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VMD-input.py
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Fri, Jun 28, 21:43

VMD-input.py
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#!/usr/local/bin/python-2.5/bin/python
import sys, os
from getopt import gnu_getopt as getopt
Info="""
Module name: VMD-input.py
Author: (c) Andres Jaramillo-Botero
California Institute of Technology
ajaramil@wag.caltech.edu
Project: pEFF
Version: August 2009
Usage: python VMD-input.py lammps_dump_filename radii_column xpos_column
Example: python VMD-input.py dump.lammpstrj 5 6
1. Extracts the electron radii from a lammps trajectory dump into %s.out
2. Creates %s.xyz file
3. Creates appropriate %.vmd file which can be sourced using TCL/TK in VMD
"""
from lmp2radii_col import makeradii
from lmp2xyz import lmp2xyz
def printHelp(input):
Info%(input,input,input)
if __name__ == '__main__':
# if no input, print help and exit
if len(sys.argv) < 2:
print "Usage: python VMD-input.py lammps_dump_filename radii_column xpos_column\n"
sys.exit(1)
else:
infile=sys.argv[1]
workdir=os.getcwd()
tools=sys.argv[0].split('VMD-input.py')[0]
# set defaults
outfile = infile.split('.')[0]
print sys.argv
if len(sys.argv) == 4:
column = int(sys.argv[2])
xpos = int(sys.argv[3])
print "Assuming xpos=eradius+1"
elif len(sys.argv) == 3:
column = int(sys.argv[2])
xpos = column+1
print "Assuming xpos=eradius+1"
elif len(sys.argv) == 2:
column=5 # default = radius for dump -> id type q spin eradius x y z
xpos=6
else: print "Incorrect number of arguments"
# check for input:
opts, argv = getopt(sys.argv[1:], 'c:o:ha')
# read options
for opt, arg in opts:
if opt == '-h': # -h: print help
Info%(input,input,input)
if opt == '-o': # output file name
outfile=arg
if opt == '-c': # select column from lammpstrj file to tabulate
column=int(arg)
print column,xpos
makeradii(infile,outfile+".out",column,True)
lmp2xyz(infile,outfile+".xyz",xpos)
print "Creating %s file ..."%(outfile+".vmd")
os.system("cat %s | sed 's/xyzfile/%s/' > %s"%(tools+"radii.vmd",outfile+".xyz","temp"))
os.system("cat %s | sed 's/radiifile/%s/' > %s; rm temp"%("temp",outfile+".out",workdir+'/'+outfile+".vmd"))
print "Done !! (you can now source %s using VMD's console) \n"%(outfile+".vmd")
print "NOTE: In VMD, set graphics representation for electrons to transparency,"
print "and change the atom types in the xyz file according to your values,"
print "for simplicity, they are set using the same mass sequence definition\nfrom your lammps data file\n"

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