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#!/usr/bin/env python
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"""principalAxisCalculator
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Opens an XYZ file and computes the moments of inertia and principal axes
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for the structure in the XYZ file. Optionally rotate the structure so that
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the long axis (that with the smallest eigenvalue) is pointing along the
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z-axis.
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Usage: principalAxisCalculator
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Options:
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-h, --help show this help
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-x, --xyz=... use specified XYZ (.xyz) file for the structure
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-o, --out=... rotate the structure so that the smallest eigenvalue
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of the rotation matrix points along the z-axis.
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Example:
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principalAxisCalculator -x junk.xyz -o rot.xyz
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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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import sys
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import getopt
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import string
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import math
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import random
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from sets import *
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import numpy
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_haveXYZFileName = 0
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_haveOutFileName = 0
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positions = []
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indices = []
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atypes = []
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Hmass = 1.0079
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Cmass = 12.011
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Omass = 15.999
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Nmass = 14.007
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Smass = 32.066
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def usage():
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print __doc__
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def add(x,y):
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return x+y
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def sum(seq):
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return reduce(add, seq)
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def readFile(XYZFileName):
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print "reading XYZ file"
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XYZFile = open(XYZFileName, 'r')
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# Find number of atoms first
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line = XYZFile.readline()
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L = line.split()
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nAtoms = int(L[0])
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# skip comment line
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line = XYZFile.readline()
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for i in range(nAtoms):
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line = XYZFile.readline()
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L = line.split()
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myIndex = i
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indices.append(myIndex)
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atomType = L[0]
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atypes.append(atomType)
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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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positions.append([x, y, z])
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XYZFile.close()
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def findCOM():
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#find center of mass
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Xcom = 0.0
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Ycom = 0.0
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Zcom = 0.0
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totalMass = 0.0
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for i in range(0,len(indices)):
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if (atypes[i] == "H"):
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myMass = Hmass
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elif (atypes[i] == "C"):
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myMass = Cmass
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elif (atypes[i] == "O"):
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myMass = Omass
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elif (atypes[i] == "N"):
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myMass = Nmass
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elif (atypes[i] == "S"):
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myMass = Smass
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else:
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print "unknown atom type!"
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Xcom = Xcom + myMass * positions[i][0]
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Ycom = Ycom + myMass * positions[i][1]
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Zcom = Zcom + myMass * positions[i][2]
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totalMass = totalMass + myMass
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Xcom = Xcom / totalMass
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Ycom = Ycom / totalMass
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Zcom = Zcom / totalMass
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COM = [Xcom, Ycom, Zcom]
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return COM
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def findMoments():
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COM = findCOM()
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#find inertia tensor matrix elements
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I = numpy.zeros((3,3), numpy.float)
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for i in range(0,len(indices)):
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if (atypes[i] == "H"):
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myMass = Hmass
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elif (atypes[i] == "C"):
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myMass = Cmass
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elif (atypes[i] == "O"):
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myMass = Omass
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elif (atypes[i] == "N"):
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myMass = Nmass
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elif (atypes[i] == "S"):
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myMass = Smass
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else:
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print "unknown atom type!"
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dx = positions[i][0] - COM[0]
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dy = positions[i][1] - COM[1]
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dz = positions[i][2] - COM[2]
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I[0,0] = I[0,0] + myMass * ( dy * dy + dz * dz )
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I[1,1] = I[1,1] + myMass * ( dx * dx + dz * dz )
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I[2,2] = I[2,2] + myMass * ( dx * dx + dy * dy )
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I[0,1] = I[0,1] - myMass * ( dx * dy )
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I[0,2] = I[0,2] - myMass * ( dx * dz )
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I[1,2] = I[1,2] - myMass * ( dy * dz )
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I[1,0] = I[0,1]
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I[2,0] = I[0,2]
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I[2,1] = I[1,2]
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print "Inertia Tensor:"
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print I
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print
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(evals, evects) = numpy.linalg.eig(I)
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print "evals:"
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print evals
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print
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print "evects:"
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print evects
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print
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return (COM, evals, evects)
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def writeFile(OutFileName):
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(COM, evals, evects) = findMoments()
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# we need to re-order the axes so that the smallest moment of inertia
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# (which corresponds to the long axis of the molecule) is along the z-axis
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# we'll just reverse the order of the three axes:
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axOrder = numpy.argsort(evals)
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RotMat = numpy.zeros((3,3), numpy.float)
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RotMat[0] = evects[axOrder[2]]
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RotMat[1] = evects[axOrder[1]]
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RotMat[2] = evects[axOrder[0]]
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nAtoms = len(indices)
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print "writing output XYZ file"
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OutFile = open(OutFileName, 'w')
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OutFile.write('%10d\n' % (nAtoms))
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OutFile.write('\n')
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for i in range(nAtoms):
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dx = positions[i][0] - COM[0]
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dy = positions[i][1] - COM[1]
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dz = positions[i][2] - COM[2]
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r = numpy.array([dx,dy,dz])
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rnew = numpy.dot(RotMat, r)
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OutFile.write('%s\t%f\t%f\t%f\t%d\n' % (atypes[i], rnew[0], rnew[1], rnew[2], i))
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OutFile.close()
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def main(argv):
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try:
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opts, args = getopt.getopt(argv, "hx:o:", ["help", "xyz=", "out="])
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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 ("-x", "--xyz"):
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XYZFileName = arg
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global _haveXYZFileName
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_haveXYZFileName = 1
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elif opt in ("-o", "--out"):
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OutFileName = arg
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global _haveOutFileName
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_haveOutFileName = 1
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if (_haveXYZFileName != 1):
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usage()
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print "No xyz file was specified"
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sys.exit()
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readFile(XYZFileName)
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if (_haveOutFileName == 1):
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writeFile(OutFileName)
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else:
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findMoments()
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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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