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#!/usr/bin/env python |
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"""Dump File Converter |
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|
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Converts old-style OOPSE md and dump files into new OpenMD style |
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combined files |
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|
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Usage: dumpConverter |
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|
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Options: |
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-h, --help show this help |
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-m, --meta-data=... use specified meta-data (.md) file |
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-c, --config-file=... use specified configuration (.in, .eor, .dump) file |
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-o, --output-file=... use specified output (.opmd) file |
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|
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|
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Example: |
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dumpConverter -m Ar.md -c Ar.dump -o Ar.opmd |
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|
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""" |
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|
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__author__ = "Dan Gezelter (gezelter@nd.edu)" |
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__version__ = "$Revision$" |
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__date__ = "$Date$" |
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__copyright__ = "Copyright (c) 2006 by the University of Notre Dame" |
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__license__ = "OpenMD" |
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|
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import sys |
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import getopt |
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import string |
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|
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_haveMDFileName = 0 |
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_haveConfFileName = 0 |
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_haveOutputFileName = 0 |
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|
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def usage(): |
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print __doc__ |
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|
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|
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def convertFiles(mdFileName, configFileName, outputFileName): |
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mdFile = open(mdFileName, 'r') |
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outputFile = open(outputFileName, 'w') |
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|
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outputFile.write("<OpenMD version=1>\n"); |
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outputFile.write(" <MetaData>\n") |
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|
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mdLines = mdFile.readlines() |
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for l in mdLines: |
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if (l.find('initialConfig') == -1): |
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outputFile.write(l) |
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|
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outputFile.write(" </MetaData>\n") |
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mdFile.close() |
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|
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framePos = 0 |
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configFile = open(configFileName, 'r') |
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for line in configFile.readlines(): |
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framePos = framePos + 1 |
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if (framePos == 1): |
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L = line.split() |
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nStuntDoubles = int(L[0]) |
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whichSD = 0 |
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outputFile.write(" <Snapshot>\n") |
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continue |
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elif (framePos == 2): |
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L = line.replace(';',' ').split() |
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time = float(L[0]) |
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outputFile.write(" <FrameData>\n"); |
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outputFile.write(" Time: %.10g\n" % (time)) |
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Hxx = float(L[1]) |
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Hxy = float(L[2]) |
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Hxz = float(L[3]) |
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Hyx = float(L[4]) |
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Hyy = float(L[5]) |
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Hyz = float(L[6]) |
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Hzx = float(L[7]) |
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Hzy = float(L[8]) |
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Hzz = float(L[9]) |
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outputFile.write(" Hmat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n" % (Hxx, Hxy, Hxz, Hyx, Hyy, Hyz, Hzx, Hzy, Hzz)) |
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if (len(L) >= 12): |
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chi = float(L[10]) |
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integChi = float(L[11]) |
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outputFile.write(" Thermostat: %.10g , %.10g\n" % (chi, integChi)) |
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if (len(L) >= 21): |
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Nxx = float(L[12]) |
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Nxy = float(L[13]) |
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Nxz = float(L[14]) |
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Nyx = float(L[15]) |
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Nyy = float(L[16]) |
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Nyz = float(L[17]) |
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Nzx = float(L[18]) |
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Nzy = float(L[19]) |
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Nzz = float(L[20]) |
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outputFile.write(" Barostat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n" % (Nxx, Nxy, Nxz, Nyx, Nyy, Nyz, Nzx, Nzy, Nzz)) |
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|
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outputFile.write(" </FrameData>\n") |
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outputFile.write(" <StuntDoubles>\n") |
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else: |
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whichSD = whichSD + 1 |
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L = line.split() |
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x = float(L[1]) |
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y = float(L[2]) |
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z = float(L[3]) |
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vx = float(L[4]) |
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vy = float(L[5]) |
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vz = float(L[6]) |
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sdFormat = 'pv' |
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if (len(L) == 10): |
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sdFormat = 'pvf' |
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fx = float(L[7]) |
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fy = float(L[8]) |
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fz = float(L[9]) |
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if (len(L) >= 14): |
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qw = float(L[7]) |
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qx = float(L[8]) |
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qy = float(L[9]) |
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qz = float(L[10]) |
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jx = float(L[11]) |
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jy = float(L[12]) |
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jz = float(L[13]) |
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if (qw == 0.0 and qx == 0.0 and qy == 0.0 and qz == 0.0): |
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sdFormat = 'pv' |
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else: |
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sdFormat = 'pvqj' |
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if (len(L) == 20): |
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fx = float(L[14]) |
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fy = float(L[15]) |
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fz = float(L[16]) |
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tx = float(L[17]) |
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ty = float(L[18]) |
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tz = float(L[19]) |
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if (qw == 0.0 and qx == 0.0 and qy == 0.0 and qz == 0.0): |
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sdFormat = 'pvf' |
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else: |
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sdFormat = 'pvqjft' |
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if (sdFormat == 'pv'): |
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outputFile.write("%10d %7s %18.10g %18.10g %18.10g %14e %13e %13e\n" % (whichSD-1, sdFormat, x, y, z, vx, vy, vz)) |
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elif (sdFormat == 'pvf'): |
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outputFile.write("%10d %7s %18.10g %18.10g %18.10g %13e %13e %13e %13e %13e %13e\n" % (whichSD-1, sdFormat, x, y, z, vx, vy, vz, fx, fy, fz)) |
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elif (sdFormat == 'pvqj'): |
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outputFile.write("%10d %7s %18.10g %18.10g %18.10g %13e %13e %13e %13e %13e %13e %13e %13e %13e %13e\n" % (whichSD-1, sdFormat, x, y, z, vx, vy, vz, qw, qx, qy, qz, jx, jy, jz)) |
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elif (sdFormat == 'pvqjft'): |
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outputFile.write("%d %s %18.10g %18.10g %18.10g %13e %13e %13e %13e %13e %13e %13e %13e %13e %13e %13e %13e %13e %13e %13e %13e\n" % (whichSD-1, sdFormat, x, y, z, vx, vy, vz, qw, qx, qy, qz, jx, jy, jz, fx, fy, fz, tx, ty, tz)) |
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if (whichSD == nStuntDoubles): |
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outputFile.write(" </StuntDoubles>\n") |
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outputFile.write(" </Snapshot>\n") |
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framePos = 0 |
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|
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|
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configFile.close() |
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outputFile.write("</OpenMD>\n") |
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outputFile.close() |
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|
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|
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def main(argv): |
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try: |
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opts, args = getopt.getopt(argv, "hm:c:o:", ["help", "meta-data=", "config-file=", "output-file="]) |
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except getopt.GetoptError: |
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usage() |
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sys.exit(2) |
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for opt, arg in opts: |
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if opt in ("-h", "--help"): |
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usage() |
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sys.exit() |
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elif opt in ("-m", "--meta-data"): |
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mdFileName = arg |
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global _haveMDFileName |
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_haveMDFileName = 1 |
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elif opt in ("-c", "--config-file"): |
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configFileName = arg |
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global _haveConfFileName |
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_haveConfFileName = 1 |
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elif opt in ("-o", "--output-file"): |
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outputFileName = arg |
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global _haveOutputFileName |
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_haveOutputFileName = 1 |
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if (_haveMDFileName != 1): |
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usage() |
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print "No meta-data file was specified" |
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sys.exit() |
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if (_haveConfFileName != 1): |
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usage() |
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print "No configuration file was specified" |
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sys.exit() |
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if (_haveOutputFileName != 1): |
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usage() |
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print "No output file was specified" |
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sys.exit() |
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convertFiles(mdFileName, configFileName, outputFileName); |
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|
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if __name__ == "__main__": |
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if len(sys.argv) == 1: |
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usage() |
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sys.exit() |
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main(sys.argv[1:]) |
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|
