Source Code for Module diffpy.Structure.expansion.makeEllipsoid

  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: makeEllipsoid.py 3032 2009-04-08 19:15:37Z juhas $" 
 19   
 20  from math import ceil 
 21  from numpy import array 
 22  from diffpy.Structure import Structure, Atom 
 23  from diffpy.Structure.expansion.shapeUtils import findCenter 
 24   
 25 -def makeSphere(S, radius): 
 26      """Create a spherical nanoparticle. 
 27   
 28      Arguments 
 29      S       --  A Structure instance 
 30      radius  --  primary equatorial radius (along x-axis) 
 31   
 32      Returns a new structure instance 
 33      """ 
 34      return makeEllipsoid(S, radius) 
 35   
 36 -def makeEllipsoid(S, a, b=None, c=None): 
 37      """Cut a structure out of another one. 
 38   
 39      Arguments 
 40      S       --  A Structure instance 
 41      a       --  primary equatorial radius (along x-axis) 
 42      b       --  secondary equatorial radius (along y-axis). If b is None 
 43                  (default) then it is set equal to a 
 44      c       --  polar radius (along z-axis). If c is None (default), then it is 
 45                  set equal to a. 
 46   
 47      Returns a new structure instance 
 48      """ 
 49      if b is None: b = a 
 50      if c is None: c = a 
 51      sabc = array([a, b, c]) 
 52   
 53      # Create a supercell large enough for the ellipsoid 
 54      frac = S.lattice.fractional(sabc) 
 55      mno = map(ceil, 2*frac) 
 56      mno = max(map(ceil, 2*frac))*array([1,1,1]) 
 57      # Make the supercell 
 58      from diffpy.Structure.expansion import supercell 
 59      newS = supercell(S, mno) 
 60      lat = newS.lattice 
 61   
 62      # Find the central atom 
 63      ncenter = findCenter(newS) 
 64   
 65      cxyz = lat.cartesian(newS[ncenter].xyz) 
 66   
 67      delList = [] 
 68      N = len(newS) 
 69      j = N 
 70      for i in xrange(N): 
 71          j -= 1 
 72   
 73          # Calculate (x/a)**2 + (y/b)**2 + (z/c)**2 
 74          xyz = lat.cartesian(newS[j].xyz) 
 75          darray = ((xyz-cxyz)/sabc)**2 
 76          d = sum(darray)**0.5 
 77   
 78          # Discard atom if (x/a)**2 + (y/b)**2 + (z/c)**2 > 1 
 79          if d > 1: 
 80              delList.append(j) 
 81   
 82      for i in delList: 
 83          newS.pop(i) 
 84   
 85      return newS 
 86   
 87  if __name__ == "__main__": 
 88   
 89      import os.path 
 90      datadir = "../../tests/testdata" 
 91      S = Structure() 
 92      S.read(os.path.join(datadir, "CdSe_bulk.stru"), "pdffit") 
 93      newS = makeEllipsoid(S, 12) 
 94      newS.write("CdSe_d24.stru", "pdffit") 
 95      newS = makeEllipsoid(S, 20, 10, 10) 
 96      newS.write("CdSe_a20_b10_c10.stru", "pdffit") 
 97      newS = makeEllipsoid(S, 20, 15, 10) 
 98      newS.write("CdSe_a20_b15_c10.stru", "pdffit") 
 99      S = Structure() 
100      S.read(os.path.join(datadir, "Ni.stru"), "pdffit") 
101      newS = makeEllipsoid(S, 10) 
102      newS.write("Ni_d20.stru", "pdffit") 
103      newS = makeEllipsoid(S, 20, 4) 
104      newS.write("Ni_a20_b4_c20.stru", "pdffit") 
105      newS = makeEllipsoid(S, 20, 15, 10) 
106      newS.write("Ni_a20_b15_c10.stru", "pdffit") 
107