Converting from existing LAMMPS input files

The Simphony-LAMMPS library provides a set of tools to convert existing lammps data files to SimPhoNy CUDS format. While these tools are not required when using the LAMMPS SimPhoNy engine, they can be helpful in converting existing LAMMPS data to SimPhoNy format. See the following examples:

Conversion from lammps data file to list CUDS `Particles`

from __future__ import print_function

import subprocess

from simlammps import read_data_file
from simlammps.cuba_extension import CUBAExtension

from simphony.core.cuba import CUBA

lammps_script = """# example of creating lammps data file (to be then used by SimPhoNy"
dimension	2
atom_style	atomic

# create geometry
lattice		hex 0.7
region		box block 0 20 0 10 -0.25 0.25
create_box	3 box
create_atoms	1 box

mass		1 1.0
mass		2 1.0
mass		3 1.0

# LJ potentials
pair_style	lj/cut 1.12246
pair_coeff	* * 1.0 1.0 1.12246

# define groups
region	     1 block INF INF INF 1.25 INF INF
group	     lower region 1
region	     2 block INF INF 8.75 INF INF INF
group	     upper region 2
group	     boundary union lower upper
group	     flow subtract all boundary

set	     group lower type 2
set	     group upper type 3

# initial velocities
compute      mobile flow temp
velocity     flow create 1.0 482748 temp mobile
velocity     boundary set 0.0 0.0 0.0

# write atoms to a lammps data file
write_data example.data"""

with open("lammps_example_script", "w") as script_file:
    script_file.write(lammps_script)

subprocess.check_call("lammps < lammps_example_script", shell=True)


particles, state_data = read_data_file("example.data")
print("\n\nFinished converting files")
print("\nA Particles data-set was read from the file:")
print("    '{}' has {} particles".format(
    particles.name,
    particles.count_of(CUBA.PARTICLE)))

for particles in particles:
    number_particles = sum(1 for _ in particles.iter(item_type=CUBA.PARTICLE))

number_materials = sum(1 for _ in state_data.iter_materials())
print("\n{} materials were read from the file.\n".format(number_materials))

box_description = \
    ""\
    "The data-set has the following simulation box description:\n"\
    "    CUBAExtension.BOX_ORIGIN: {}\n" \
    "    CUBAExtension.BOX_VECTORS: {}"

print(box_description.format(
    particles.data_extension[CUBAExtension.BOX_ORIGIN],
    particles.data_extension[CUBAExtension.BOX_VECTORS]))

Note

There needs to be an executable called “lammps” that can be found in the PATH for the example to work.