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root/OpenMD/trunk/src/applications/utilities/affineScale

Comparing trunk/src/applications/utilities/affineScale (file contents):
Revision 1383 by gezelter, Thu Oct 22 19:12:14 2009 UTC vs.
Revision 1919 by jmarr, Wed Jul 31 18:03:35 2013 UTC

#	Line 1 | Line 1
1	<	#!/usr/bin/env python
1	>	#!@PYTHON_EXECUTABLE@
2		"""MetaData affine scaling transform
3
4		Takes a MetaData file and scales both the periodic box and the
#	Line 24 | Line 24 | __author__ = "Dan Gezelter (gezelter@nd.edu)"
24		"""
25
26		__author__ = "Dan Gezelter (gezelter@nd.edu)"
27	<	__version__ = "$Revision: 1.3 $"
28	<	__date__ = "$Date: 2009-10-22 19:12:14 $"
27	>	__version__ = "$Revision$"
28	>	__date__ = "$Date$"
29		__copyright__ = "Copyright (c) 2009 by the University of Notre Dame"
30		__license__ = "OpenMD"
31
#	Line 41 | Line 41 | p = []
41		indices = []
42		pvqj = []
43		p = []
44	+	wrap = []
45		v = []
46		q = []
47		j = []
#	Line 52 | Line 53 | def readFile(mdFileName):
53
54		def readFile(mdFileName):
55		mdFile = open(mdFileName, 'r')
56	<	# Find OOPSE version info first
56	>	# Find OpenMD version info first
57		line = mdFile.readline()
58		while 1:
59	<	if '<OOPSE version=' in line:
60	<	OOPSEversion = line
59	>	if '<OOPSE version=' in line or '<OpenMD version=' in line:
60	>	OpenMDversion = line
61		break
62		line = mdFile.readline()
63
#	Line 123 | Line 124 | def readFile(mdFileName):
124		y = float(L[3])
125		z = float(L[4])
126		p.append([x, y, z])
127	+	wrap.append([0,0,0])
128		vx = float(L[5])
129		vy = float(L[6])
130		vz = float(L[7])
#	Line 153 | Line 155 | def writeFile(outputFileName,repeatX,repeatY,repeatZ):
155		def writeFile(outputFileName,repeatX,repeatY,repeatZ):
156		outputFile = open(outputFileName, 'w')
157
158	<	outputFile.write("<OOPSE version=4>\n");
158	>	outputFile.write("<OpenMD version=1>\n");
159
160		print "writing MetaData"
161		for metaline in metaData:
#	Line 206 | Line 208 | def writeFile(outputFileName,repeatX,repeatY,repeatZ):
208
209		outputFile.write("    </StuntDoubles>\n")
210		outputFile.write("  </Snapshot>\n")
211	<	outputFile.write("</OOPSE>\n")
211	>	outputFile.write("</OpenMD>\n")
212		outputFile.close()
213
214		def roundMe(x):
#	Line 217 | Line 219 | def wrapVector(myVect):
219
220		def wrapVector(myVect):
221		scaled = [0.0, 0.0, 0.0]
222	+	wrappingNumber = [0,0,0]
223		for i in range(3):
224		scaled[i] = myVect[i] * BoxInv[i]
225	<	scaled[i] = scaled[i] - roundMe(scaled[i])
225	>	wrappingNumber[i] = roundMe(scaled[i])
226	>	scaled[i] = scaled[i] - wrappingNumber[i]
227		myVect[i] = scaled[i] * Hmat[i][i]
228	<	return myVect
228	>	return myVect, wrappingNumber
229
230		def dot(L1, L2):
231		myDot = 0.0
#	Line 251 | Line 255 | def mapToBox():
255		dpos.append(p[i][0])
256		dpos.append(p[i][1])
257		dpos.append(p[i][2])
258	<	p[i] = wrapVector(dpos)
258	>	p[i], wrap[i] = wrapVector(dpos)
259
260		def scaleBox(scaleX, scaleY, scaleZ):
261		for i in range(3):
#	Line 265 | Line 269 | def scaleCoordinates(scaleX, scaleY, scaleZ):
269
270		def scaleCoordinates(scaleX, scaleY, scaleZ):
271		for i in range(len(indices)):
272	<	p[i][0] = p[i][0]*scaleX
273	<	p[i][1] = p[i][1]*scaleY
274	<	p[i][2] = p[i][2]*scaleZ
272	>	p[i][0] = p[i][0]*scaleX + wrap[i][0] * Hmat[0][0]
273	>	p[i][1] = p[i][1]*scaleY + wrap[i][1] * Hmat[1][1]
274	>	p[i][2] = p[i][2]*scaleZ + wrap[i][2] * Hmat[2][2]
275
276		def main(argv):
277		_haveMDFileName = 0

Comparing trunk/src/applications/utilities/affineScale (property svn:keywords):
Revision 1383 by gezelter, Thu Oct 22 19:12:14 2009 UTC vs.
Revision 1919 by jmarr, Wed Jul 31 18:03:35 2013 UTC

#	Line 0 | Line 1
1	+	Author Id Revision Date

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