forked from lijiext/lammps
84 lines
1.9 KiB
Python
Executable File
84 lines
1.9 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_pymol.py
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# Purpose: viz running LAMMPS simulation via PyMol
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# Syntax: viz_pymol.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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from __future__ import print_function
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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_pymol.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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# dump a file in native LAMMPS dump format for Pizza.py dump tool
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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 PyMol
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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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import pymol
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pymol.finish_launching()
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from dump import dump
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from pdbfile import pdbfile
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from pymol import cmd as pm
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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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pm.load("tmp.pdb")
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pm.show("spheres","tmp")
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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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pm.load("tmp.pdb")
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pm.forward()
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lmp.command("run 0 pre no post yes")
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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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