mirror of https://github.com/lammps/lammps.git
92 lines
2.0 KiB
Python
Executable File
92 lines
2.0 KiB
Python
Executable File
#!/usr/bin/env python -i
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# preceeding line should have path for Python on your machine
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# viz_vmd.py
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# Purpose: viz running LAMMPS simulation via VMD
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# Syntax: viz_vmd.py in.lammps Nfreq Nsteps
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# in.lammps = LAMMPS input script
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# Nfreq = dump and viz shapshot every this many steps
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# Nsteps = run for this many steps
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import sys
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sys.path.append("./pizza")
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# parse command line
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argv = sys.argv
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if len(argv) != 4:
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print "Syntax: viz_vmd.py in.lammps Nfreq Nsteps"
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sys.exit()
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infile = sys.argv[1]
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nfreq = int(sys.argv[2])
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nsteps = int(sys.argv[3])
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me = 0
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# uncomment if running in parallel via Pypar
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#import pypar
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#me = pypar.rank()
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#nprocs = pypar.size()
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from lammps import lammps
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lmp = lammps()
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# run infile all at once
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# assumed to have no run command in it
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lmp.file(infile)
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lmp.command("thermo %d" % nfreq)
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lmp.command("dump python all atom %d tmp.dump" % nfreq)
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# initial 0-step run to generate dump file and image
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lmp.command("run 0 pre yes post no")
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ntimestep = 0
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# wrapper on VMD window via Pizza.py vmd tool
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# just proc 0 handles reading of dump file and viz
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if me == 0:
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from vmd import vmd
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v = vmd()
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v('menu main off')
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v.rep('VDW')
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from dump import dump
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from pdbfile import pdbfile
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d = dump('tmp.dump',0)
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p = pdbfile(d)
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d.next()
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d.unscale()
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p.single(ntimestep)
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v.new('tmp.pdb','pdb')
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# run nfreq steps at a time w/out pre/post, read dump snapshot, display it
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while ntimestep < nsteps:
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lmp.command("run %d pre no post no" % nfreq)
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ntimestep += nfreq
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if me == 0:
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d.next()
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d.unscale()
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p.single(ntimestep)
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# add frame to current data set
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v.append('tmp.pdb','pdb')
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# delete all frame and add new.
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#v.update('tmp.dump')
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lmp.command("run 0 pre no post yes")
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if me == 0:
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v.flush()
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# uncomment the following, if you want to work with the viz some more.
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#v('menu main on')
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#print "type quit to terminate."
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#v.enter()
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#v.stop()
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# uncomment if running in parallel via Pypar
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#print "Proc %d out of %d procs has" % (me,nprocs), lmp
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#pypar.finalize()
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