git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5229 f3b2605a-c512-4ea7-a41b-209d697bcdaa

python/examples/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 GL window via Pizza.py gl tool
+# 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()