bigd4
commented
1 year ago You can use ase to read .traj file by from ase.io import read; frames = read('xxx.traj',':'). Or you can save the structures as .xyz by use write('selected.xyz', [a[i] for i in selected_i]), format='extxyz' to replace write('selected.traj', [a[i] for i in selected_i]) in plot_select_structure.py
I got plot_select_structure.py to run and produce a plot. It also produces a file 'selected.traj', but that is a binary file. If I want to use this for active learning/retraining my NEP, how to add it to my original .xyz training file? Also, in the GPUMD paper as in Fig 7 and 8, how to plot Fig 7, and how to see which points represent certain structures as in Fig 8? Thanks.