Source Code for Module diffpy.Structure.expansion.shapeUtils

 1  #!/usr/bin/env python 
 2  ############################################################################## 
 3  # 
 4  # PDFgui            by DANSE Diffraction group 
 5  #                   Simon J. L. Billinge 
 6  #                   (c) 2008 trustees of the Michigan State University. 
 7  #                   All rights reserved. 
 8  # 
 9  # File coded by:    Chris Farrow 
10  # 
11  # See AUTHORS.txt for a list of people who contributed. 
12  # See LICENSE.txt for license information. 
13  # 
14  ############################################################################## 
15   
16  """Utilities for making shapes.""" 
17   
18  __id__ = "$Id: shapeUtils.py 2980 2009-04-02 00:14:33Z juhas $" 
19   
20 -def findCenter(S): 
21      """Find the approximate center atom of a structure. 
22   
23      The center of the structure is the atom closest to (0.5, 0.5, 0.5) 
24   
25      Returns the index of the atom. 
26      """ 
27      best = -1 
28      bestd = len(S) 
29      center = [0.5, 0.5, 0.5] # the cannonical center 
30   
31      for i in range(len(S)): 
32          d = S.lattice.dist(S[i].xyz, center) 
33          if d < bestd: 
34              bestd = d 
35              best = i 
36   
37      return best 
38   
39  if __name__ == "__main__": 
40   
41      import os.path 
42      datadir = "../../tests/testdata" 
43      S = Structure() 
44      S.read(os.path.join(datadir, "CdSe_bulk.stru"), "pdffit") 
45      newS = makeEllipsoid(S, 20) 
46      newS.write("CdSe_d20.stru", "pdffit") 
47      newS = makeEllipsoid(S, 20, 10, 10) 
48      newS.write("CdSe_a20_b10_c10.stru", "pdffit") 
49      newS = makeEllipsoid(S, 20, 15, 10) 
50      newS.write("CdSe_a20_b15_c10.stru", "pdffit") 
51      S = Structure() 
52      S.read(os.path.join(datadir, "Ni.stru"), "pdffit") 
53      newS = makeEllipsoid(S, 20) 
54      newS.write("Ni_d20.stru", "pdffit") 
55      newS = makeEllipsoid(S, 20, 4) 
56      newS.write("Ni_a20_b4_c20.stru", "pdffit") 
57      newS = makeEllipsoid(S, 20, 15, 10) 
58      newS.write("Ni_a20_b15_c10.stru", "pdffit") 
59