Untitled

import os
import pandas as pd
import matplotlib.pyplot as plt
from ase import Atoms
from ase.visualize import view
from ase.io import read
import numpy as np
import pickle

log = pd.read_csv('traj-3/dynamics.csv') # path to whichever trajectory you want to inspect

NATOM    = 48
FORMULA  = "O6C2Ru40"
BOX      = [[4,0,0],[1,1.73205081,0],[0,0,10.99]]
BOX      = np.dot(BOX,2.75)
POSFLAGS = ["{}_{}".format(u,i) for i in range(1,NATOM+1) for u in ['x','y','z']]

NTIME   = log['time'].count()
TRAJPOS = log[["time"]+POSFLAGS].to_numpy()[:,1:].reshape(NTIME,NATOM,3)
traj = []
for i in range(len(TRAJPOS)):
     traj.append(Atoms(FORMULA,cell=BOX,pbc=[True,True,True],positions=TRAJPOS[i]
                 ))