Originally written by @YuanbinLiu during his time at @vldgroup.
voidkit is a Python tool for identifying and analysing voids in atomistic structures of materials.
Voids are defined as connected empty regions identified using a regular probing grid.
The code outputs the Cartesian coordinates of individual voids, which can be used for visualisation.
In addition, an effective void radius is computed as a global quantity characterising the entire structure.
The code supports the following input formats:
.extxyzfiles- LAMMPS dump files
The input file may contain either a single structure or multiple frames.
- For a single structure, results are computed for that frame.
- For multiple frames, the code returns the average value.
A typical command is shown below:
python void_multi_process.py \
--input traj.extxyz \
--cutoff 2.9 \
--grid_spacing 0.29 \
--min_points 5 \
--threads 1Install the required Python dependencies using:
pip install -r requirements.txtIf you use this code in your work, please consider citing the following work:
Medium-range structural order in amorphous arsenic
Yuanbin Liu, Yuxing Zhou, Richard Ademuwagun, Luc Walterbos,
Janine George, Stephen R. Elliott, Volker L. Deringer
The voidkit code is published and distributed under the MIT License.