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#!/usr/bin/env python |
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"""Water Replacer |
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|
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Finds atomistic waters in an xyz file and generates a meta-data file |
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with center of mass and orientational coordinates for rigid body |
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waters. |
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|
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Usage: waterReplacer |
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|
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Options: |
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-h, --help show this help |
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-x, use the specified input (.xyz) file |
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-o, --output-file=... use specified output (.md) file |
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|
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|
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Example: |
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waterReplacer -x basal.xyz -o basal.md |
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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: 1646 $" |
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__date__ = "$Date: 2011-09-26 09:30:00 -0400 (Mon, 26 Sep 2011) $" |
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__copyright__ = "Copyright (c) 2011 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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import numpy |
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|
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_haveXYZFileName = 0 |
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_haveOutputFileName = 0 |
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|
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atypes = [] |
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positions = [] |
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metaData = [] |
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frameData = [] |
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WaterPos = [] |
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WaterQuats = [] |
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indices = [] |
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Hmat = [] |
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BoxInv = [] |
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H = [] |
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Eliminate = [] |
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|
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#Hmat = zeros([3,3],Float) |
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#BoxInv = zeros([3],Float) |
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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 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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def findWaters(): |
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print "finding water molecules" |
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# simpler since we only have to find H atoms within a few |
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# angstroms of each water: |
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|
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hCovRad = 0.32 |
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oCovRad = 0.73 |
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covTol = 0.45 |
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OHbond = hCovRad + oCovRad + covTol |
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Hmass = 1.0079 |
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Omass = 15.9994 |
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# initialize H array to an error condition |
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H.append(-1) |
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H.append(-1) |
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|
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for i in range(len(indices)): |
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if (atypes[i] == "O"): |
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nH = 0 |
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H[0] = -1 |
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H[1] = -1 |
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COM = [0.0, 0.0, 0.0] |
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opos = positions[i] |
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for j in range(len(indices)): |
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if (atypes[j] == "H"): |
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hpos = positions[j] |
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dx = opos[0] - hpos[0] |
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dy = opos[1] - hpos[1] |
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dz = opos[2] - hpos[2] |
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dist = math.sqrt(dx*dx + dy*dy + dz*dz) |
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if (dist < OHbond): |
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if (nH >= 2): |
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print "oxygen %d had too many hydrogens" % (i) |
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sys.exit(1) |
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H[nH] = j |
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nH = nH + 1 |
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if (nH != 2): |
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print "oxygen %d had %d hydrogens, skipping" % (i, nH) |
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if (nH == 2): |
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Xcom = Omass * opos[0] + Hmass*(positions[H[0]][0] + positions[H[1]][0]) |
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Ycom = Omass * opos[1] + Hmass*(positions[H[0]][1] + positions[H[1]][1]) |
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Zcom = Omass * opos[2] + Hmass*(positions[H[0]][2] + positions[H[1]][2]) |
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|
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totalMass = Omass + 2.0*Hmass |
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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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WaterPos.append(COM) |
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bisector = [0.0, 0.0, 0.0] |
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ux = [0.0, 0.0, 0.0] |
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uy = [0.0, 0.0, 0.0] |
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uz = [0.0, 0.0, 0.0] |
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RotMat = numpy.zeros((3,3), numpy.float) |
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|
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for j in range(3): |
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bisector[j] = 0.5*(positions[H[0]][j] + positions[H[1]][j]) |
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uz[j] = bisector[j] - opos[j] |
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uy[j] = positions[H[0]][j] - positions[H[1]][j] |
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|
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uz = normalize(uz) |
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uy = normalize(uy) |
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ux = cross(uy, uz) |
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ux = normalize(ux) |
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|
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q = [0.0, 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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RotMat[0] = ux |
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RotMat[1] = uy |
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RotMat[2] = uz |
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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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q[3] = 0.25 / s |
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|
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WaterQuats.append(q) |
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Eliminate.append(i) |
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Eliminate.append(H[0]) |
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Eliminate.append(H[1]) |
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|
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|
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def writeFile(outputFileName): |
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outputFile = open(outputFileName, 'w') |
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|
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outputFile.write("<OpenMD version=1>\n"); |
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|
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for metaline in metaData: |
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outputFile.write(metaline) |
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|
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outputFile.write(" <Snapshot>\n") |
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|
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for frameline in frameData: |
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outputFile.write(frameline) |
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|
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outputFile.write(" <StuntDoubles>\n") |
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|
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sdFormat = 'pvqj' |
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|
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index = 0 |
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for i in range(len(WaterPos)): |
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outputFile.write("%10d %7s %18.10g %18.10g %18.10g %13e %13e %13e %13e %13e %13e %13e %13e %13e %13e\n" % (index, sdFormat, WaterPos[i][0], WaterPos[i][1], WaterPos[i][2], 0.0, 0.0, 0.0, WaterQuats[i][0], WaterQuats[i][1], WaterQuats[i][2], WaterQuats[i][3], 0.0, 0.0, 0.0)) |
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index = index + 1 |
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|
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|
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sdFormat = 'pv' |
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for i in range(len(indices)): |
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if i not in Eliminate: |
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outputFile.write("%10d %7s %18.10g %18.10g %18.10g %13e %13e %13e \n" % (index, sdFormat, positions[i][0], positions[i][1], positions[i][2], 0.0, 0.0, 0.0)) |
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|
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outputFile.write(" </StuntDoubles>\n") |
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outputFile.write(" </Snapshot>\n") |
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outputFile.write("</OpenMD>\n") |
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outputFile.close() |
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|
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def dot(L1, L2): |
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myDot = 0.0 |
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for i in range(len(L1)): |
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myDot = myDot + L1[i]*L2[i] |
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return myDot |
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|
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def normalize(L1): |
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L2 = [] |
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myLength = math.sqrt(dot(L1, L1)) |
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for i in range(len(L1)): |
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L2.append(L1[i] / myLength) |
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return L2 |
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|
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def cross(L1, L2): |
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# don't call this with anything other than length 3 lists please |
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# or you'll be sorry |
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L3 = [0.0, 0.0, 0.0] |
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L3[0] = L1[1]*L2[2] - L1[2]*L2[1] |
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L3[1] = L1[2]*L2[0] - L1[0]*L2[2] |
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L3[2] = L1[0]*L2[1] - L1[1]*L2[0] |
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return L3 |
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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-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 ("-x", "--xyz-file"): |
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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", "--output-file"): |
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outputFileName = arg |
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global _haveOutputFileName |
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_haveOutputFileName = 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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if (_haveOutputFileName != 1): |
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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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readFile(xyzFileName) |
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findWaters() |
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writeFile(outputFileName) |
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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:]) |
