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split.py
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Wed, Nov 6, 23:17

split.py
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#!/usr/bin/env python -i
# preceding line should have path for Python on your machine
# split.py
# Purpose: similar to simple.py, but first the world communicator
# is split in two halves and LAMMPS is run only on one partition
# Syntax: split.py in.lammps
# in.lammps = LAMMPS input script
from __future__ import print_function
import sys
# parse command line
argv = sys.argv
if len(argv) != 2:
print("Syntax: simple.py in.lammps")
sys.exit()
infile = sys.argv[1]
me = 0
# this example *only* works with mpi4py version 2.0.0 or later
from mpi4py import MPI
comm = MPI.COMM_WORLD
me = comm.Get_rank()
nprocs = comm.Get_size()
# create two subcommunicators
if me < nprocs // 2: color = 0
else: color = 1
split = comm.Split(color,key=0)
if color == 0:
from lammps import lammps
lmp = lammps(comm=split)
# 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)
epsilon = 0.1
x[0] += epsilon
lmp.scatter_atoms("x",1,3,x)
lmp.command("run 1");
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])
print("Proc %d out of %d procs has" % (me,nprocs), lmp)
print("Calculation on partition 0 complete")
else:
# could run a 2nd calculation on second partition
# with different LAMMPS instance or another code
# in this case, just sleep on second partition
import time
time.sleep(2)
print("Calculation on partition 1 complete")
# shutdown mpi4py
comm.Barrier()
MPI.Finalize()

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