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#!@PYTHON_EXECUTABLE@ |
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"""A script that computes the static dielectric constant |
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|
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Accumulates the static dielectric constant from an OpenMD stat file |
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that has been run with the SYSTEM_DIPOLE added to the statFileFormat. |
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|
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This assumes the fluctuation formula appropriate for conducting |
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boundaries: |
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|
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<M^2> - <M>^2 |
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epsA = 1 + ----------------- |
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3 kB <T> <V> eps0 |
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|
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epsA: dielectric constant |
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M: total dipole moment of the box |
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<V>: average volume of the box |
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<T>: average temperature |
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eps0: vacuum permittivity |
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kB: Boltzmann constant |
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|
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See M. Neumann, O. Steinhauser, and G. S. Pawley, Mol. Phys. 52, 97 (1984). |
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|
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Also, optionally applies a correction factor as follows: |
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|
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((Q + 2) (epsA - 1) + 3) |
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eps = ------------------------ |
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((Q - 1) (epsA - 1) + 3) |
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|
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Where Q depends on the method used to compute the electrostatic interaction. |
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See M. Neumann and O. Steinhauser, Chem. Phys. Lett. 95, 417 (1983)) |
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|
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Usage: stat2dielectric |
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|
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Options: |
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-h, --help show this help |
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-f, --stat-file=... use specified stat file |
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-o, --output-file=... use specified output (.dielectric) file |
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-q, --Q-value=... use the specified Q value to correct the dielectric |
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|
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To use this, the OpenMD file for the run should specify: |
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|
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statFileFormat = "TIME|TOTAL_ENERGY|POTENTIAL_ENERGY|KINETIC_ENERGY|TEMPERATURE|PRESSURE|VOLUME|CONSERVED_QUANTITY|SYSTEM_DIPOLE"; |
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|
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This line will get OpenMD to compute the total system dipole and place |
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it in the final three columns of the stat file. The stat2dielectric |
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script looks for the temperature in column 5, the volume in column 7, |
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and the dipole vector in the last 3 columns of the stat file. |
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|
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Example: |
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stat2dielectric -f stockmayer.stat -o stockmayer.dielectric |
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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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|
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__copyright__ = "Copyright (c) 2014 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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import math |
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|
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def usage(): |
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print __doc__ |
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|
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def readStatFile(statFileName): |
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global time |
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global temperature |
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global volume |
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global boxDipole |
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time = [] |
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temperature = [] |
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volume = [] |
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boxDipole = [] |
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|
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statFile = open(statFileName, 'r') |
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line = statFile.readline() |
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|
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print "reading File" |
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line = statFile.readline() |
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while 1: |
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L = line.split() |
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|
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time.append(float(L[0])) |
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temperature.append(float(L[4])) |
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volume.append(float(L[6])) |
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dipX = float(L[-3]) |
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dipY = float(L[-2]) |
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dipZ = float(L[-1]) |
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boxDipole.append([dipX, dipY, dipZ]) |
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|
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line = statFile.readline() |
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if not line: break |
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|
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statFile.close() |
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|
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def computeAverages(outFileName, Q): |
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|
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# permittivity in C^2 N^-1 m^-2 |
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eps0 = 8.854187817620E-12 |
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# Boltzmann constant in J / K |
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kB = 1.380648E-23 |
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# Convert angstroms^3 to m^3 |
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a3tom3 = 1.0E-30 |
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|
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M2 = 0.0 |
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M = 0.0 |
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Dx = 0.0 |
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Dy = 0.0 |
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Dz = 0.0 |
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Temp = 0.0 |
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Vol = 0.0 |
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|
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print "computing Dielectrics" |
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outFile = open(outFileName, 'w') |
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|
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for i in range(len(time)): |
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|
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dipX = boxDipole[i][0] |
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dipY = boxDipole[i][1] |
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dipZ = boxDipole[i][2] |
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|
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length2 = dipX*dipX + dipY*dipY + dipZ*dipZ |
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M2 += length2 |
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M2avg = M2 / float(1+i) |
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|
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Dx += dipX |
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Dy += dipY |
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Dz += dipZ |
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|
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# the average of each of the three components of the box dipole |
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Mx = Dx / float(1+i) |
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My = Dy / float(1+i) |
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Mz = Dz / float(1+i) |
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Mavg = Mx*Mx + My*My + Mz*Mz |
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|
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# the average of the box dipole vector length |
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M += math.sqrt(length2) |
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Mavg2 = M / float(1+i) |
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|
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Temp += temperature[i] |
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Tavg = Temp / float(1+i) |
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|
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Vol += volume[i] * a3tom3 |
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Vavg = Vol / float(1+i) |
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|
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d1 = 1.0 + (M2avg - Mavg) / (3.0*eps0*kB*Tavg*Vavg) |
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d2 = 1.0 + (M2avg - Mavg2*Mavg2) / (3.0*eps0*kB*Tavg*Vavg) |
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|
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|
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corrected1 = ((Q+2.0)*(d1 - 1.0) + 3.0)/((Q-1.0) * (d1 - 1.0) + 3.0) |
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corrected2 = ((Q+2.0)*(d2 - 1.0) + 3.0)/((Q-1.0) * (d2 - 1.0) + 3.0) |
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|
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outFile.write("%lf\t%lf\t%lf\t%lf\t%lf\n" % (time[i], d1, d2, corrected1, corrected2)) |
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|
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outFile.close() |
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|
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|
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def main(argv): |
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global haveStatFileName |
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global haveOutputFileName |
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global haveQValue |
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|
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haveStatFileName = False |
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haveOutputFileName = False |
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haveQValue = False |
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|
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try: |
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opts, args = getopt.getopt(argv, "hq:f:o:", ["help", "Q-value=", "stat-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 ("-q", "--Q-value="): |
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Q = float(arg) |
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haveQValue = True |
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elif opt in ("-f", "--stat-file"): |
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statFileName = arg |
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haveStatFileName = True |
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elif opt in ("-o", "--output-file"): |
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outputFileName = arg |
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haveOutputFileName = True |
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if (not haveStatFileName): |
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usage() |
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print "No stat file was specified" |
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sys.exit() |
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if (not haveOutputFileName): |
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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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|
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|
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readStatFile(statFileName) |
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if (not haveQValue): |
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computeAverages(outputFileName, 1.0) |
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else: |
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computeAverages(outputFileName, Q) |
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|
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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:]) |
