Parallel cell-based 3D voronoi tessellations

multivoro is a python library that allows building 3D Voronoi/Laguerre tessellations with voro++ exposed in python via the nanobind library. It leverages the latest multi-threaded extension of Voro++ to allow computing the voronoi cells in parallel.

Codebases

• Voro++
• nanobind

Installation

Wheels

There are available pre-compiled wheels to pip install for Linux and macOS. However, note that these wheels are compiled without multithreading support.

To install them in your system:

pip install multivoro

Source

To build multivoro from source in Ubuntu:

Setup a python virtual environment:

# python versions to choose from: [python3.8-python3.12]
sudo apt install python3.10-dev python3.10-venv
python3.10 -mvenv venv
source ./venv/bin/activate

Install openmp runtime and compile the wheel:

sudo apt install libomp-dev
git clone --recurse-submodules https://github.com/eleftherioszisis/multivoro.git
cd multivoro
USE_OpenMP=ON pip install .

USE_OpenMP environment variable is used as an option in multivoro cmake. By default it is set to 'OFF'.

Usage

from multivoro import compute_voronoi

cells = compute_voronoi(
    points=[[-1.0, 0.0, 0.0], [1.0, 0.0, 0.0]],
    radii=[1.0, 1.0],
    limits=[[-2.0, -1.0, -1.0], [2.0, 1.0, 1.0]],
    n_threads=6,
)

for cell in cells:
    print(cell.get_vertices())
    print(cell.get_neighbors())
    print(cell.get_face_vertices())

Voro++ Copyright And Acknowledgments

Copyright Notice

Voro++ Copyright (c) 2008, The Regents of the University of California, through Lawrence Berkeley National Laboratory (subject to receipt of any required approvals from the U.S. Dept. of Energy). All rights reserved.

If you have questions about your rights to use or distribute this software, please contact Berkeley Lab's Technology Transfer Department at [email protected].

NOTICE. This software was developed under partial funding from the U.S. Department of Energy. As such, the U.S. Government has been granted for itself and others acting on its behalf a paid-up, nonexclusive, irrevocable, worldwide license in the Software to reproduce, prepare derivative works, and perform publicly and display publicly. Beginning five (5) years after the date permission to assert copyright is obtained from the U.S. Department of Energy, and subject to any subsequent five (5) year renewals, the U.S. Government is granted for itself and others acting on its behalf a paid-up, nonexclusive, irrevocable, worldwide license in the Software to reproduce, prepare derivative works, distribute copies to the public, perform publicly and display publicly, and to permit others to do so.

Acknowledgments

This work (voro++) was supported by the Director, Office of Science, Computational and Technology Research, U.S. Department of Energy under Contract No. DE-AC02-05CH11231.