Introduction

This script is designed to convert molecular dynamics (MD) trajectories generated by GPUMD into a single unit-cell configuration. A detailed methodology for visualizing atomic distributions from such simulations is described in National Science Review 11, nwae216 (2024).

Input Files

Please prepare the following two input files:

1. inp.dat: specifies the supercell size, number of atomic types, and other basic settings;
2. dump.xyz: contains the MD trajectory coordinates.

We have included a complete example for Cs₃Bi₂I₆Cl₃, with inp.dat, dump.xyz, and all supporting files.