Source Code for Module diffpy.Structure.expansion.makeCuboctahedron

 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  """Make a spheroid nanoparticle from a template structure.""" 
17   
18  __id__ = "$Id: makeCuboctahedron.py 3032 2009-04-08 19:15:37Z juhas $" 
19   
20  from math import ceil 
21  from diffpy.Structure import Structure, Atom 
22  from diffpy.Structure.expansion.shapeUtils import findCenter 
23   
24 -def makeCuboctahedron(S, dist): 
25      """Make a cuboctahedron nanoparticle. 
26   
27      Arguments 
28      S       --  A Structure instance 
29      dist    --  Distance from center to nearest face 
30   
31      Returns a new structure instance 
32      """ 
33   
34      # Create a supercell large enough for the ellipsoid 
35      frac = S.lattice.fractional((dist, dist, dist)) 
36      mno = map(ceil, 2*frac) 
37      # Make the supercell 
38      from diffpy.Structure.expansion import supercell 
39      newS = supercell(S, mno) 
40      lat = newS.lattice 
41   
42      # Find the central atom 
43      ncenter = findCenter(newS) 
44   
45      # Make the cuboctahedron template 
46      from geometry.composites import cuboctahedron 
47      from geometry.operations import translate, rotate 
48      c0 = translate(cuboctahedron(dist), lat.cartesian(newS[ncenter].xyz)) 
49   
50      # Cut out an octahedron 
51      from geometry import locate 
52   
53      N = len(newS) 
54      j = N 
55      for i in xrange(N): 
56   
57          xyz = lat.cartesian(newS[N-1-i].xyz) 
58          if locate(xyz, c0) == 1: 
59              newS.pop(N-1-i) 
60   
61      return newS 
62   
63  if __name__ == "__main__": 
64   
65      import os.path 
66      datadir = "../../tests/testdata" 
67      S = Structure() 
68      S.read(os.path.join(datadir, "CdSe_bulk.stru"), "pdffit") 
69      newS = makeCuboctahedron(S, 12) 
70      newS.write("CdSe_cuboct24.stru", "pdffit") 
71      S = Structure() 
72      S.read(os.path.join(datadir, "Ni.stru"), "pdffit") 
73      newS = makeCuboctahedron(S, 10) 
74      newS.write("Ni_cuboct20.stru", "pdffit") 
75