In reading trajectory file from LAMMPS dump file

dynasor
1

Hello,

I’m currently trying to import a LAMMPS dump file of a system with two elements, but dynasor keeps reading my file as a system with only one element. I basically followed your example of aluminum_liquid_dynamic, but since the example has one element, I guess I might have to provide some additional code/file for dynasor to handle two-element system… (or I simply might have made a mistake in the code) Can you help me work this out?

These are the lines that I ran to import dump file:

import numpy as np
import matplotlib.pyplot as plt

from dynasor import compute_dynamic_structure_factors, Trajectory
from dynasor.qpoints import get_spherical_qpoints
from dynasor.post_processing import compute_spherical_qpoint_average
from dynasor.logging_tools import set_logging_level

set_logging_level(‘INFO’)

trajectory_filename = ‘dump_test’
traj = Trajectory(
trajectory_filename,
trajectory_format=‘lammps_internal’,
frame_stop=1)

and this was the output that I got

INFO: Trajectory file: dump_test
INFO: Total number of particles: 816
INFO: Number of atom types: 1
INFO: Number of atoms of type X: 816
INFO: Simulation cell (in Angstrom):
[[26.95202407 0. 0. ]
[ 0. 26.95202407 0. ]
[ 0. 0. 26.95202407]]

and this is first part of my dump file

ITEM: TIMESTEP
0
ITEM: NUMBER OF ATOMS
816
ITEM: BOX BOUNDS pp pp pp
0.0000000000000000e+00 2.6952024070000000e+01
0.0000000000000000e+00 2.6952024070000000e+01
0.0000000000000000e+00 2.6952024070000000e+01
ITEM: ATOMS id type x y z
560 2 5.05721 5.82974 5.58473
532 2 1.34249 0.276115 1.55615
509 2 1.1969 3.94284 5.19856
187 1 3.68259 4.29029 3.64209
771 2 5.53167 5.82983 1.63569

2

Hi Jimin_Lee,

Only some trajectory types support automatic reading of atomic types. For your case, with a lammps dump file, you need to specify atomic_indices when setting up your Trajectory. This can be done either in the form of a dictionary or in the form of an index file. See here and here for more information.

Feel free to reach out again if you have any further questions.

3

Thank you for your kind reply!