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#!/usr/bin/env python |
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"""Computes predicted diffusion constants and rotational relaxation |
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times from a diff file. Explains the values in the diff file in |
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terms of properties that can be calculated from a molecular dynamics |
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simulation. |
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|
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Usage: diffExplainer |
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|
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Options: |
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-h, --help show this help |
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-d, --diff-file=... use specified diff file |
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-t, --temperature=... temperature in Kelvin |
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|
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|
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Example: |
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diffExplainer -d ellipsoid.diff -t 300 |
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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: 1.1 $" |
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__date__ = "$Date: 2008-01-16 20:19:28 $" |
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|
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__copyright__ = "Copyright (c) 2008 by the University of Notre Dame" |
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__license__ = "OOPSE" |
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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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_haveDiffFileName = 0 |
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_haveTemperature = 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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def readDiffFile(diffFileName): |
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diffFile = open(diffFileName, 'r') |
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|
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global DTTxx |
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global DTTyy |
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global DTTzz |
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|
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global XiRRxx |
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global XiRRyy |
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global XiRRzz |
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|
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global DRRxx |
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global DRRyy |
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global DRRzz |
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|
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line = diffFile.readline() |
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while 1: |
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L = line.split() |
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XiRRxx = float(L[31]) |
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XiRRyy = float(L[35]) |
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XiRRzz = float(L[39]) |
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DTTxx = float(L[115]) |
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DTTyy = float(L[119]) |
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DTTzz = float(L[123]) |
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DRRxx = float(L[142]) |
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DRRyy = float(L[146]) |
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DRRzz = float(L[150]) |
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line = diffFile.readline() |
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if not line: break |
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|
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diffFile.close() |
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|
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def computeProperties(temperature): |
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|
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kb = 1.9872156E-3 |
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kt = kb * temperature |
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|
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print |
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print "Translational Diffusion Constant (angstroms^2 fs^-1): %.3e" % ((DTTxx + DTTyy + DTTzz)/3.0) |
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|
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Delta = math.sqrt(math.pow((DRRxx-DRRyy),2) +(DRRzz-DRRxx)*(DRRzz-DRRyy)) |
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a = math.sqrt(3.0)*(DRRxx-DRRyy) |
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b = (2.0*DRRzz - DRRxx - DRRyy + 2.0*Delta) |
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N = 2.0*math.sqrt(Delta)*math.sqrt(b) |
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Di = (DRRxx + DRRyy + DRRzz)/3.0 |
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f1 = 6.0*Di + 2.0*Delta |
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f2 = 6.0*Di - 2.0*Delta |
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f3 = 3.0*(DRRxx + Di) |
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f4 = 3.0*(DRRyy + Di) |
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f5 = 3.0*(DRRzz + Di) |
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|
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f0 = (f1 + f2 + f3 + f4 + f5)/5.0 |
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|
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print |
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print "l=2 Orientational correlation functions:" |
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print |
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print "In general only the C^2(0,0) correlation function relates to the lcorr" |
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print "computed via the DynamicProps correlation function routine." |
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print |
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print "To get any of the specific correlation functions, multiply each amplitude" |
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print "by exp(-t/t_i) where t_i is the relevant decay time printed in the first row:" |
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print |
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print "decay times (fs): %.3e %.3e %.3e %.3e %.3e" % (1.0/f1, 1.0/f2, 1.0/f3, 1.0/f4, 1.0/f5 ) |
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print |
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print " C^2(0, 0): %.3e %.3e %.3e %.3e %.3e" % (pow(a/N,2), pow(b/N,2), 0, 0, 0 ) |
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print " C^2(1, 1): %.3e %.3e %.3e %.3e %.3e" % (0,0,0.5,0.5,0) |
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print " C^2(1,-1): %.3e %.3e %.3e %.3e %.3e" % (0,0,-0.5,0.5,0) |
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print " C^2(2, 2): %.3e %.3e %.3e %.3e %.3e" % (0.5*pow(b/N,2), 0.5*pow(a/N,2), 0, 0, 0.5) |
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print " C^2(2,-2): %.3e %.3e %.3e %.3e %.3e" % (0.5*pow(b/N,2), 0.5*pow(a/N,2), 0, 0,-0.5) |
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print " C^2(2, 0): %.3e %.3e %.3e %.3e %.3e" % (math.sqrt(2.0)*a*b/pow(N,2),-math.sqrt(2.0)*a*b/pow(N,2),0,0,0) |
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print |
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print |
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print "average (or characteristic) relaxation time:\t%.3e" % (1.0/f0) |
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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, "hd:t:", ["help", "diff-file=", "temperature="]) |
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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 ("-d", "--diff-file"): |
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diffFileName = arg |
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global _haveDiffFileName |
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_haveDiffFileName = 1 |
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elif opt in ("-t", "--temperature"): |
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temperature = float(arg) |
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global _haveTemperature |
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_haveTemperature = 1 |
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if (_haveDiffFileName != 1): |
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usage() |
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print "No diff file was specified" |
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sys.exit() |
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if (_haveTemperature != 1): |
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usage() |
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print "No temperature was specified" |
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sys.exit() |
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|
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readDiffFile(diffFileName); |
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computeProperties(temperature); |
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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:]) |
