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viz_atomeye.py
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Tue, May 14, 16:18

viz_atomeye.py
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#!/usr/bin/env python -i
# preceding line should have path for Python on your machine
# viz_atomeye.py
# Purpose: viz running LAMMPS simulation via AtomEye
# Syntax: viz_atomeye.py in.lammps Nfreq Nsteps
# in.lammps = LAMMPS input script
# Nfreq = dump and viz shapshot every this many steps
# Nsteps = run for this many steps
from __future__ import print_function
import sys,os
# set this to point to AtomEye version 3 executable
# first line if want AtomEye output to screen, 2nd line to file
#ATOMEYE3 = "/home/sjplimp/tools/atomeye3/A3.i686-20060530"
ATOMEYE3 = "/home/sjplimp/tools/atomeye3/A3.i686-20060530 > atomeye.out"
# parse command line
argv = sys.argv
if len(argv) != 4:
print("Syntax: viz_atomeye.py in.lammps Nfreq Nsteps")
sys.exit()
infile = sys.argv[1]
nfreq = int(sys.argv[2])
nsteps = int(sys.argv[3])
me = 0
# uncomment if running in parallel via Pypar
#import pypar
#me = pypar.rank()
#nprocs = pypar.size()
from lammps import lammps
lmp = lammps()
# run infile all at once
# assumed to have no run command in it
# dump a file in extended CFG format for AtomEye
lmp.file(infile)
lmp.command("thermo %d" % nfreq)
lmp.command("dump python all cfg %d tmp.cfg.* mass type xs ys zs id" % nfreq)
# initial 0-step run to generate dump file and image
lmp.command("run 0 pre yes post no")
ntimestep = 0
# wrapper on GL window via Pizza.py gl tool
# just proc 0 handles reading of dump file and viz
if me == 0:
a = os.popen(ATOMEYE3,'w')
a.write("load_config tmp.cfg.0\n")
a.flush()
# run nfreq steps at a time w/out pre/post, read dump snapshot, display it
while ntimestep < nsteps:
lmp.command("run %d pre no post no" % nfreq)
ntimestep += nfreq
if me == 0:
a.write("load_config tmp.cfg.%d\n" % ntimestep)
a.flush()
lmp.command("run 0 pre no post yes")
# uncomment if running in parallel via Pypar
#print("Proc %d out of %d procs has" % (me,nprocs), lmp)
#pypar.finalize()

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