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viz_vmd.py
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Tue, Nov 19, 08:30

viz_vmd.py
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#!/usr/local/bin/python -i
# preceeding line should have path for Python on your machine
# viz_vmd.py
# Purpose: viz running LAMMPS simulation via VMD
# Syntax: viz_vmd.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
import sys
sys.path.append("./pizza")
# parse command line
argv = sys.argv
if len(argv) != 4:
print "Syntax: viz_vmd.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
lmp.file(infile)
lmp.command("thermo %d" % nfreq)
lmp.command("dump python all atom %d tmp.dump" % nfreq)
# initial 0-step run to generate dump file and image
lmp.command("run 0 pre yes post no")
ntimestep = 0
# wrapper on VMD window via Pizza.py vmd tool
# just proc 0 handles reading of dump file and viz
if me == 0:
from vmd import vmd
v = vmd()
v('menu main off')
v.rep('VDW')
from dump import dump
from pdbfile import pdbfile
d = dump('tmp.dump',0)
p = pdbfile(d)
d.next()
d.unscale()
p.single(ntimestep)
v.new('tmp.pdb','pdb')
# 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:
d.next()
d.unscale()
p.single(ntimestep)
# add frame to current data set
v.append('tmp.pdb','pdb')
# delete all frame and add new.
#v.update('tmp.dump')
lmp.command("run 0 pre no post yes")
if me == 0:
v.flush()
# uncomment the following, if you want to work with the viz some more.
#v('menu main on')
#print "type quit to terminate."
#v.enter()
#v.stop()
# uncomment if running in parallel via Pypar
#print "Proc %d out of %d procs has" % (me,nprocs), lmp
#pypar.finalize()

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