| 1 |
#!/usr/bin/env python |
| 2 |
"""Ice Cube Solvator |
| 3 |
|
| 4 |
Opens two md files, one with water in an ice structure, |
| 5 |
and one with water in a liquid phase. Deletes any overlapping |
| 6 |
liquid molecules and merges the two md files. |
| 7 |
|
| 8 |
Usage: waterRotator |
| 9 |
|
| 10 |
Options: |
| 11 |
-h, --help show this help |
| 12 |
-u, --solute=... use specified meta-data (.md) file as the solute |
| 13 |
-v, --solvent=... use specified meta-data (.md) file as the solvent |
| 14 |
-r, --rcut=... specify the cutoff radius for deleting solvent |
| 15 |
-o, --output-file=... use specified output (.md) file |
| 16 |
|
| 17 |
|
| 18 |
Example: |
| 19 |
iceCubeSolvator -u frosty.md -v tepid.md -r 4.0 -o lukewarm.md |
| 20 |
|
| 21 |
""" |
| 22 |
|
| 23 |
__author__ = "Dan Gezelter (gezelter@nd.edu)" |
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__version__ = "$Revision: 1.7 $" |
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__date__ = "$Date: 2008-06-26 15:50:22 $" |
| 26 |
__copyright__ = "Copyright (c) 2006 by the University of Notre Dame" |
| 27 |
__license__ = "OOPSE" |
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|
| 29 |
import sys |
| 30 |
import getopt |
| 31 |
import string |
| 32 |
import math |
| 33 |
import random |
| 34 |
from sets import * |
| 35 |
#from Numeric import * |
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|
| 37 |
_haveMDFileName1 = 0 |
| 38 |
_haveMDFileName2 = 0 |
| 39 |
_haveRcut = 0 |
| 40 |
_haveOutputFileName = 0 |
| 41 |
_haveNSoluteAtoms = 1 |
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_haveNSolventAtoms = 1 |
| 43 |
|
| 44 |
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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pvqj1 = [] |
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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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pvqj2 = [] |
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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() |
| 100 |
while 1: |
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if '<Snapshot>' in line: |
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line = mdFile.readline() |
| 103 |
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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if 'pvqj' in L[1]: |
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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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else: |
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quaternions1.append([0.0, 0.0, 0.0, 0.0]) |
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angVels1.append([0.0, 0.0, 0.0]) |
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|
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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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if 'pvqj' in L[1]: |
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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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else: |
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quaternions1.append([0.0, 0.0, 0.0, 0.0]) |
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angVels1.append([0.0, 0.0, 0.0]) |
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|
| 266 |
line = mdFile.readline() |
| 267 |
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() |
| 274 |
|
| 275 |
def writeFile(outputFileName): |
| 276 |
outputFile = open(outputFileName, 'w') |
| 277 |
|
| 278 |
outputFile.write("<OOPSE version=4>\n"); |
| 279 |
|
| 280 |
for metaline in metaData1: |
| 281 |
outputFile.write(metaline) |
| 282 |
|
| 283 |
outputFile.write(" <Snapshot>\n") |
| 284 |
|
| 285 |
for frameline in frameData1: |
| 286 |
outputFile.write(frameline) |
| 287 |
|
| 288 |
outputFile.write(" <StuntDoubles>\n") |
| 289 |
|
| 290 |
|
| 291 |
newIndex = 0 |
| 292 |
for i in range(len(indices1)): |
| 293 |
if (pvqj[i] == 'pv'): |
| 294 |
outputFile.write("%10d %7s %18.10g %18.10g %18.10g %14e %13e %13e\n" % (newIndex, pvqj1[i], positions1[i][0], positions1[i][1], positions1[i][2], velocities1[i][0], velocities1[i][1], velocities1[i][2])) |
| 295 |
elif(pvqj[i] == 'pvqj'): |
| 296 |
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])) |
| 297 |
|
| 298 |
newIndex = newIndex + 1 |
| 299 |
|
| 300 |
outputFile.write(" </StuntDoubles>\n") |
| 301 |
outputFile.write(" </Snapshot>\n") |
| 302 |
outputFile.write("</OOPSE>\n") |
| 303 |
outputFile.close() |
| 304 |
|
| 305 |
def roundMe(x): |
| 306 |
if (x >= 0.0): |
| 307 |
return math.floor(x + 0.5) |
| 308 |
else: |
| 309 |
return math.ceil(x - 0.5) |
| 310 |
|
| 311 |
def frange(start,stop,step=1.0): |
| 312 |
while start < stop: |
| 313 |
yield start |
| 314 |
start += step |
| 315 |
|
| 316 |
|
| 317 |
def wrapVector(myVect): |
| 318 |
scaled = [0.0, 0.0, 0.0] |
| 319 |
for i in range(3): |
| 320 |
scaled[i] = myVect[i] * BoxInv1[i] |
| 321 |
scaled[i] = scaled[i] - roundMe(scaled[i]) |
| 322 |
myVect[i] = scaled[i] * Hmat1[i][i] |
| 323 |
return myVect |
| 324 |
|
| 325 |
def dot(L1, L2): |
| 326 |
myDot = 0.0 |
| 327 |
for i in range(len(L1)): |
| 328 |
myDot = myDot + L1[i]*L2[i] |
| 329 |
return myDot |
| 330 |
|
| 331 |
def normalize(L1): |
| 332 |
L2 = [] |
| 333 |
myLength = math.sqrt(dot(L1, L1)) |
| 334 |
for i in range(len(L1)): |
| 335 |
L2.append(L1[i] / myLength) |
| 336 |
return L2 |
| 337 |
|
| 338 |
def cross(L1, L2): |
| 339 |
# don't call this with anything other than length 3 lists please |
| 340 |
# or you'll be sorry |
| 341 |
L3 = [0.0, 0.0, 0.0] |
| 342 |
L3[0] = L1[1]*L2[2] - L1[2]*L2[1] |
| 343 |
L3[1] = L1[2]*L2[0] - L1[0]*L2[2] |
| 344 |
L3[2] = L1[0]*L2[1] - L1[1]*L2[0] |
| 345 |
return L3 |
| 346 |
|
| 347 |
def removeOverlaps(rcut,nSolventAtoms,nSoluteAtoms): |
| 348 |
|
| 349 |
rcut2 = rcut*rcut |
| 350 |
nextMol = 0 |
| 351 |
|
| 352 |
|
| 353 |
for i in range(0,len(indices2),nSolventAtoms): |
| 354 |
keepThisMolecule = 1 |
| 355 |
for atom1 in range (i, (i+nSolventAtoms)): |
| 356 |
iPos = positions2[atom1] |
| 357 |
|
| 358 |
for j in range(0,len(indices1),nSoluteAtoms): |
| 359 |
for atom2 in range (j, (j+nSoluteAtoms)): |
| 360 |
jPos = positions1[j] |
| 361 |
dpos = [jPos[0]-iPos[0], jPos[1]-iPos[1], jPos[2]-iPos[2]] |
| 362 |
dpos = wrapVector(dpos) |
| 363 |
dist2 = dot(dpos,dpos) |
| 364 |
|
| 365 |
if (dist2 < rcut2): |
| 366 |
keepThisMolecule = 0 |
| 367 |
break |
| 368 |
|
| 369 |
keepers.append(keepThisMolecule) |
| 370 |
|
| 371 |
for i in range(0,len(indices2),nSolventAtoms): |
| 372 |
if (keepers[i] == 1): |
| 373 |
for j in range (i, i+nSolventAtoms): |
| 374 |
if (pvqj2[j] == 'pv'): |
| 375 |
positions1.append(positions2[j]) |
| 376 |
velocities1.append(velocities2[j]) |
| 377 |
quaternions1.append(quaternions2[j]) |
| 378 |
angVels1.append(angVels2[j]) |
| 379 |
indices1.append(indices2[j]) |
| 380 |
|
| 381 |
def main(argv): |
| 382 |
try: |
| 383 |
opts, args = getopt.getopt(argv, "hu:v:n:p:r:o:", ["help", "solute=","solvent=","nSoluteAtoms=","nSolventAtoms=", "rcut=" "output-file="]) |
| 384 |
except getopt.GetoptError: |
| 385 |
usage() |
| 386 |
sys.exit(2) |
| 387 |
for opt, arg in opts: |
| 388 |
if opt in ("-h", "--help"): |
| 389 |
usage() |
| 390 |
sys.exit() |
| 391 |
elif opt in ("-u", "--solute"): |
| 392 |
mdFileName1 = arg |
| 393 |
global _haveMDFileName1 |
| 394 |
_haveMDFileName1 = 1 |
| 395 |
elif opt in ("-v", "--solvent"): |
| 396 |
mdFileName2 = arg |
| 397 |
global _haveMDFileName2 |
| 398 |
_haveMDFileName2 = 1 |
| 399 |
elif opt in ("-n", "--nSoluteAtoms"): |
| 400 |
nSoluteAtoms = int(arg) |
| 401 |
global _haveNSoluteAtoms |
| 402 |
_haveNSoluteAtoms = 1 |
| 403 |
elif opt in ("-p", "--nSolventAtoms"): |
| 404 |
nSolventAtoms = int(arg) |
| 405 |
global _haveNSolventAtoms |
| 406 |
_haveNSolventAtoms = 1 |
| 407 |
elif opt in ("-r", "--rcut"): |
| 408 |
rcut = float(arg) |
| 409 |
global _haveRcut |
| 410 |
_haveRcut = 1 |
| 411 |
elif opt in ("-o", "--output-file"): |
| 412 |
outputFileName = arg |
| 413 |
global _haveOutputFileName |
| 414 |
_haveOutputFileName = 1 |
| 415 |
|
| 416 |
if (_haveMDFileName1 != 1): |
| 417 |
usage() |
| 418 |
print "No meta-data file was specified for the solute" |
| 419 |
sys.exit() |
| 420 |
|
| 421 |
if (_haveMDFileName2 != 1): |
| 422 |
usage() |
| 423 |
print "No meta-data file was specified for the solvent" |
| 424 |
sys.exit() |
| 425 |
|
| 426 |
if (_haveOutputFileName != 1): |
| 427 |
usage() |
| 428 |
print "No output file was specified" |
| 429 |
sys.exit() |
| 430 |
|
| 431 |
if (_haveRcut != 1): |
| 432 |
print "No cutoff radius was specified, using 4 angstroms" |
| 433 |
rcut = 4.0 |
| 434 |
|
| 435 |
if (_haveNSoluteAtoms != 1): |
| 436 |
nSoluteAtoms = 1 |
| 437 |
|
| 438 |
if (_haveNSolventAtoms != 1): |
| 439 |
nSolventAtoms = 1 |
| 440 |
|
| 441 |
readFile1(mdFileName1) |
| 442 |
readFile2(mdFileName2) |
| 443 |
removeOverlaps(rcut,nSolventAtoms,nSoluteAtoms) |
| 444 |
writeFile(outputFileName) |
| 445 |
|
| 446 |
if __name__ == "__main__": |
| 447 |
if len(sys.argv) == 1: |
| 448 |
usage() |
| 449 |
sys.exit() |
| 450 |
main(sys.argv[1:]) |
