1.0,
+                             point_in_geometry_algorithm)
+
+trixi2vtk(shape_sampled)
diff --git a/examples/preprocessing/data/bar.stl b/examples/preprocessing/data/bar.stl
diff --git a/examples/preprocessing/data/circle.asc b/examples/preprocessing/data/circle.asc
@@ -0,0 +1,65 @@
+# ASCII
+1 0 0
+0.995004 0.0998334 0
+0.980067 0.198669 0
+0.955337 0.29552 0
+0.921061 0.389418 0
+0.877583 0.479426 0
+0.825336 0.564642 0
+0.764842 0.644218 0
+0.696707 0.717356 0
+0.62161 0.783327 0
+0.540302 0.841471 0
+0.453596 0.891207 0
+0.362358 0.932039 0
+0.267499 0.963558 0
+0.169967 0.98545 0
+0.0707372 0.997495 0
+-0.0291995 0.999574 0
+-0.128845 0.991665 0
+-0.227202 0.973848 0
+-0.32329 0.9463 0
+-0.416147 0.909297 0
+-0.504846 0.863209 0
+-0.588501 0.808496 0
+-0.666276 0.745705 0
+-0.737394 0.675463 0
+-0.801144 0.598472 0
+-0.856889 0.515501 0
+-0.904072 0.42738 0
+-0.942222 0.334988 0
+-0.970958 0.239249 0
+-0.989992 0.14112 0
+-0.999135 0.0415806 0
+-0.998295 -0.0583742 0
+-0.98748 -0.157746 0
+-0.966798 -0.255541 0
+-0.936457 -0.350783 0
+-0.896758 -0.44252 0
+-0.8481 -0.529836 0
+-0.790968 -0.611858 0
+-0.725932 -0.687766 0
+-0.653644 -0.756803 0
+-0.574824 -0.818277 0
+-0.490261 -0.871576 0
+-0.400799 -0.916166 0
+-0.307333 -0.951602 0
+-0.210796 -0.97753 0
+-0.112152 -0.993691 0
+-0.0123886 -0.999923 0
+0.0874991 -0.996165 0
+0.186512 -0.982453 0
+0.283662 -0.958924 0
+0.377978 -0.925815 0
+0.468517 -0.883455 0
+0.554374 -0.832267 0
+0.634693 -0.772764 0
+0.70867 -0.70554 0
+0.775566 -0.631267 0
+0.834713 -0.550685 0
+0.88552 -0.464602 0
+0.927478 -0.373877 0
+0.96017 -0.279415 0
+0.983268 -0.182162 0
+0.996542 -0.0830893 0
+1 0 0
diff --git a/examples/preprocessing/data/gear.stl b/examples/preprocessing/data/gear.stl
diff --git a/examples/preprocessing/data/hexagon.asc b/examples/preprocessing/data/hexagon.asc
@@ -0,0 +1,8 @@
+# ASCII
+0.866025 0.5 0
+0 1 0
+-0.866025 0.5 0
+-0.866025 -0.5 0
+-1.11022e-16 -1 0
+0.866025 -0.5 0
+0.866025 0.5 0