Topology¶

Importing structure¶

To create bond topology you first need a LAMMPS data file with the Masses and Atoms sections. This can be generated from any structure file (cif, xyz, pdb, vesta, etc.) by the command-line tool atomsk:

atomsk structure.cif lmp

It can also be generated other ways such as topotools or pymatgen:

import pymatgen.io.lammps.data as pgld
from pymatgen import Structure

pg_structure = Structure.from_file('structure.cif')
ld_object = pgld.LammpsData.from_structure(pg_structure)
ld_object.write_file('structure.lmp')

The Masses section must have a comment after each mass with the name of the element. Element names are added automatically by atomsk but not by pymatgen. For example:

Masses

 207.200000000 # Pb
  14.006700000 # N
  12.010700000 # C
 126.904470000 # I

The Atoms section lists all atom coordinates. It can optionally have a column with the atomic charges.

Creating bond topology¶

First specify pairs of atoms to bond and the maximum distance for bonding. The following will create bonds between nitrogen and carbon atoms up to 1.5 Angstroms and between carbon atoms up to 1.52 Angstroms:

import pandas as pd

bond_pairs = pd.DataFrame(data = dict(element1 = ['N',  'C'],
                                      element2 = ['C',  'C'],
                                      cutoff   = [1.5, 1.52]))

To add bond, angle and dihedral information to the LAMMPS file:

import lammps_helper as lh
bonds =  lh.add_bond_data('lammps_data.lmp', bond_pairs)
angles, dihedrals = lh.add_angle_dihedral_data('lammps_data.lmp', bonds)

Keep in mind that the topology must be very simple. This code probably cannot handle cyclic molecules. If your structure has molecules with rings, I suggest you use moltemplate to generate the structure or lammps-interface to convert the structure from a .cif file.