pymatgen.io.lammps.utils module
This module defines utility classes and functions.
- class LammpsRunner(input_filename='lammps.in', bin='lammps')[source]
Bases:
object
LAMMPS wrapper
- Parameters:
input_filename (str) – input file name
bin (str) – command to run, excluding the input file name
- 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).
- 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