PyLammpsMPI

Install with pip

pip install pylammpsmpi

Example usage

Setting up a simulation

from pylammpsmpi import LammpsLibrary

Set up a job which runs on 2 cores

lmp = LammpsLibrary(cores=2)

Read an input file

lmp.file("tests/in.simple")

Check version of lammps

lmp.version

20190807

Check number of atoms

lmp.natoms

256

Run commands

lmp.command("run 1")

lmp.command(["run 1", "run 1"])

Commands can also be direct

lmp.run(10)

lmp.mass(1, 20)

Extract a global property

lmp.extract_global("boxxhi", 1)

6.718384765530029

Access thermo quantities

lmp.get_thermo("temp")

array(1.12985322)

Thermo quantities can also be accessed directly,

lmp.temp

array(1.12985322)

lmp.press

array(-2.60581752)

Accessing simulation box

lmp.extract_box()

([0.0, 0.0, 0.0],
 [6.718384765530029, 6.718384765530029, 6.718384765530029],
 0.0,
 0.0,
 0.0,
 [1, 1, 1],
 0)

Accessing and changing atom properties

Get individual atom properties, for example force on each atoms

ff = lmp.gather_atoms("f")
print(type(ff))
print(len(ff))

<class 'numpy.ndarray'>
256

Get atom properties by their ids

ids = lmp.gather_atoms("id")

ff = lmp.gather_atoms("f", ids=ids[:10])
len(ff)

10

Change atom properties

ff = ff*0.5
lmp.scatter_atoms("f", ff, ids=ids[:10])

Access value of variables

temp = lmp.extract_variable("tt", "all", 0)
temp

0.8846341461467611

Access value of computes

ke = lmp.extract_compute("ke", 1, 1)
len(ke)

256

v = lmp.extract_compute("v", 1, 2, width=3)
v.shape

(256, 3)

lmp.extract_compute("1", 0, 0)

0.8846341461467611

msd = lmp.extract_compute("msd", 0, 1, length=4)
msd[0]

0.005507481618069701

Access values from fix

x = lmp.extract_fix("2", 0, 1, 1)
x

-2.605817524153117

Change the simulation box

lmp.reset_box([0.0,0.0,0.0], [8.0,8.0,8.0], 0.0,0.0,0.0)