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#!/usr/bin/env python -i
# preceeding line should have path for Python on your machine
# simple.py
# Purpose: mimic operation of examples/COUPLE/simple/simple.cpp via Python
# Serial syntax: simple.py in.lammps
# in.lammps = LAMMPS input script
# Parallel syntax: mpirun -np 4 simple.py in.lammps
# in.lammps = LAMMPS input script
# also need to uncomment either Pypar or mpi4py sections below
from __future__ import print_function
import sys
import numpy as np
import ctypes
# parse command line
argv = sys.argv
if len(argv) != 2:
print("Syntax: simple.py in.lammps")
sys.exit()
infile = sys.argv[1]
me = 0
# uncomment this if running in parallel via Pypar
#import pypar
#me = pypar.rank()
#nprocs = pypar.size()
# uncomment this if running in parallel via mpi4py
#from mpi4py import MPI
#me = MPI.COMM_WORLD.Get_rank()
#nprocs = MPI.COMM_WORLD.Get_size()
from lammps import lammps
lmp = lammps()
# run infile one line at a time
lines = open(infile,'r').readlines()
for line in lines: lmp.command(line)
# run 10 more steps
# get coords from LAMMPS
# change coords of 1st atom
# put coords back into LAMMPS
# run a single step with changed coords
lmp.command("run 10")
x = lmp.gather_atoms("x",1,3)
v = lmp.gather_atoms("v",1,3)
epsilon = 0.1
x[0] += epsilon
lmp.scatter_atoms("x",1,3,x)
lmp.command("run 1");
# extract force on single atom two different ways
f = lmp.extract_atom("f",3)
print("Force on 1 atom via extract_atom: ",f[0][0])
fx = lmp.extract_variable("fx","all",1)
print("Force on 1 atom via extract_variable:",fx[0])
# use commands_string() and commands_list() to invoke more commands
strtwo = "run 10\nrun 20"
lmp.commands_string(strtwo)
cmds = ["run 10","run 20"]
lmp.commands_list(cmds)
# delete all atoms
# create_atoms() to create new ones with old coords, vels
# initial thermo should be same as step 20
natoms = lmp.get_natoms()
type = natoms*[1]
lmp.command("delete_atoms group all");
lmp.create_atoms(natoms,None,type,x,v);
lmp.command("run 10");
# uncomment if running in parallel via Pypar
#print("Proc %d out of %d procs has" % (me,nprocs), lmp)
#pypar.finalize()
# uncomment if running in parallel via mpi4py
#print "Proc %d out of %d procs has" % (me,nprocs), lmp
#MPI.Finalize()
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