pymatgen.io.lammps.utils module

This module defines utility classes and functions.

class LammpsRunner(input_filename='lammps.in', bin='lammps')

Bases: object

LAMMPS wrapper

Parameters:

• input_filename (string) – input file name

• bin (string) – command to run, excluding the input file name

run()

Write the input/data files and run LAMMPS.

class Polymer(start_monomer, s_head, s_tail, monomer, head, tail, end_monomer, e_head, e_tail, n_units, link_distance=1.0, linear_chain=False)

Bases: object

Generate polymer chain via Random walk. At each position there are a total of 5 possible moves(excluding the previous direction).

Parameters:

• start_monomer (Molecule) – Starting molecule

• s_head (int) – starting atom index of the start_monomer molecule

• s_tail (int) – tail atom index of the start_monomer

• monomer (Molecule) – The monomer

• head (int) – index of the atom in the monomer that forms the head

• tail (int) – tail atom index. monomers will be connected from tail to head

• end_monomer (Molecule) – Terminal molecule

• e_head (int) – starting atom index of the end_monomer molecule

• e_tail (int) – tail atom index of the end_monomer

• n_units (int) – number of monomer units excluding the start and terminal molecules

• link_distance (float) – distance between consecutive monomers

• linear_chain (bool) – linear or random walk polymer chain