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#!/usr/bin/env python |
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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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#!@PYTHON_EXECUTABLE@ |
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"""principalAxisCalculator |
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|
| 4 |
> |
Opens an XYZ file and computes the moments of inertia and principal axes |
| 5 |
> |
for the structure in the XYZ file. Optionally rotate the structure so that |
| 6 |
> |
the long axis (that with the smallest eigenvalue) is pointing along the |
| 7 |
> |
z-axis. |
| 8 |
> |
|
| 9 |
> |
Usage: principalAxisCalculator |
| 10 |
> |
|
| 11 |
> |
Options: |
| 12 |
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-h, --help show this help |
| 13 |
> |
-x, --xyz=... use specified XYZ (.xyz) file for the structure |
| 14 |
> |
-o, --out=... rotate the structure so that the smallest eigenvalue |
| 15 |
> |
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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|
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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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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) |
| 216 |
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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="]) |
| 223 |
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except getopt.GetoptError: |
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usage() |
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sys.exit(2) |
| 226 |
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for opt, arg in opts: |
| 227 |
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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 |
| 234 |
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elif opt in ("-o", "--out"): |
| 235 |
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OutFileName = arg |
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global _haveOutFileName |
| 237 |
< |
_haveOutFileName = 1 |
| 238 |
< |
|
| 239 |
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|
| 240 |
< |
if (_haveXYZFileName != 1): |
| 241 |
< |
usage() |
| 242 |
< |
print "No xyz file was specified" |
| 243 |
< |
sys.exit() |
| 244 |
< |
|
| 245 |
< |
readFile(XYZFileName) |
| 246 |
< |
|
| 247 |
< |
if (_haveOutFileName == 1): |
| 248 |
< |
writeFile(OutFileName) |
| 249 |
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else: |
| 250 |
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findMoments() |
| 251 |
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|
| 252 |
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if __name__ == "__main__": |
| 253 |
< |
if len(sys.argv) == 1: |
| 254 |
< |
usage() |
| 255 |
< |
sys.exit() |
| 256 |
< |
main(sys.argv[1:]) |
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|
| 52 |
> |
def usage(): |
| 53 |
> |
print __doc__ |
| 54 |
> |
|
| 55 |
> |
def add(x,y): |
| 56 |
> |
return x+y |
| 57 |
> |
|
| 58 |
> |
def sum(seq): |
| 59 |
> |
return reduce(add, seq) |
| 60 |
> |
|
| 61 |
> |
def readFile(XYZFileName): |
| 62 |
> |
print "reading XYZ file" |
| 63 |
> |
|
| 64 |
> |
XYZFile = open(XYZFileName, 'r') |
| 65 |
> |
# Find number of atoms first |
| 66 |
> |
line = XYZFile.readline() |
| 67 |
> |
L = line.split() |
| 68 |
> |
nAtoms = int(L[0]) |
| 69 |
> |
# skip comment line |
| 70 |
> |
line = XYZFile.readline() |
| 71 |
> |
for i in range(nAtoms): |
| 72 |
> |
line = XYZFile.readline() |
| 73 |
> |
L = line.split() |
| 74 |
> |
myIndex = i |
| 75 |
> |
indices.append(myIndex) |
| 76 |
> |
atomType = L[0] |
| 77 |
> |
atypes.append(atomType) |
| 78 |
> |
x = float(L[1]) |
| 79 |
> |
y = float(L[2]) |
| 80 |
> |
z = float(L[3]) |
| 81 |
> |
positions.append([x, y, z]) |
| 82 |
> |
XYZFile.close() |
| 83 |
> |
|
| 84 |
> |
|
| 85 |
> |
def findCOM(): |
| 86 |
> |
#find center of mass |
| 87 |
> |
Xcom = 0.0 |
| 88 |
> |
Ycom = 0.0 |
| 89 |
> |
Zcom = 0.0 |
| 90 |
> |
totalMass = 0.0 |
| 91 |
> |
|
| 92 |
> |
for i in range(0,len(indices)): |
| 93 |
> |
if (atypes[i] == "H"): |
| 94 |
> |
myMass = Hmass |
| 95 |
> |
elif (atypes[i] == "C"): |
| 96 |
> |
myMass = Cmass |
| 97 |
> |
elif (atypes[i] == "O"): |
| 98 |
> |
myMass = Omass |
| 99 |
> |
elif (atypes[i] == "N"): |
| 100 |
> |
myMass = Nmass |
| 101 |
> |
elif (atypes[i] == "S"): |
| 102 |
> |
myMass = Smass |
| 103 |
> |
elif (atypes[i] == "Au1"): |
| 104 |
> |
myMass = Au1mass |
| 105 |
> |
elif (atypes[i] == "Au2"): |
| 106 |
> |
myMass = Au2mass |
| 107 |
> |
elif (atypes[i] == "Au"): |
| 108 |
> |
myMass = Aumass |
| 109 |
> |
else: |
| 110 |
> |
print "unknown atom type! %s" % (atypes[i]) |
| 111 |
> |
|
| 112 |
> |
Xcom = Xcom + myMass * positions[i][0] |
| 113 |
> |
Ycom = Ycom + myMass * positions[i][1] |
| 114 |
> |
Zcom = Zcom + myMass * positions[i][2] |
| 115 |
> |
totalMass = totalMass + myMass |
| 116 |
> |
|
| 117 |
> |
Xcom = Xcom / totalMass |
| 118 |
> |
Ycom = Ycom / totalMass |
| 119 |
> |
Zcom = Zcom / totalMass |
| 120 |
> |
|
| 121 |
> |
COM = [Xcom, Ycom, Zcom] |
| 122 |
> |
|
| 123 |
> |
return COM |
| 124 |
> |
|
| 125 |
> |
def findMoments(): |
| 126 |
> |
|
| 127 |
> |
COM = findCOM() |
| 128 |
> |
|
| 129 |
> |
#find inertia tensor matrix elements |
| 130 |
> |
|
| 131 |
> |
I = numpy.zeros((3,3), numpy.float) |
| 132 |
> |
|
| 133 |
> |
for i in range(0,len(indices)): |
| 134 |
> |
if (atypes[i] == "H"): |
| 135 |
> |
myMass = Hmass |
| 136 |
> |
elif (atypes[i] == "C"): |
| 137 |
> |
myMass = Cmass |
| 138 |
> |
elif (atypes[i] == "O"): |
| 139 |
> |
myMass = Omass |
| 140 |
> |
elif (atypes[i] == "N"): |
| 141 |
> |
myMass = Nmass |
| 142 |
> |
elif (atypes[i] == "S"): |
| 143 |
> |
myMass = Smass |
| 144 |
> |
elif (atypes[i] == "Au1"): |
| 145 |
> |
myMass = Au1mass |
| 146 |
> |
elif (atypes[i] == "Au2"): |
| 147 |
> |
myMass = Au2mass |
| 148 |
> |
elif (atypes[i] == "Au"): |
| 149 |
> |
myMass = Aumass |
| 150 |
> |
else: |
| 151 |
> |
print "unknown atom type!" |
| 152 |
> |
|
| 153 |
> |
dx = positions[i][0] - COM[0] |
| 154 |
> |
dy = positions[i][1] - COM[1] |
| 155 |
> |
dz = positions[i][2] - COM[2] |
| 156 |
> |
|
| 157 |
> |
I[0,0] = I[0,0] + myMass * ( dy * dy + dz * dz ) |
| 158 |
> |
I[1,1] = I[1,1] + myMass * ( dx * dx + dz * dz ) |
| 159 |
> |
I[2,2] = I[2,2] + myMass * ( dx * dx + dy * dy ) |
| 160 |
> |
|
| 161 |
> |
I[0,1] = I[0,1] - myMass * ( dx * dy ) |
| 162 |
> |
I[0,2] = I[0,2] - myMass * ( dx * dz ) |
| 163 |
> |
|
| 164 |
> |
I[1,2] = I[1,2] - myMass * ( dy * dz ) |
| 165 |
> |
|
| 166 |
> |
I[1,0] = I[0,1] |
| 167 |
> |
I[2,0] = I[0,2] |
| 168 |
> |
I[2,1] = I[1,2] |
| 169 |
> |
|
| 170 |
> |
print "Inertia Tensor:" |
| 171 |
> |
print I |
| 172 |
> |
print |
| 173 |
> |
|
| 174 |
> |
(evals, evects) = numpy.linalg.eig(I) |
| 175 |
> |
print "evals:" |
| 176 |
> |
print evals |
| 177 |
> |
print |
| 178 |
> |
print "evects:" |
| 179 |
> |
print evects |
| 180 |
> |
print |
| 181 |
> |
|
| 182 |
> |
return (COM, evals, evects) |
| 183 |
> |
|
| 184 |
> |
def writeFile(OutFileName): |
| 185 |
> |
|
| 186 |
> |
(COM, evals, evects) = findMoments() |
| 187 |
> |
|
| 188 |
> |
|
| 189 |
> |
# we need to re-order the axes so that the smallest moment of inertia |
| 190 |
> |
# (which corresponds to the long axis of the molecule) is along the z-axis |
| 191 |
> |
# we'll just reverse the order of the three axes: |
| 192 |
> |
|
| 193 |
> |
axOrder = numpy.argsort(evals) |
| 194 |
> |
RotMat = numpy.zeros((3,3), numpy.float) |
| 195 |
> |
RotMat[0] = evects[axOrder[2]] |
| 196 |
> |
RotMat[1] = evects[axOrder[1]] |
| 197 |
> |
RotMat[2] = evects[axOrder[0]] |
| 198 |
> |
|
| 199 |
> |
nAtoms = len(indices) |
| 200 |
> |
|
| 201 |
> |
print "writing output XYZ file" |
| 202 |
> |
|
| 203 |
> |
OutFile = open(OutFileName, 'w') |
| 204 |
> |
|
| 205 |
> |
OutFile.write('%10d\n' % (nAtoms)) |
| 206 |
> |
OutFile.write('\n') |
| 207 |
> |
|
| 208 |
> |
for i in range(nAtoms): |
| 209 |
> |
|
| 210 |
> |
dx = positions[i][0] - COM[0] |
| 211 |
> |
dy = positions[i][1] - COM[1] |
| 212 |
> |
dz = positions[i][2] - COM[2] |
| 213 |
> |
|
| 214 |
> |
r = numpy.array([dx,dy,dz]) |
| 215 |
> |
rnew = numpy.dot(RotMat, r) |
| 216 |
> |
|
| 217 |
> |
OutFile.write('%s\t%f\t%f\t%f\t%d\n' % (atypes[i], rnew[0], rnew[1], rnew[2], i)) |
| 218 |
> |
OutFile.close() |
| 219 |
> |
|
| 220 |
> |
def main(argv): |
| 221 |
> |
try: |
| 222 |
> |
opts, args = getopt.getopt(argv, "hx:o:", ["help", "xyz=", "out="]) |
| 223 |
> |
except getopt.GetoptError: |
| 224 |
> |
usage() |
| 225 |
> |
sys.exit(2) |
| 226 |
> |
for opt, arg in opts: |
| 227 |
> |
if opt in ("-h", "--help"): |
| 228 |
> |
usage() |
| 229 |
> |
sys.exit() |
| 230 |
> |
elif opt in ("-x", "--xyz"): |
| 231 |
> |
XYZFileName = arg |
| 232 |
> |
global _haveXYZFileName |
| 233 |
> |
_haveXYZFileName = 1 |
| 234 |
> |
elif opt in ("-o", "--out"): |
| 235 |
> |
OutFileName = arg |
| 236 |
> |
global _haveOutFileName |
| 237 |
> |
_haveOutFileName = 1 |
| 238 |
> |
|
| 239 |
> |
|
| 240 |
> |
if (_haveXYZFileName != 1): |
| 241 |
> |
usage() |
| 242 |
> |
print "No xyz file was specified" |
| 243 |
> |
sys.exit() |
| 244 |
> |
|
| 245 |
> |
readFile(XYZFileName) |
| 246 |
> |
|
| 247 |
> |
if (_haveOutFileName == 1): |
| 248 |
> |
writeFile(OutFileName) |
| 249 |
> |
else: |
| 250 |
> |
findMoments() |
| 251 |
> |
|
| 252 |
> |
if __name__ == "__main__": |
| 253 |
> |
if len(sys.argv) == 1: |
| 254 |
> |
usage() |
| 255 |
> |
sys.exit() |
| 256 |
> |
main(sys.argv[1:]) |
