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viz_pymol.py
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Sat, Nov 9, 10:25

viz_pymol.py
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#!/usr/local/bin/python -i
# preceeding line should have path for Python on your machine
# viz_pymol.py
# Purpose: viz running LAMMPS simulation via PyMol
# Syntax: viz_pymol.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_pymol.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 native LAMMPS dump format for Pizza.py dump tool
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 PyMol
# just proc 0 handles reading of dump file and viz
if me == 0:
import pymol
pymol.finish_launching()
from dump import dump
from pdbfile import pdbfile
from pymol import cmd as pm
d = dump("tmp.dump",0)
p = pdbfile(d)
d.next()
d.unscale()
p.single(ntimestep)
pm.load("tmp.pdb")
pm.show("spheres","tmp")
# 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)
pm.load("tmp.pdb")
pm.forward()
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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