distanceprinter.py

#!/usr/bin/env python

"""Demonstration of using PairQuantity class for a printout
of pair distances in periodic and non-periodic structures.
"""

from diffpy.srreal.pairquantity import PairQuantity
from diffpy.structure import Structure

class DistancePrinter(PairQuantity):

    '''This PairQuantity class simply prints the visited pair distances
    and the indices of the contributing atoms.
    '''

    def _resetValue(self):
        self.count = 0

    def _addPairContribution(self, bnds, sumscale):
        self.count += bnds.multiplicity() * sumscale / 2.0
        print("%i %g %i %i" % (
            self.count, bnds.distance(), bnds.site0(), bnds.site1()))
        return

# class DistancePrinter

# define nickel structure data
nickel_discus_data = '''
title   Ni
spcgr   P1
cell    3.523870,  3.523870,  3.523870, 90.000000, 90.000000, 90.000000
ncell          1,         1,         1,         4
atoms
NI          0.00000000        0.00000000        0.00000000       0.1000
NI          0.00000000        0.50000000        0.50000000       0.1000
NI          0.50000000        0.00000000        0.50000000       0.1000
NI          0.50000000        0.50000000        0.00000000       0.1000
'''

nickel = Structure()
nickel.readStr(nickel_discus_data, format='discus')

bucky = Structure(filename='datafiles/C60bucky.stru', format='discus')
distprint = DistancePrinter()
distprint._setDoubleAttr('rmax', 10)

def get_pyobjcryst_sphalerite():
    from pyobjcryst.crystal import create_crystal_from_cif
    crst = create_crystal_from_cif('datafiles/sphalerite.cif')
    return crst

def main():
    s = input('Enter rmin: ')
    if s.strip():  distprint.rmin = float(s)
    print("rmin = %g" % distprint.rmin)
    s = input('Enter rmax: ')
    if s.strip():  distprint.rmax = float(s)
    print("rmax = %g" % distprint.rmax)
    print()
    linesep = 78 * '-'
    # C60bucky
    print(linesep)
    input('Press enter for distances in C60 molecule.')
    distprint.eval(bucky)
    # nickel
    print(linesep)
    input('Press enter for distances in a nickel crystal.')
    distprint.eval(nickel)
    # objcryst sphalerite
    print(linesep)
    input('Press enter for distances in objcryst loaded sphalerite.cif.')
    crst = get_pyobjcryst_sphalerite()
    distprint.eval(crst)
    print(linesep)
    input('Press enter for distances in diffpy.structure sphalerite.cif.')
    crst = Structure(filename='datafiles/sphalerite.cif')
    distprint.eval(crst)
    return

if __name__ == '__main__':
    main()