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#!/usr/bin/env python |
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"""MetaData file remapper |
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|
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Takes a MetaData file and maps all StuntDoubles back to the periodic box. |
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Will optionally replicate the system in the three box directions, or |
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translate every object in the box and before writing out a new MetaData file. |
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|
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Usage: md2md |
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|
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Options: |
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-h, --help show this help |
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-m, --meta-data=... use specified meta-data (.md, .eor) file |
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-o, --output-file=... use specified output file |
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-x, --repeatX=... make the system repeat in the x direction |
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-y, --repeatY=... make the system repeat in the y direction |
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-z, --repeatZ=... make the system repeat in the z direction |
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-t, --translateX=... translate all x coordinates by some amount |
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-u, --translateY=... translate all y coordinates by some amount |
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-v, --translateZ=... translate all z coordinates by some amount |
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|
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Example: |
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md2md -m lipidSystem.md -o bigLipidSystem.md -x 2 -y 2 -z 1 -v 35.0 |
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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) 2009 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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|
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metaData = [] |
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frameData = [] |
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indices = [] |
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pvqj = [] |
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p = [] |
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v = [] |
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q = [] |
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j = [] |
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Hmat = [] |
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BoxInv = [] |
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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(mdFileName): |
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mdFile = open(mdFileName, 'r') |
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# Find OpenMD 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 or '<OpenMD version=' in line: |
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OpenMDversion = 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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metaData.append(line) |
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line = mdFile.readline() |
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if '</MetaData>' in line: |
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metaData.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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frameData.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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Hmat.append([Hxx, Hxy, Hxz]) |
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Hmat.append([Hyx, Hyy, Hyz]) |
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Hmat.append([Hzx, Hzy, Hzz]) |
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BoxInv.append(1.0/Hxx) |
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BoxInv.append(1.0/Hyy) |
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BoxInv.append(1.0/Hzz) |
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line = mdFile.readline() |
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if '</FrameData>' in line: |
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frameData.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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indices.append(myIndex) |
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pvqj.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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p.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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v.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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q.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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j.append([jx, jy, jz]) |
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else: |
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q.append([0.0, 0.0, 0.0, 0.0]) |
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j.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 writeFile(outputFileName,repeatX,repeatY,repeatZ): |
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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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print "writing MetaData" |
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for metaline in metaData: |
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if 'nMol' in metaline: |
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metasplit = metaline.split() |
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nMol = float(metasplit[2].strip(';')) |
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newNmol = nMol * repeatX * repeatY * repeatZ |
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outputFile.write(' nMol = %10d;\n' % (newNmol)) |
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else: |
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outputFile.write(metaline) |
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|
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print "writing Snapshot" |
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outputFile.write(" <Snapshot>\n") |
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|
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print "writing FrameData" |
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for frameline in frameData: |
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if 'Hmat:' in frameline: |
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myH = [] |
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myH.append([repeatX * Hmat[0][0], repeatX * Hmat[0][1], repeatX * Hmat[0][2]]) |
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myH.append([repeatY * Hmat[1][0], repeatY * Hmat[1][1], repeatY * Hmat[1][2]]) |
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myH.append([repeatZ * Hmat[2][0], repeatZ * Hmat[2][1], repeatZ * Hmat[2][2]]) |
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outputFile.write(" Hmat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n" % (myH[0][0], myH[0][1], myH[0][2], myH[1][0], myH[1][1], myH[1][2], myH[2][0], myH[2][1], myH[2][2])) |
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else: |
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outputFile.write(frameline) |
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|
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print "writing StuntDoubles" |
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outputFile.write(" <StuntDoubles>\n") |
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|
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print repeatX, repeatY, repeatZ |
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|
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deco = [ (index, i) for i, index in enumerate(indices) ] |
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deco.sort() |
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whichSD = 0 |
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for ii in range(repeatX): |
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for jj in range(repeatY): |
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for kk in range(repeatZ): |
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for index in range(len(deco)): |
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(index,i) = deco[index] |
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print i |
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myP = [] |
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myP.append(p[i][0] + ii*Hmat[0][0] + jj*Hmat[1][0] + kk*Hmat[2][0]) |
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myP.append(p[i][1] + ii*Hmat[0][1] + jj*Hmat[1][1] + kk*Hmat[2][1]) |
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myP.append(p[i][2] + ii*Hmat[0][2] + jj*Hmat[1][2] + kk*Hmat[2][2]) |
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|
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if (pvqj[i] == 'pv'): |
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outputFile.write("%10d %7s %18.10g %18.10g %18.10g %14e %13e %13e\n" % (whichSD, pvqj[i], myP[0], myP[1], myP[2], v[i][0], v[i][1], v[i][2])) |
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elif (pvqj[i] == 'pvqj'): |
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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" % (whichSD, pvqj[i], myP[0], myP[1], myP[2], v[i][0], v[i][1], v[i][2], q[i][0], q[i][1], q[i][2], q[i][3], j[i][0], j[i][1], j[i][2])) |
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whichSD = whichSD + 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("</OpenMD>\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] * BoxInv[i] |
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scaled[i] = scaled[i] - roundMe(scaled[i]) |
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myVect[i] = scaled[i] * Hmat[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 |
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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 mapToBox(translateX, translateY, translateZ): |
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print "translating by %f\t%f\t%f" % (translateX, translateY, translateZ) |
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for i in range(len(indices)): |
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dpos = [] |
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dpos.append(p[i][0] + translateX) |
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dpos.append(p[i][1] + translateY) |
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dpos.append(p[i][2] + translateZ) |
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p[i] = wrapVector(dpos) |
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|
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def main(argv): |
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repeatX = 1 |
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repeatY = 1 |
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repeatZ = 1 |
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translateX = 0.0 |
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translateY = 0.0 |
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translateZ = 0.0 |
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_haveMDFileName = 0 |
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_haveOutputFileName = 0 |
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try: |
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opts, args = getopt.getopt(argv, "hm:o:x:y:z:t:u:v:", ["help", "meta-data=", "output-file=", "repeatX=", "repeatY=", "repeatZ=","translateX=","translateY=","translateZ="]) |
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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 ("-m", "--meta-data"): |
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mdFileName = arg |
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_haveMDFileName = 1 |
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elif opt in ("-o", "--output-file"): |
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outputFileName = arg |
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_haveOutputFileName = 1 |
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elif opt in ("-x", "--repeatX"): |
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repeatX = int(arg) |
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elif opt in ("-y", "--repeatY"): |
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repeatY = int(arg) |
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elif opt in ("-z", "--repeatZ"): |
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repeatZ = int(arg) |
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elif opt in ("-t", "--translateX"): |
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translateX = float(arg) |
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elif opt in ("-u", "--translateY"): |
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translateY = float(arg) |
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elif opt in ("-v", "--translateZ"): |
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translateZ = float(arg) |
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if (_haveMDFileName != 1): |
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usage() |
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print "No meta-data 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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|
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readFile(mdFileName) |
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mapToBox(translateX, translateY, translateZ) |
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writeFile(outputFileName, repeatX, repeatY, repeatZ) |
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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:]) |
