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#!/usr/bin/env python |
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"""Ice Cube Solvator |
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|
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Opens two md files, one with water in an ice structure, |
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and one with water in a liquid phase. Deletes any overlapping |
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liquid molecules and merges the two md files. |
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|
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Usage: waterRotator |
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|
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Options: |
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-h, --help show this help |
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-u, --solute=... use specified meta-data (.md) file as the solute |
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-v, --solvent=... use specified meta-data (.md) file as the solvent |
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-r, --rcut=... specify the cutoff radius for deleting solvent |
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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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iceCubeSolvator -u frosty.md -v tepid.md -r 4.0 -o lukewarm.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: 1.4 $" |
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__date__ = "$Date: 2008-06-25 18:22:08 $" |
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__copyright__ = "Copyright (c) 2006 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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import random |
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from sets import * |
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#from Numeric import * |
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|
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_haveMDFileName1 = 0 |
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_haveMDFileName2 = 0 |
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_haveRcut = 0 |
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_haveOutputFileName = 0 |
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|
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metaData1 = [] |
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frameData1 = [] |
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positions1 = [] |
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velocities1 = [] |
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quaternions1 = [] |
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angVels1 = [] |
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indices1 = [] |
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Hmat1 = [] |
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BoxInv1 = [] |
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|
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metaData2 = [] |
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frameData2 = [] |
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positions2 = [] |
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velocities2 = [] |
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quaternions2 = [] |
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angVels2 = [] |
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indices2 = [] |
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Hmat2 = [] |
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BoxInv2 = [] |
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|
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keepers = [] |
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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 readFile1(mdFileName): |
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mdFile = open(mdFileName, 'r') |
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# Find OOPSE version info first |
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line = mdFile.readline() |
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while 1: |
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if '<OOPSE version=' in line: |
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OOPSEversion = line |
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break |
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line = mdFile.readline() |
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|
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# Rewind file and find start of MetaData block |
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|
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mdFile.seek(0) |
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line = mdFile.readline() |
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print "reading MetaData" |
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while 1: |
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if '<MetaData>' in line: |
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while 2: |
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metaData1.append(line) |
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line = mdFile.readline() |
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if '</MetaData>' in line: |
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metaData1.append(line) |
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break |
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break |
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line = mdFile.readline() |
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|
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mdFile.seek(0) |
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print "reading Snapshot" |
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line = mdFile.readline() |
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while 1: |
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if '<Snapshot>' in line: |
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line = mdFile.readline() |
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while 1: |
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print "reading FrameData" |
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if '<FrameData>' in line: |
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while 2: |
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frameData1.append(line) |
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if 'Hmat:' in line: |
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L = line.split() |
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Hxx = float(L[2].strip(',')) |
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Hxy = float(L[3].strip(',')) |
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Hxz = float(L[4].strip(',')) |
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Hyx = float(L[7].strip(',')) |
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Hyy = float(L[8].strip(',')) |
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Hyz = float(L[9].strip(',')) |
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Hzx = float(L[12].strip(',')) |
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Hzy = float(L[13].strip(',')) |
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Hzz = float(L[14].strip(',')) |
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Hmat1.append([Hxx, Hxy, Hxz]) |
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Hmat1.append([Hyx, Hyy, Hyz]) |
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Hmat1.append([Hzx, Hzy, Hzz]) |
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print Hmat1 |
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BoxInv1.append(1.0/Hxx) |
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BoxInv1.append(1.0/Hyy) |
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BoxInv1.append(1.0/Hzz) |
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print BoxInv1 |
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line = mdFile.readline() |
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if '</FrameData>' in line: |
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frameData1.append(line) |
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break |
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break |
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|
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line = mdFile.readline() |
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while 1: |
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if '<StuntDoubles>' in line: |
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line = mdFile.readline() |
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while 2: |
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L = line.split() |
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myIndex = int(L[0]) |
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indices1.append(myIndex) |
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pvqj1.append(L[1]) |
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x = float(L[2]) |
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y = float(L[3]) |
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z = float(L[4]) |
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positions1.append([x, y, z]) |
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vx = float(L[5]) |
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vy = float(L[6]) |
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vz = float(L[7]) |
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velocities1.append([vx, vy, vz]) |
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qw = float(L[8]) |
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qx = float(L[9]) |
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qy = float(L[10]) |
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qz = float(L[11]) |
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quaternions1.append([qw, qx, qy, qz]) |
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jx = float(L[12]) |
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jy = float(L[13]) |
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jz = float(L[14]) |
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angVels1.append([jx, jy, jz]) |
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line = mdFile.readline() |
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if '</StuntDoubles>' in line: |
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break |
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break |
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line = mdFile.readline() |
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if not line: break |
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|
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mdFile.close() |
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|
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def readFile2(mdFileName): |
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mdFile = open(mdFileName, 'r') |
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# Find OOPSE version info first |
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line = mdFile.readline() |
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while 1: |
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if '<OOPSE version=' in line: |
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OOPSEversion = line |
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break |
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line = mdFile.readline() |
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|
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# Rewind file and find start of MetaData block |
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|
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mdFile.seek(0) |
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line = mdFile.readline() |
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print "reading MetaData" |
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while 1: |
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if '<MetaData>' in line: |
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while 2: |
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metaData2.append(line) |
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line = mdFile.readline() |
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if '</MetaData>' in line: |
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metaData2.append(line) |
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break |
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break |
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line = mdFile.readline() |
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|
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mdFile.seek(0) |
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print "reading Snapshot" |
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line = mdFile.readline() |
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while 1: |
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if '<Snapshot>' in line: |
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line = mdFile.readline() |
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while 1: |
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print "reading FrameData" |
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if '<FrameData>' in line: |
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while 2: |
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frameData2.append(line) |
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if 'Hmat:' in line: |
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L = line.split() |
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Hxx = float(L[2].strip(',')) |
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Hxy = float(L[3].strip(',')) |
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Hxz = float(L[4].strip(',')) |
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Hyx = float(L[7].strip(',')) |
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Hyy = float(L[8].strip(',')) |
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Hyz = float(L[9].strip(',')) |
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Hzx = float(L[12].strip(',')) |
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Hzy = float(L[13].strip(',')) |
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Hzz = float(L[14].strip(',')) |
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Hmat2.append([Hxx, Hxy, Hxz]) |
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Hmat2.append([Hyx, Hyy, Hyz]) |
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Hmat2.append([Hzx, Hzy, Hzz]) |
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print Hmat2 |
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BoxInv2.append(1.0/Hxx) |
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BoxInv2.append(1.0/Hyy) |
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BoxInv2.append(1.0/Hzz) |
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print BoxInv2 |
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line = mdFile.readline() |
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if '</FrameData>' in line: |
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frameData2.append(line) |
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break |
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break |
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|
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line = mdFile.readline() |
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while 1: |
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if '<StuntDoubles>' in line: |
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line = mdFile.readline() |
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while 2: |
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L = line.split() |
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myIndex = int(L[0]) |
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indices2.append(myIndex) |
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pvqj2.append(L[1]) |
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x = float(L[2]) |
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y = float(L[3]) |
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z = float(L[4]) |
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positions2.append([x, y, z]) |
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vx = float(L[5]) |
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vy = float(L[6]) |
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vz = float(L[7]) |
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velocities2.append([vx, vy, vz]) |
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qw = float(L[8]) |
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qx = float(L[9]) |
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qy = float(L[10]) |
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qz = float(L[11]) |
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quaternions2.append([qw, qx, qy, qz]) |
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jx = float(L[12]) |
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jy = float(L[13]) |
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jz = float(L[14]) |
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angVels2.append([jx, jy, jz]) |
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line = mdFile.readline() |
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if '</StuntDoubles>' in line: |
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break |
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break |
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line = mdFile.readline() |
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if not line: break |
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|
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mdFile.close() |
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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("<OOPSE version=4>\n"); |
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|
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for metaline in metaData1: |
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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 frameData1: |
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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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newIndex = 0 |
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for i in range(len(indices1)): |
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|
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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" % (newIndex, pvqj1[i], positions1[i][0], positions1[i][1], positions1[i][2], velocities1[i][0], velocities1[i][1], velocities1[i][2], quaternions1[i][0], quaternions1[i][1], quaternions1[i][2], quaternions1[i][3], angVels1[i][0], angVels1[i][1], angVels1[i][2])) |
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newIndex = newIndex + 1 |
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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("</OOPSE>\n") |
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outputFile.close() |
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|
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def roundMe(x): |
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if (x >= 0.0): |
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return math.floor(x + 0.5) |
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else: |
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return math.ceil(x - 0.5) |
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|
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def wrapVector(myVect): |
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scaled = [0.0, 0.0, 0.0] |
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for i in range(3): |
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scaled[i] = myVect[i] * BoxInv1[i] |
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scaled[i] = scaled[i] - roundMe(scaled[i]) |
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myVect[i] = scaled[i] * Hmat1[i][i] |
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return myVect |
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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 |
| 307 |
|
| 308 |
def normalize(L1): |
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L2 = [] |
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myLength = math.sqrt(dot(L1, L1)) |
| 311 |
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] |
| 319 |
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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|
| 324 |
def removeOverlaps(rcut): |
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|
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rcut2 = rcut*rcut |
| 327 |
for i in range(len(indices2)): |
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keepThisMolecule = 1 |
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|
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iPos = positions2[i] |
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|
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for j in range(len(indices1)): |
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jPos = positions1[j] |
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dpos = [jPos[0]-iPos[0], jPos[1]-iPos[1], jPos[2]-iPos[2]] |
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dpos = wrapVector(dpos) |
| 336 |
dist2 = dot(dpos,dpos) |
| 337 |
|
| 338 |
if (dist2 < rcut2): |
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keepThisMolecule = 0 |
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break |
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|
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keepers.append(keepThisMolecule) |
| 343 |
|
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for i in range(len(indices2)): |
| 345 |
if (keepers[i] == 1): |
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positions1.append(positions2[i]) |
| 347 |
velocities1.append(velocities2[i]) |
| 348 |
quaternions1.append(quaternions2[i]) |
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angVels1.append(angVels2[i]) |
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indices1.append(indices2[i]) |
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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, "hu:v:r:o:", ["help", "solute=","solvent=", "rcut" "output-file="]) |
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except getopt.GetoptError: |
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usage() |
| 357 |
sys.exit(2) |
| 358 |
for opt, arg in opts: |
| 359 |
if opt in ("-h", "--help"): |
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usage() |
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sys.exit() |
| 362 |
elif opt in ("-u", "--solute"): |
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mdFileName1 = arg |
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global _haveMDFileName1 |
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_haveMDFileName1 = 1 |
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elif opt in ("-v", "--solvent"): |
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mdFileName2 = arg |
| 368 |
global _haveMDFileName2 |
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_haveMDFileName2 = 1 |
| 370 |
elif opt in ("-r", "--rcut"): |
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rcut = float(arg) |
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global _haveRcut |
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_haveRcut = 1 |
| 374 |
elif opt in ("-o", "--output-file"): |
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outputFileName = arg |
| 376 |
global _haveOutputFileName |
| 377 |
_haveOutputFileName = 1 |
| 378 |
|
| 379 |
if (_haveMDFileName1 != 1): |
| 380 |
usage() |
| 381 |
print "No meta-data file was specified for the solute" |
| 382 |
sys.exit() |
| 383 |
|
| 384 |
if (_haveMDFileName2 != 1): |
| 385 |
usage() |
| 386 |
print "No meta-data file was specified for the solvent" |
| 387 |
sys.exit() |
| 388 |
|
| 389 |
if (_haveOutputFileName != 1): |
| 390 |
usage() |
| 391 |
print "No output file was specified" |
| 392 |
sys.exit() |
| 393 |
|
| 394 |
if (_haveRcut != 1): |
| 395 |
print "No cutoff radius was specified, using 4 angstroms" |
| 396 |
rcut = 4.0 |
| 397 |
|
| 398 |
readFile1(mdFileName1) |
| 399 |
readFile2(mdFileName2) |
| 400 |
removeOverlaps(rcut) |
| 401 |
writeFile(outputFileName) |
| 402 |
|
| 403 |
if __name__ == "__main__": |
| 404 |
if len(sys.argv) == 1: |
| 405 |
usage() |
| 406 |
sys.exit() |
| 407 |
main(sys.argv[1:]) |
