conversionTools

#!/usr/bin/env python

import control as ctrl
import optparse
import sys
import os

# create a parser for the argv[]
parser = optparse.OptionParser()

parser.add_option('-i',
                  action='store', 
                  dest='iFile', 
                  default='olcao.skl',
                  help='''
The input file. Default is "olcao.skl".''')

parser.add_option('-o',
                  action='store', 
                  dest='oFile', 
                  default='new.olcao.skl',
                  help='''
The output file. Default is "new.olcao.skl".''')

parser.add_option('-c',
                  action='store_true', 
                  dest='convCoors', 
                  default=False,
                  help='''
Convert coordinates from cart to frac and vice versa. The default is to not 
do any conversion.''')

parser.add_option('-b',
                  action='store', 
                  dest='buf', 
                  default=0.0, 
                  type='float',
                  help='''
The buffer that is needed when reading or writing *.xyz files. This buffer will 
pad the structure on all sides, and is needed for molecular systems. Default is 
0.0 (no padding).''')

# parse the arguments
options, args = parser.parse_args()

out_extension = os.path.splitext(options.oFile)[1]
if out_extension != ".skl" and out_extension != ".xyz" and out_extension != ".lmp":
    sys.exit("Sorry, Can only write to *.skl or *.xyz or *.lmp files currently.")

in_extension = os.path.splitext(options.iFile)[1]
if in_extension == ".xyz":
    s = ctrl.Structure(options.iFile, buf=options.buf)
else:
    s = ctrl.Structure(options.iFile)

# convert
if options.convCoors:
    if s.coordType == "F":
        s.toCart()
    elif s.coordType == "C":
        s.toFrac()
    else:
        sys.exit("unknow coordinate type: " + s.coordType)

if out_extension == ".skl":
    s.writeSkl(fileName = options.oFile)
elif out_extension == ".xyz":
    s.writeXyz(fileName = options.oFile)
elif out_extension == ".lmp":
    s.writeLAMMPS(fileName = options.oFile)
else:
    print "Dont know how to print this output file" + options.oFile