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Comparing trunk/src/applications/utilities/md2md (file contents):
Revision 1243 by xsun, Wed May 14 20:49:17 2008 UTC vs.
Revision 1383 by gezelter, Thu Oct 22 19:12:14 2009 UTC

# Line 2 | Line 2 | Takes a MetaData file and maps all StuntDoubles back t
2   """MetaData file remapper
3  
4   Takes a MetaData file and maps all StuntDoubles back to the periodic box.
5 < Will optionally replicate the system in the three box directions, and
6 < then writes out a new MetaData file.
5 > Will optionally replicate the system in the three box directions, or
6 > translate every object in the box and before writing out a new MetaData file.
7  
8   Usage: md2md
9  
10   Options:
11 <  -h, --help              show this help
12 <  -m, --meta-data=...     use specified meta-data (.md, .eor) file
13 <  -o, --output-file=...   use specified output file
14 <  -x, --repeatX=...       make the system repeat in the x direction
15 <  -y, --repeatY=...       make the system repeat in the y direction
16 <  -z, --repeatZ=...       make the system repeat in the z direction
11 >  -h,  --help             show this help
12 >  -m,  --meta-data=...    use specified meta-data (.md, .eor) file
13 >  -o,  --output-file=...  use specified output file
14 >  -x,  --repeatX=...      make the system repeat in the x direction
15 >  -y,  --repeatY=...      make the system repeat in the y direction
16 >  -z,  --repeatZ=...      make the system repeat in the z direction
17 >  -t,  --translateX=...   translate all x coordinates by some amount
18 >  -u,  --translateY=...   translate all y coordinates by some amount
19 >  -v,  --translateZ=...   translate all z coordinates by some amount
20  
18 –
21   Example:
22 <  md2md -m lipidSystem.md -o bigLipidSystem.md -x 2 -y 2 -z 1
22 >  md2md -m lipidSystem.md -o bigLipidSystem.md -x 2 -y 2 -z 1 -v 35.0
23  
24   """
25  
26   __author__ = "Dan Gezelter (gezelter@nd.edu)"
27 < __version__ = "$Revision: 1.2 $"
28 < __date__ = "$Date: 2008-05-14 20:49:17 $"
29 < __copyright__ = "Copyright (c) 2008 by the University of Notre Dame"
27 > __version__ = "$Revision: 1.4 $"
28 > __date__ = "$Date: 2009-10-22 19:12:14 $"
29 > __copyright__ = "Copyright (c) 2009 by the University of Notre Dame"
30   __license__ = "OOPSE"
31  
32   import sys
# Line 34 | Line 36 | from sets import *
36   import random
37   from sets import *
38  
37 – _haveMDFileName = 0
38 – _haveOutputFileName = 0
39 –
40 – repeatX = 1
41 – repeatY = 1
42 – repeatZ = 1
43 –
39   metaData = []
40   frameData = []
41   indices = []
# Line 155 | Line 150 | def readFile(mdFileName):
150      
151      mdFile.close()
152  
153 < def writeFile(outputFileName):
153 > def writeFile(outputFileName,repeatX,repeatY,repeatZ):
154      outputFile = open(outputFileName, 'w')
155  
156      outputFile.write("<OOPSE version=4>\n");
# Line 186 | Line 181 | def writeFile(outputFileName):
181  
182      print "writing StuntDoubles"
183      outputFile.write("    <StuntDoubles>\n")
189 –    whichSD = 0
184  
185      print repeatX, repeatY, repeatZ
186  
187 <    for i in range(len(indices)):
187 >    deco = [ (index, i) for i, index in enumerate(indices) ]
188 >    deco.sort()
189 >    whichSD = 0
190 >    for index in range(len(deco)):
191 >        (index,i) = deco[index]
192 >        print i
193          for ii in range(repeatX):
194              for jj in range(repeatY):
195 <                for kk in range(repeatZ):
197 <                  
195 >                for kk in range(repeatZ):                    
196                      myP = []
197                      myP.append(p[i][0] + ii*Hmat[0][0] + jj*Hmat[1][0] + kk*Hmat[2][0])
198                      myP.append(p[i][1] + ii*Hmat[0][1] + jj*Hmat[1][1] + kk*Hmat[2][1])
199                      myP.append(p[i][2] + ii*Hmat[0][2] + jj*Hmat[1][2] + kk*Hmat[2][2])
200 <
200 >                        
201                      if (pvqj[i] == 'pv'):
202                          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]))
203                      elif (pvqj[i] == 'pvqj'):
204                          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]))
207 –                        
205                      whichSD = whichSD + 1
206  
207      outputFile.write("    </StuntDoubles>\n")
# Line 248 | Line 245 | def cross(L1, L2):
245      L3[2] = L1[0]*L2[1] - L1[1]*L2[0]
246      return L3
247  
248 < def mapToBox():
248 > def mapToBox(translateX, translateY, translateZ):
249 >    print "translating by %f\t%f\t%f" % (translateX, translateY, translateZ)
250      for i in range(len(indices)):
251 <        dpos = p[i]
251 >        dpos = []
252 >        dpos.append(p[i][0] + translateX)
253 >        dpos.append(p[i][1] + translateY)
254 >        dpos.append(p[i][2] + translateZ)
255          p[i] = wrapVector(dpos)
256  
256 –
257   def main(argv):
258 +    repeatX = 1
259 +    repeatY = 1
260 +    repeatZ = 1
261 +    translateX = 0.0
262 +    translateY = 0.0
263 +    translateZ = 0.0
264 +    _haveMDFileName = 0
265 +    _haveOutputFileName = 0
266      try:                                
267 <        opts, args = getopt.getopt(argv, "hm:o:x:y:z:", ["help", "meta-data=", "output-file=", "repeatX=", "repeatY=", "repeatZ="])
267 >        opts, args = getopt.getopt(argv, "hm:o:x:y:z:t:u:v:", ["help", "meta-data=", "output-file=", "repeatX=", "repeatY=", "repeatZ=","translateX=","translateY=","translateZ="])
268      except getopt.GetoptError:          
269          usage()                          
270          sys.exit(2)                    
# Line 266 | Line 274 | def main(argv):
274              sys.exit()                  
275          elif opt in ("-m", "--meta-data"):
276              mdFileName = arg
269 –            global _haveMDFileName
277              _haveMDFileName = 1
278          elif opt in ("-o", "--output-file"):
279              outputFileName = arg
273 –            global _haveOutputFileName
280              _haveOutputFileName = 1
281          elif opt in ("-x", "--repeatX"):
276 –            global repeatX
282              repeatX = int(arg)
283          elif opt in ("-y", "--repeatY"):
279 –            global repeatY
284              repeatY = int(arg)
285          elif opt in ("-z", "--repeatZ"):
282 –            global repeatZ
286              repeatZ = int(arg)
287 +        elif opt in ("-t", "--translateX"):
288 +            translateX = float(arg)
289 +        elif opt in ("-u", "--translateY"):
290 +            translateY = float(arg)
291 +        elif opt in ("-v", "--translateZ"):
292 +            translateZ = float(arg)
293      if (_haveMDFileName != 1):
294          usage()
295          print "No meta-data file was specified"
# Line 289 | Line 298 | def main(argv):
298          usage()
299          print "No output file was specified"
300          sys.exit()
301 +
302      readFile(mdFileName)
303 <    mapToBox()    
304 <    writeFile(outputFileName)
303 >    mapToBox(translateX, translateY, translateZ)    
304 >    writeFile(outputFileName, repeatX, repeatY, repeatZ)
305  
306   if __name__ == "__main__":
307      if len(sys.argv) == 1:

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