Source Code for Module diffpy.Structure.expansion.supercell_mod

 1  ############################################################################## 
 2  # 
 3  # Structure         by DANSE Diffraction group 
 4  #                   Simon J. L. Billinge 
 5  #                   (c) 2008 trustees of the Michigan State University. 
 6  #                   All rights reserved. 
 7  # 
 8  # File coded by:    Chris Farrow, Pavol Juhas 
 9  # 
10  # See AUTHORS.txt for a list of people who contributed. 
11  # See LICENSE.txt for license information. 
12  # 
13  ############################################################################## 
14   
15  """This module contains functions for simple structure manipulation. 
16  """ 
17   
18  __id__ = "$Id: supercell_mod.py 3032 2009-04-08 19:15:37Z juhas $" 
19   
20   
21  import numpy 
22  from diffpy.Structure import Structure, Atom 
23   
24   
25 -def supercell(S, mno): 
26      """Perform supercell expansion for a structure. 
27   
28      New lattice parameters are multiplied and fractional coordinates 
29      divided by corresponding multiplier.  New atoms are grouped with 
30      their source in the original cell. 
31   
32      S   -- an instance of Structure from diffpy.Structure. 
33      mno -- sequence of 3 integers for cell multipliers along 
34             the a, b and c axes. 
35   
36      Return a new expanded structure instance. 
37      Raise TypeError when S is not Structure instance. 
38      Raise ValueError for invalid mno argument. 
39      """ 
40      # check arguments 
41      if len(mno) != 3: 
42          emsg = "Argument mno must contain 3 numbers." 
43          raise ValueError, emsg 
44      elif min(mno) < 1: 
45          emsg = "Multipliers must be greater or equal 1" 
46          raise ValueError, emsg 
47      if not isinstance(S, Structure): 
48          emsg = "The first argument must be a Structure instance." 
49          raise TypeError, emsg 
50   
51      # convert mno to a tuple of integers so it can be used as range limit. 
52      mno = (int(mno[0]), int(mno[1]), int(mno[2])) 
53   
54      # create return instance 
55      newS = Structure(S) 
56      if mno == (1, 1, 1): 
57          return newS 
58   
59      # back to business 
60      ijklist = [(i,j,k) 
61                  for i in range(mno[0]) 
62                      for j in range(mno[1]) 
63                          for k in range(mno[2])] 
64      # numpy.floor returns float array 
65      mnofloats = numpy.array(mno, dtype=float) 
66   
67      # build a list of new atoms 
68      newAtoms = [] 
69      for a in S: 
70          for ijk in ijklist: 
71              adup = Atom(a) 
72              adup.xyz = (a.xyz + ijk)/mnofloats 
73              newAtoms.append(adup) 
74      # newS can own references in newAtoms, no need to make copies 
75      newS.__setslice__(0, len(newS), newAtoms, copy=False) 
76   
77      # take care of lattice parameters 
78      newS.lattice.setLatPar( 
79              a=mno[0]*S.lattice.a, 
80              b=mno[1]*S.lattice.b, 
81              c=mno[2]*S.lattice.c ) 
82      return newS 
83   
84  # End of supercell 
85