This module defines utility classes and functions.

class LammpsRunner(input_filename='', bin='lammps')[source]

Bases: object

LAMMPS wrapper

  • input_filename (str) – input file name

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


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)[source]

Bases: object

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

  • 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