cd166c6f2f
this wrapper allows to spawn an instance of VMD as an ancillary process under python and supports a few simple manipulations through converting them to tcl commands. also arbitrary tcl commands can be forwarded by the object to the vmd instance.
92 lines
2.0 KiB
Python
Executable File
92 lines
2.0 KiB
Python
Executable File
#!/usr/local/bin/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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