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