/usr/share/pyshared/ase/xrdebye.py is in python-ase 3.6.0.2515-1.
This file is owned by root:root, with mode 0o644.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 | from math import exp, pi, sin, sqrt, cos, acos
import numpy as np
from ase.data import atomic_numbers
# Table (1) of
# D. WAASMAIER AND A. KIRFEL, Acta Cryst. (1995). A51, 416-431
waasmaier = {
# a1 b1 a2 b2 a3 b3 a4 b4 a5 b5 c
'C' : [2.657506, 14.780758, 1.078079, 0.776775, 1.490909, 42.086843, -4.241070, -0.000294, 0.713791, 0.239535, 4.297983],
'S' : [6.372157, 1.514347, 5.154568, 22.092528, 1.473732, 0.061373, 1.635073, 55.445176, 1.209372, 0.646925, 0.154722],
'Pd': [6.121511, 0.062549, 4.784063, 0.784031, 16.631683, 8.751391, 4.318258, 34.489983, 13.246773, 0.784031, 0.883099],
'Ag': [6.073874, 0.055333, 17.155437, 7.896512, 4.173344, 28.443739, 0.852238, 110.376108, 17.988685, 0.716809, 0.756603],
'Au': [16.777389, 0.122737, 19.317156, 8.621570, 32.979682, 1.256902, 5.595453, 38.008821, 10.576854, 0.000601, -6.279078],
'P' : [1.950541, 0.908139, 4.146930, 27.044953, 1.494560, 0.071280, 1.522042, 67.520190, 5.729711, 1.981173, 0.155233],
'Cl': [1.446071, 0.052357, 6.870609, 1.193165, 6.151801, 18.343416, 1.750347, 46.398394, 0.634168, 0.401005, 0.146773],
}
class XrDebye:
def __init__(self, wavelength, alpha=1.01, damping=0.04, warn=True,
method='Iwasa'):
"""
Obtain powder x-ray spectra.
wavelength in Angstrom
damping in Angstrom**2
"""
self.wavelength = wavelength
self.damping = damping
self.alpha = alpha
self.warn = warn
self.method = method
def set_damping(self, damping):
self.damping = damping
def get(self, atoms, s):
"""Get the powder x-ray (XRD) pattern using the Debye-Formula.
After: T. Iwasa and K. Nobusada, J. Phys. Chem. C 111 (2007) 45
s is assumed to be in 1/Angstrom
"""
sinth = self.wavelength * s / 2.
costh = sqrt(1. - sinth**2)
cos2th = cos(2. * acos(costh))
pre = exp(- self.damping * s**2 / 2)
if self.method == 'Iwasa':
pre *= costh / (1. + self.alpha * cos2th**2)
f = {}
def atomic(symbol):
if not f.has_key(symbol):
if self.method == 'Iwasa':
f[symbol] = self.get_waasmaier(symbol, s)
else:
f[symbol] = atomic_numbers[symbol]
return f[symbol]
def sinc(x):
if x < 1.e-6:
x2 = x * x
return 1 - x2 / 6. + x2 * x2 / 120.
else:
return sin(x) / x
I = 0.
for a in atoms:
fa = atomic(a.symbol)
# print a.symbol, fa
for b in atoms:
fb = atomic(b.symbol)
if a == b:
twopis = 0.
else:
vrij = a.position - b.position
rij = np.sqrt(np.dot(vrij, vrij))
twopisr = 2 * pi * s * rij
I += fa * fb * sinc(twopisr)
return pre * I
def get_waasmaier(self, symbol, s):
"""Scattering factor for free atoms."""
if symbol == 'H':
# XXXX implement analytical H
return 0
elif waasmaier.has_key(symbol):
abc = waasmaier[symbol]
f = abc[10]
s2 = s*s
for i in range(5):
f += abc[2 * i] * exp(-abc[2 * i + 1] * s2)
return f
if self.warn:
print '<xrdebye::get_atomic> Element', symbol, 'not available'
return 0
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