Source Code for Module diffpy.srrietveld.addon.structurefile

 1  ############################################################################## 
 2  # 
 3  # diffpy.srrietveld by DANSE Diffraction group 
 4  #                   Simon J. L. Billinge 
 5  #                   (c) 2009 Trustees of the Columbia University 
 6  #                   in the City of New York.  All rights reserved. 
 7  # 
 8  # File coded by:    Peng Tian 
 9  # 
10  # See AUTHORS.txt for a list of people who contributed. 
11  # See LICENSE.txt for license information. 
12  # 
13  ############################################################################## 
14   
15  """ structurefile.py is to convert different format structure files to a dictionary. 
16      currently only cif file can be converted. Assume one cif for one structure. 
17  """ 
18   
19  __id__ = "$Id: structurefile.py 5657 2010-07-09 19:43:17Z juhas $" 
20   
21  from diffpy.Structure import Structure 
22   
23 -class StructureFileConverter: 
24      """ Convert input structure file to a dictionary """ 
25   
26 -    def __init__(self, structurefile): 
27          """ Initialization """ 
28          import os 
29          self.strufile = structurefile 
30          filename = os.path.basename(structurefile) 
31          self.name = os.path.splitext(filename)[0] 
32          self.structure = Structure() 
33          self.atominfo = self.structure.read(structurefile) 
34          self.strudict = {'PHASE':[]} 
35          return 
36   
37 -    def cifToDict(self): 
38          """ put cif content to dictionary """ 
39          import re 
40   
41          # set single Phase section 
42          phase = {} 
43          phase['Name'] = self.name 
44          phase['a'] = self.structure.lattice.a 
45          phase['b'] = self.structure.lattice.b 
46          phase['c'] = self.structure.lattice.c 
47          phase['alpha'] = self.structure.lattice.alpha 
48          phase['beta'] = self.structure.lattice.beta 
49          phase['gamma'] = self.structure.lattice.gamma 
50          phase['Spacegroup'] = self.atominfo.cif_sgname 
51          atomlist = self.atominfo.asymmetric_unit 
52          for atom in atomlist: 
53              atomkey = 'ATOM' + str(atomlist.index(atom)+1) 
54              phase[atomkey] = [] 
55              tempdict = {} 
56              # find the atom name 
57              res = re.search(r'([^0-9]*)', atom.name) 
58              if res and res.groups(): 
59                  atomname = res.groups()[0] 
60              else: 
61                  atomname = atom.name 
62              tempdict['Name'] = atomname 
63              tempdict['Symbol'] = atomname 
64              tempdict['Typ'] = atomname 
65              if atom.Bisoequiv <= 0.0: 
66                  tempdict['Biso'] = 1.0 
67              else: 
68                  tempdict['Biso'] = atom.Bisoequiv 
69              xyz = map(None, atom.xyz) 
70              tempdict['X'] = xyz[0] 
71              tempdict['Y'] = xyz[1] 
72              tempdict['Z'] = xyz[2] 
73              phase[atomkey].append(tempdict) 
74          self.strudict['PHASE'].append(phase) 
75          return self.strudict 
76