I was trying to read the lammps trajectory file using:
from ase.io.lammpsrun import read_lammps_dump
a = read_lammps_dump(‘tiny_EQLB_120_EQLB.lammpstrj’, index=0)
As I assigned the atom symbols, my trajectory file has a str ‘Si’ ‘Ge’, and above command preventing me from reading the dump file. I can use sed and convert the str to int but I need atom symbol to collect the some other parameters from trajectory file.
for example to grab the atom indexes:
t = np.array([atom.index for atom in trj[0] if atom.symbol == target])
Earlier I use to convert lammps trajectory file to extendedxyz (only because atom symbols). Do you have any solution to above problem so everything can be done in ASE?
Best,
Abhi
te = np.array([atom.index for atom in trj[0] if atom.symbol == target])