polypy

polygon (ring network) discovery from XYZ files.

polypy is a python script to analyze (shortest-path) rings in structures read from xyz-files. It can be used to identify defects in crystal structures or molecules.

Features

• Shortest-path ring search using Franzblau statistics [Phys. Rev. B 44, 4925]
• Generate xyz files with atoms marked for visualization of rings
• Detect subgraphs; defect clusters; atom chains; neighbor shells
• Progress bars!

Obtain code

The only file required is "polypy", simply download it or clone this repository.

Example use

polypy file.xyz                                 *use default settings*
polypy -s -d0 --pbc "15.0 21.0 12.0" file.xyz   *simplified info file, (d0) inifinite depth search, and periodic boundary conditions*
polypy -h                                       *print standard help*