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Merge pull request #201 from InteractiveComputerGraphics/remove_octree
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Remove octree-based domain decomposition
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@w1th0utnam3
w1th0utnam3 authored Oct 13, 2023
2 parents e668d88 + 0469cb7 commit 73bc254
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5 changes: 4 additions & 1 deletion CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,10 @@

The following changes are present in the `main` branch of the repository and are not yet part of a release:

- N/A
- Lib: Remove octree-based domain decomposition (superseded by regular grid subdivision approach `--subdomain-grid`)
- CLI: Set `--subdomain-grid=on` by default
- CLI: Remove all arguments for octree-based domain decomposition
- CLI: Remove options to output some debug files (octree grid, density map, etc.)

## Version 0.10.0

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212 changes: 7 additions & 205 deletions splashsurf/src/reconstruction.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -4,10 +4,10 @@ use clap::value_parser;
use indicatif::{ProgressBar, ProgressStyle};
use log::info;
use rayon::prelude::*;
use splashsurf_lib::mesh::{AttributeData, Mesh3d, MeshAttribute, MeshWithData, PointCloud3d};
use splashsurf_lib::mesh::{AttributeData, Mesh3d, MeshAttribute, MeshWithData};
use splashsurf_lib::nalgebra::{Unit, Vector3};
use splashsurf_lib::sph_interpolation::SphInterpolator;
use splashsurf_lib::{density_map, profile, Aabb3d, Index, Real};
use splashsurf_lib::{profile, Aabb3d, Index, Real};
use std::borrow::Cow;
use std::convert::TryFrom;
use std::path::PathBuf;
Expand Down Expand Up @@ -122,7 +122,7 @@ pub struct ReconstructSubcommandArgs {
#[arg(
help_heading = ARGS_OCTREE,
long,
default_value = "off",
default_value = "on",
value_name = "off|on",
ignore_case = true,
require_equals = true
Expand All @@ -132,55 +132,6 @@ pub struct ReconstructSubcommandArgs {
#[arg(help_heading = ARGS_OCTREE, long, default_value="64")]
pub subdomain_cubes: u32,

/// Enable spatial decomposition using an octree (faster) instead of a global approach
#[arg(
help_heading = ARGS_OCTREE,
long,
default_value = "on",
value_name = "off|on",
ignore_case = true,
require_equals = true
)]
pub octree_decomposition: Switch,
/// Enable stitching of the disconnected local meshes resulting from the reconstruction when spatial decomposition is enabled (slower, but without stitching meshes will not be closed)
#[arg(
help_heading = ARGS_OCTREE,
long,
default_value = "on",
value_name = "off|on",
ignore_case = true,
require_equals = true
)]
pub octree_stitch_subdomains: Switch,
/// The maximum number of particles for leaf nodes of the octree, default is to compute it based on the number of threads and particles
#[arg(help_heading = ARGS_OCTREE, long)]
pub octree_max_particles: Option<usize>,
/// Safety factor applied to the kernel compact support radius when it's used as a margin to collect ghost particles in the leaf nodes when performing the spatial decomposition
#[arg(help_heading = ARGS_OCTREE, long)]
pub octree_ghost_margin_factor: Option<f64>,
/// Enable computing particle densities in a global step before domain decomposition (slower)
#[arg(
help_heading = ARGS_OCTREE,
long,
default_value = "off",
value_name = "off|on",
ignore_case = true,
require_equals = true
)]
pub octree_global_density: Switch,
/// Enable computing particle densities per subdomain but synchronize densities for ghost-particles (faster, recommended).
/// Note: if both this and global particle density computation is disabled the ghost particle margin has to be increased to at least 2.0
/// to compute correct density values for ghost particles.
#[arg(
help_heading = ARGS_OCTREE,
long,
default_value = "on",
value_name = "off|on",
ignore_case = true,
require_equals = true
)]
pub octree_sync_local_density: Switch,

/// Enable omputing surface normals at the mesh vertices and write them to the output file
#[arg(
help_heading = ARGS_INTERP,
Expand Down Expand Up @@ -337,15 +288,6 @@ pub struct ReconstructSubcommandArgs {
)]
pub output_raw_mesh: Switch,

/// Optional filename for writing the point cloud representation of the intermediate density map to disk
#[arg(help_heading = ARGS_DEBUG, long, value_parser = value_parser!(PathBuf))]
pub output_dm_points: Option<PathBuf>,
/// Optional filename for writing the grid representation of the intermediate density map to disk
#[arg(help_heading = ARGS_DEBUG, long, value_parser = value_parser!(PathBuf))]
pub output_dm_grid: Option<PathBuf>,
/// Optional filename for writing the octree used to partition the particles to disk
#[arg(help_heading = ARGS_DEBUG, long, value_parser = value_parser!(PathBuf))]
pub output_octree: Option<PathBuf>,
/// Enable checking the final mesh for holes and non-manifold edges and vertices
#[arg(
help_heading = ARGS_DEBUG,
Expand Down Expand Up @@ -472,7 +414,7 @@ mod arguments {
use log::info;
use regex::{escape, Regex};
use splashsurf_lib::nalgebra::Vector3;
use splashsurf_lib::{Aabb3d, ParticleDensityComputationStrategy};
use splashsurf_lib::Aabb3d;
use std::convert::TryFrom;
use std::fs;
use std::path::{Path, PathBuf};
Expand Down Expand Up @@ -577,37 +519,7 @@ mod arguments {
Some(splashsurf_lib::SpatialDecomposition::UniformGrid(
splashsurf_lib::GridDecompositionParameters {
subdomain_num_cubes_per_dim: args.subdomain_cubes,
},
))
} else if args.octree_decomposition.into_bool() {
let subdivision_criterion = if let Some(max_particles) = args.octree_max_particles {
splashsurf_lib::SubdivisionCriterion::MaxParticleCount(max_particles)
} else {
splashsurf_lib::SubdivisionCriterion::MaxParticleCountAuto
};
let ghost_particle_safety_factor = args.octree_ghost_margin_factor;
let enable_stitching = args.octree_stitch_subdomains.into_bool();

let particle_density_computation = if args.octree_global_density.into_bool()
&& args.octree_sync_local_density.into_bool()
{
return Err(anyhow!("Cannot enable both global and merged local particle density computation at the same time. Switch off at least one."));
} else {
if args.octree_global_density.into_bool() {
ParticleDensityComputationStrategy::Global
} else if args.octree_sync_local_density.into_bool() {
ParticleDensityComputationStrategy::SynchronizeSubdomains
} else {
ParticleDensityComputationStrategy::IndependentSubdomains
}
};

Some(splashsurf_lib::SpatialDecomposition::Octree(
splashsurf_lib::OctreeDecompositionParameters {
subdivision_criterion,
ghost_particle_safety_factor,
enable_stitching,
particle_density_computation,
..Default::default()
},
))
} else {
Expand Down Expand Up @@ -673,9 +585,6 @@ mod arguments {
is_sequence: bool,
input_file: PathBuf,
output_file: PathBuf,
output_density_map_points_file: Option<PathBuf>,
output_density_map_grid_file: Option<PathBuf>,
output_octree_file: Option<PathBuf>,
sequence_range: (Option<usize>, Option<usize>),
}

Expand All @@ -685,17 +594,11 @@ mod arguments {
input_file: P,
output_base_path: Option<P>,
output_file: P,
output_density_map_points_file: Option<P>,
output_density_map_grid_file: Option<P>,
output_octree_file: Option<P>,
sequence_range: (Option<usize>, Option<usize>),
) -> Result<Self, anyhow::Error> {
let input_file = input_file.into();
let output_base_path = output_base_path.map(|p| p.into());
let output_file = output_file.into();
let output_density_map_points_file = output_density_map_points_file.map(|p| p.into());
let output_density_map_grid_file = output_density_map_grid_file.map(|p| p.into());
let output_octree_file = output_octree_file.map(|p| p.into());

if let (Some(start), Some(end)) = sequence_range {
if start > end {
Expand Down Expand Up @@ -727,21 +630,13 @@ mod arguments {
is_sequence,
input_file,
output_file,
output_density_map_points_file: output_density_map_points_file
.map(|f| output_base_path.join(f)),
output_density_map_grid_file: output_density_map_grid_file
.map(|f| output_base_path.join(f)),
output_octree_file: output_octree_file.map(|f| output_base_path.join(f)),
sequence_range,
})
} else {
Ok(Self {
is_sequence,
input_file,
output_file,
output_density_map_points_file,
output_density_map_grid_file,
output_octree_file,
sequence_range,
})
}
Expand Down Expand Up @@ -821,14 +716,7 @@ mod arguments {
let output_filename_i = output_pattern.replace("{}", index);
let output_file_i = output_dir.join(output_filename_i);

paths.push(ReconstructionRunnerPaths::new(
input_file_i,
output_file_i,
// Don't write density maps etc. when processing a sequence of files
None,
None,
None,
));
paths.push(ReconstructionRunnerPaths::new(input_file_i, output_file_i));
}
}

Expand All @@ -851,9 +739,6 @@ mod arguments {
ReconstructionRunnerPaths::new(
self.input_file.clone(),
self.output_file.clone(),
self.output_density_map_points_file.clone(),
self.output_density_map_grid_file.clone(),
self.output_octree_file.clone(),
);
1
]
Expand Down Expand Up @@ -950,9 +835,6 @@ mod arguments {
args.input_file_or_sequence.clone(),
args.output_dir.clone(),
output_filename,
args.output_dm_points.clone(),
args.output_dm_grid.clone(),
args.output_octree.clone(),
(args.start_index, args.end_index),
)
}
Expand All @@ -963,25 +845,13 @@ mod arguments {
pub(crate) struct ReconstructionRunnerPaths {
pub input_file: PathBuf,
pub output_file: PathBuf,
pub output_density_map_points_file: Option<PathBuf>,
pub output_density_map_grid_file: Option<PathBuf>,
pub output_octree_file: Option<PathBuf>,
}

impl ReconstructionRunnerPaths {
fn new(
input_file: PathBuf,
output_file: PathBuf,
output_density_map_points_file: Option<PathBuf>,
output_density_map_grid_file: Option<PathBuf>,
output_octree_file: Option<PathBuf>,
) -> Self {
fn new(input_file: PathBuf, output_file: PathBuf) -> Self {
ReconstructionRunnerPaths {
input_file,
output_file,
output_density_map_points_file,
output_density_map_grid_file,
output_octree_file,
}
}
}
Expand Down Expand Up @@ -1423,74 +1293,6 @@ pub(crate) fn reconstruction_pipeline_generic<I: Index, R: Real>(
info!("Done.");
}

// Store octree leaf nodes as hex cells
if let Some(output_octree_file) = &paths.output_octree_file {
info!("Writing octree to \"{}\"...", output_octree_file.display());
io::vtk_format::write_vtk(
reconstruction.octree().unwrap().hexmesh(grid, true),
output_octree_file,
"mesh",
)
.with_context(|| {
format!(
"Failed to write octree to output file \"{}\"",
output_octree_file.display()
)
})?;
info!("Done.");
}

// Store point cloud density map
if let Some(output_density_map_points_file) = &paths.output_density_map_points_file {
info!("Constructing density map point cloud...");
let density_map = reconstruction
.density_map()
.ok_or_else(|| anyhow::anyhow!("No density map was created during reconstruction"))?;

let point_cloud: PointCloud3d<R> = {
let mut points = Vec::with_capacity(density_map.len());
density_map.for_each(|flat_point_index, _| {
let point = grid.try_unflatten_point_index(flat_point_index).unwrap();
points.push(grid.point_coordinates(&point));
});

PointCloud3d::new(points)
};

info!(
"Saving density map point cloud to \"{}\"...",
output_density_map_points_file.display()
);

io::vtk_format::write_vtk(
&point_cloud,
output_density_map_points_file,
"density_map_points",
)?;

info!("Done.");
}

// Store hex-mesh density map
if let Some(output_density_map_grid_file) = &paths.output_density_map_grid_file {
info!("Constructing density map hex mesh...");
let density_map = reconstruction
.density_map()
.ok_or_else(|| anyhow::anyhow!("No density map was created during reconstruction"))?;

let density_mesh =
density_map::sparse_density_map_to_hex_mesh(&density_map, &grid, R::zero());

info!(
"Saving density map hex mesh to \"{}\"...",
output_density_map_grid_file.display()
);

io::vtk_format::write_vtk(density_mesh, output_density_map_grid_file, "density_map")?;

info!("Done.");
}

if postprocessing.check_mesh_closed
|| postprocessing.check_mesh_manifold
|| postprocessing.check_mesh_debug
Expand Down
6 changes: 4 additions & 2 deletions splashsurf_lib/README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -37,13 +37,15 @@ For each of the features, `splashsurf_lib` re-exports the corresponding dependen

Currently, only one method based on a "spatial hashing" strategy is implemented.

`TODO: This section is missing a description of the domain decomposition for more efficient parallelization`

**Short summary**: The fluid density is evaluated or mapped onto a sparse grid using spatial hashing in the support radius of each fluid particle. This implies that memory is only allocated in areas where the fluid density is non-zero. This is in contrast to a naive approach where the marching cubes background grid is allocated for the whole domain. Finally, the marching cubes reconstruction is performed only in those grid cells where an edge crosses the surface threshold. Cells completely in the interior of the fluid are skipped in the marching cubes phase.

**Individual steps**:
1. Construct a "virtual background grid" with the desired resolution of the marching cubes algorithm. In the end, the procedure will place a single surface mesh vertex on each edge of this virtual grid, where the fluid surface crosses the edge (or rather, where the fluid density crosses the specified threshold). Virtual means that no storage is actually allocated for this grid yet; only its topology is used implicitly later.
2. Compute the density of each fluid particle
- Perform a neighborhood search
- Per particle, evaluate an SPH sum over the neighbors to compute its density (based on input parameters of kernel radius and particle rest mass)
- Perform a neighborhood search
- Per particle, evaluate an SPH sum over the neighbors to compute its density (based on input parameters of kernel radius and particle rest mass)
3. Optional: filter out (or rather mask as inactive) single particles if the user provided a "splash detection radius". This is done by performing an additional neighborhood search using this splash detection radius instead of the kernel radius.
4. Compute a "sparse density map": a map from the index of a vertex of the virtual background grid to the corresponding fluid density value. The map will only contain entries for vertices where the fluid density is non-zero. Construction of the map:
- Iterate over all active particles
Expand Down
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