How to generate lammps file with full type rather than atomic/charge?

[dapang201]

Thank you for your help! I would like to ask how to generate lammps file with full type.

Best regards.

[casarziga]

'Atoms' section for different atom types:
Full: atom-ID molecule-ID atom-type q x y z
Atomic: atom-ID atom-type x y z
Charge: atom-ID atom-type q x y z

The differences are only in columns, whereby moleculeI-D can be 1, and q (charge) is a function of atom-type. You can also set q=0, and specify the charge in the lammps input file (set group X charge Y, or something like this)

I recommend to use python pandas to manipulate your 'Atoms' section: to add or remove columns that you need to generate a different atom-style. Use something like:

import pandas as pd
df = pd.read_csv('datafile.data', delim_whitespace=True, skiprows=X, nrows=Y, names=['atom-ID', 'atom-type', 'x', 'y', 'z'])

And then manipulate df, and export it: df.to_csv('new.data', sep=' ', header=None, index=None).