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#!@PYTHON_EXECUTABLE@ |
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"""principalAxisCalculator |
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|
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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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|
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Usage: principalAxisCalculator |
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|
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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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|
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Example: |
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principalAxisCalculator -x junk.xyz -o rot.xyz |
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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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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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|
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|
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_haveXYZFileName = 0 |
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_haveOutFileName = 0 |
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|
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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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Aumass = 196.466569 |
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Au1mass = 196.466569 |
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Au2mass = 0.5 |
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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 add(x,y): |
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return x+y |
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|
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def sum(seq): |
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return reduce(add, seq) |
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|
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def readFile(XYZFileName): |
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print "reading XYZ file" |
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|
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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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|
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|
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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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|
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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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elif (atypes[i] == "Au1"): |
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myMass = Au1mass |
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elif (atypes[i] == "Au2"): |
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myMass = Au2mass |
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elif (atypes[i] == "Au"): |
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myMass = Aumass |
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else: |
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print "unknown atom type! %s" % (atypes[i]) |
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|
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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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|
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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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|
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COM = [Xcom, Ycom, Zcom] |
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|
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return COM |
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|
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def findMoments(): |
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|
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COM = findCOM() |
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|
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#find inertia tensor matrix elements |
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|
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I = numpy.zeros((3,3), numpy.float) |
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|
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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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elif (atypes[i] == "Au1"): |
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myMass = Au1mass |
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elif (atypes[i] == "Au2"): |
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myMass = Au2mass |
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elif (atypes[i] == "Au"): |
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myMass = Aumass |
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else: |
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print "unknown atom type!" |
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|
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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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|
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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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|
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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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|
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I[1,2] = I[1,2] - myMass * ( dy * dz ) |
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|
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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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|
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print "Inertia Tensor:" |
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print I |
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print |
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|
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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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|
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return (COM, evals, evects) |
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|
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def writeFile(OutFileName): |
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|
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(COM, evals, evects) = findMoments() |
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|
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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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|
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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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|
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q = [0.0, 0.0, 0.0, 0.0] |
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myEuler = [0.0, 0.0, 0.0] |
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|
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# RotMat to Quat code is out of OpenMD's SquareMatrix3.hpp code: |
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|
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t = RotMat[0][0] + RotMat[1][1] + RotMat[2][2] + 1.0 |
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|
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if( t > 1e-6 ): |
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s = 0.5 / math.sqrt( t ) |
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q[0] = 0.25 / s |
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q[1] = (RotMat[1][2] - RotMat[2][1]) * s |
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q[2] = (RotMat[2][0] - RotMat[0][2]) * s |
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q[3] = (RotMat[0][1] - RotMat[1][0]) * s |
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else: |
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ad1 = RotMat[0][0] |
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ad2 = RotMat[1][1] |
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ad3 = RotMat[2][2] |
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|
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if( ad1 >= ad2 and ad1 >= ad3 ): |
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s = 0.5 / math.sqrt( 1.0 + RotMat[0][0] - RotMat[1][1] - RotMat[2][2] ) |
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q[0] = (RotMat[1][2] - RotMat[2][1]) * s |
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q[1] = 0.25 / s |
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q[2] = (RotMat[0][1] + RotMat[1][0]) * s |
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q[3] = (RotMat[0][2] + RotMat[2][0]) * s |
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elif ( ad2 >= ad1 and ad2 >= ad3 ): |
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s = 0.5 / math.sqrt( 1.0 + RotMat[1][1] - RotMat[0][0] - RotMat[2][2] ) |
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q[0] = (RotMat[2][0] - RotMat[0][2] ) * s |
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q[1] = (RotMat[0][1] + RotMat[1][0]) * s |
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q[2] = 0.25 / s |
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q[3] = (RotMat[1][2] + RotMat[2][1]) * s |
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else: |
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s = 0.5 / math.sqrt( 1.0 + RotMat[2][2] - RotMat[0][0] - RotMat[1][1] ) |
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q[0] = (RotMat[0][1] - RotMat[1][0]) * s |
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q[1] = (RotMat[0][2] + RotMat[2][0]) * s |
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q[2] = (RotMat[1][2] + RotMat[2][1]) * s |
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|
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print "Quaternions:" |
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print q |
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|
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theta = math.acos(RotMat[2][2]) |
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ctheta = RotMat[2][2] |
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stheta = math.sqrt(1.0 - ctheta * ctheta) |
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|
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if (math.fabs(stheta) < 1e-6): |
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psi = 0.0 |
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phi = math.atan2(-RotMat[1][0], RotMat[0][0]) |
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else: |
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phi = math.atan2(RotMat[2][0], -RotMat[2][1]) |
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psi = math.atan2(RotMat[0][2], RotMat[1][2]) |
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|
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if (phi < 0): |
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phi = phi + 2.0 * math.pi; |
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|
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if (psi < 0): |
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psi = psi + 2.0 * math.pi; |
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|
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myEuler[0] = phi * 180.0 / math.pi; |
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myEuler[1] = theta * 180.0 / math.pi; |
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myEuler[2] = psi * 180.0 / math.pi; |
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|
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print "Euler Angles:" |
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print myEuler |
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|
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nAtoms = len(indices) |
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|
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print "writing output XYZ file" |
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|
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OutFile = open(OutFileName, 'w') |
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|
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OutFile.write('%10d\n' % (nAtoms)) |
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OutFile.write('\n') |
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|
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for i in range(nAtoms): |
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|
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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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|
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r = numpy.array([dx,dy,dz]) |
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rnew = numpy.dot(RotMat, r) |
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|
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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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|
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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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|
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|
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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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|
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readFile(XYZFileName) |
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|
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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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|
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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:]) |
