LAMMPSrun

Introduction

LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) is a classical molecular dynamics code.

“LAMMPS has potentials for soft materials (biomolecules, polymers) and solid-state materials (metals, semiconductors) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale.”

This is LAMMPSrun ASE implementation of the interface to LAMMPSRUN.

Environment variables

The environment variable ASE_LAMMPSRUN_COMMAND should contain the path to the lammps binary, or more generally, a command line possibly also including an MPI-launcher command. For example (in a Bourne-shell compatible environment):

$ export ASE_LAMMPSRUN_COMMAND=/path/to/lmp_binary

or possibly something similar to

$ export ASE_LAMMPSRUN_COMMAND="/path/to/mpirun --np 4 lmp_binary"

LAMMPS Calculator

The LAMMPSRUN calculator first appeared in ASE version 3.5.0. At the time of the release of ASE 3.17.0, the LAMMPS calculator is still a thin wrapper containing basic features to enable the use of LAMMPS in ASE (missing some feature might have been added in the source code development tree or some more recent version of ASE).

class ase.calculators.LAMMPSrun.LAMMPS(..., keyword=value, ...)

Below follows a list with a selection of parameters

keyword

type

default value

description

specorder

list

None

List containing the atom species;

always_triclinic

bool

False

LAMMPS treats orthorhombic and tilted cells differently (extra parameters in input and output-files).

keep_alive

bool

True

Do not restart LAMMPS for each query; perform only a reset to a clean state.

keep_tmp_files

bool

False

Generated LAMMPS input and output-files are not deleted.

tmp_dir

string

None

Location to write tmp-files.

files

list

[]

List of files needed by LAMMPS. Typically a list of potential files.

verbose

bool

False

Print additional debugging output to STDOUT.

write_velocities

bool

False

Forward ASE velocities to LAMMPS.

Example

A simple example.

from ase import Atoms, Atom
from ase.calculators.lammpsrun import LAMMPS

a = [6.5, 6.5, 7.7]
d = 2.3608
NaCl = Atoms([Atom('Na', [0, 0, 0]),
              Atom('Cl', [0, 0, d])],
             cell=a, pbc=True)

calc = LAMMPS()
NaCl.set_calculator(calc)

print(NaCl.get_stress())

Setting up an OPLS calculation

There are some modules to facilitate the setup of an OPLS force field calculation, see ase.io.opls.