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#!@PYTHON_EXECUTABLE@ |
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"""MetaData affine scaling transform |
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|
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Takes a MetaData file and scales both the periodic box and the |
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coordinates of all StuntDoubles in the system by the same amount. |
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|
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You can either specify a new volume scaling for isotropic scaling, |
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or specify one (or more) of the coordinates for non-isotropic scaling. |
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|
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Usage: affineScale |
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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, --newX=... scale the system to a new x dimension |
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-y, --newY=... scale the system to a new y dimension |
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-z, --newZ=... scale the system to a new z dimension |
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-v, --newV=... scale the system to a new volume |
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|
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Example: |
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affineScale -m lipidSystem.md -o scaledSystem.md -v 77000.0 |
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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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wrap = [] |
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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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wrap.append([0,0,0]) |
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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 index in range(len(deco)): |
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(index,i) = deco[index] |
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print i |
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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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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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wrappingNumber = [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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wrappingNumber[i] = roundMe(scaled[i]) |
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scaled[i] = scaled[i] - wrappingNumber[i] |
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myVect[i] = scaled[i] * Hmat[i][i] |
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return myVect, wrappingNumber |
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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(): |
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for i in range(len(indices)): |
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dpos = [] |
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dpos.append(p[i][0]) |
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dpos.append(p[i][1]) |
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dpos.append(p[i][2]) |
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p[i], wrap[i] = wrapVector(dpos) |
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|
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def scaleBox(scaleX, scaleY, scaleZ): |
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for i in range(3): |
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Hmat[0][i] = scaleX * Hmat[0][i] |
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for i in range(3): |
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Hmat[1][i] = scaleY * Hmat[1][i] |
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for i in range(3): |
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Hmat[2][i] = scaleZ * Hmat[2][i] |
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for i in range(3): |
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BoxInv[i] = 1.0/Hmat[i][i] |
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|
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def scaleCoordinates(scaleX, scaleY, scaleZ): |
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for i in range(len(indices)): |
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p[i][0] = p[i][0]*scaleX + wrap[i][0] * Hmat[0][0] |
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p[i][1] = p[i][1]*scaleY + wrap[i][1] * Hmat[1][1] |
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p[i][2] = p[i][2]*scaleZ + wrap[i][2] * Hmat[2][2] |
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|
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def main(argv): |
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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:v:", ["help", "meta-data=", "output-file=", "newX=", "newY=", "newZ=","newV="]) |
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except getopt.GetoptError: |
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usage() |
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sys.exit(2) |
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doV = 0 |
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doX = 0 |
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doY = 0 |
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doZ = 0 |
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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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if opt in ("-x", "--newX"): |
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newX = float(arg) |
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doX = 1 |
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elif opt in ("-y", "--newY"): |
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newY = float(arg) |
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doY = 1 |
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elif opt in ("-z", "--newZ"): |
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newZ = float(arg) |
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doZ = 1 |
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elif opt in ("-v", "--newV"): |
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newV = float(arg) |
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doV = 1 |
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|
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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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if not (doV or doX or doY or doZ): |
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usage() |
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print "no scaling options given. Nothing to do!" |
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sys.exit() |
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|
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if doV and (doX or doY or doZ): |
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usage() |
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print "-v is mutually exclusive with any of the -x, -y, and -z options" |
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sys.exit() |
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|
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readFile(mdFileName) |
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|
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scaleX = 1.0 |
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scaleY = 1.0 |
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scaleZ = 1.0 |
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|
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if doX: |
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scaleX = newX / Hmat[0][0] |
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if doY: |
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scaleY = newY / Hmat[1][1] |
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if doZ: |
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scaleZ = newZ / Hmat[2][2] |
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|
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if doV: |
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oldV = Hmat[0][0] * Hmat[1][1] * Hmat[2][2] |
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scaleX = pow(newV/oldV, 1.0/3.0) |
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scaleY = scaleX |
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scaleZ = scaleX |
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|
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mapToBox() |
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scaleBox(scaleX, scaleY, scaleZ) |
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scaleCoordinates(scaleX, scaleY, scaleZ) |
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writeFile(outputFileName, 1, 1, 1) |
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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:]) |
