def test_xrdebye():
tolerance = 1E-5
# previously calculated values
expected_get = 116850.37344
expected_xrd = np.array([18549.274677, 52303.116995, 38502.372027])
expected_saxs = np.array([372650934.006398, 280252013.563702,
488123.103628])
# test system -- cluster of 587 silver atoms
atoms = FaceCenteredCubic('Ag', [(1, 0, 0), (1, 1, 0), (1, 1, 1)],
[6, 8, 8], 4.09)
xrd = XrDebye(atoms=atoms, wavelength=wavelengths['CuKa1'], damping=0.04,
method='Iwasa', alpha=1.01, warn=True)
# test get()
obtained_get = xrd.get(s=0.09)
assert np.abs((obtained_get - expected_get) / expected_get) < tolerance
# test XRD
obtained_xrd = xrd.calc_pattern(x=np.array([15, 30, 50]), mode='XRD')
assert np.allclose(obtained_xrd, expected_xrd, rtol=tolerance)
# test SAXS
obtained_saxs = xrd.calc_pattern(x=np.array([0.021, 0.09, 0.53]),
mode='SAXS')
assert np.allclose(obtained_saxs, expected_saxs, rtol=tolerance)
def getXRD(self, **kwargs):
"""
calculate XRD
"""
wavelength = None
if 'wavelength' in kwargs:
wavelength = kwargs['wavelength']
if 'structure' not in kwargs:
raise NameError("Structure not found!")
structure = kwargs['structure']
if wavelength is None or structure is None:
raise RuntimeError(
"ASE Calculator cannot evaluate XRD - not enough parameters!")
ase_atoms = structure.aseStructure()
xrd_object = XrDebye(atoms=ase_atoms, wavelength=wavelength)
# Equally spaced list of 2theta values
angles_list = np.arange(15, 30, 0.1)
# Get the xray diffraction pattern for these points
intensity_list = xrd_object.calc_pattern(x=np.arange(15, 30, 0.1),
mode='XRD')
# Return the list of tuples
return zip(angles_list, intensity_list)
def xrd():
# test system -- cluster of 587 silver atoms
atoms = FaceCenteredCubic('Ag', [(1, 0, 0), (1, 1, 0), (1, 1, 1)],
[6, 8, 8], 4.09)
return XrDebye(atoms=atoms,
wavelength=wavelengths['CuKa1'],
damping=0.04,
method='Iwasa',
alpha=1.01,
warn=True)
def getSANS(self, **kwargs):
"""
calculate XRD
"""
wavelength = None
if 'wavelength' in kwargs:
wavelength = kwargs['wavelength']
if 'structure' not in kwargs:
raise NameError("Structure not found!")
structure = kwargs['structure']
if wavelength is None or structure is None:
raise RuntimeError(
"ASE Calculator cannot evaluate SANS - not enough parameters!")
ase_atoms = structure.aseStructure()
xrd_object = XrDebye(atoms=ase_atoms, wavelength=wavelength)
xrd_object.calc_pattern(x=np.logspace(-2, -0.3, 50), mode='SAXS')
xrd_object.plot_pattern(filename=None)
from ase.utils.xrdebye import XrDebye, wavelengths
from ase.cluster.cubic import FaceCenteredCubic
import numpy as np
tolerance = 1E-5
# previously calculated values
expected_get = 116850.37344
expected_xrd = np.array([18549.274677, 52303.116995, 38502.372027])
expected_saxs = np.array([372650934.006398, 280252013.563702, 488123.103628])
# test system -- cluster of 587 silver atoms
atoms = FaceCenteredCubic('Ag', [(1, 0, 0), (1, 1, 0), (1, 1, 1)], [6, 8, 8],
4.09)
xrd = XrDebye(atoms=atoms,
wavelength=wavelengths['CuKa1'],
damping=0.04,
method='Iwasa',
alpha=1.01,
warn=True)
# test get()
obtained_get = xrd.get(s=0.09)
assert np.abs((obtained_get - expected_get) / expected_get) < tolerance
# test XRD
obtained_xrd = xrd.calc_pattern(x=np.array([15, 30, 50]), mode='XRD')
assert np.allclose(obtained_xrd, expected_xrd, rtol=tolerance)
# test SAXS
obtained_saxs = xrd.calc_pattern(x=np.array([0.021, 0.09, 0.53]), mode='SAXS')
assert np.allclose(obtained_xrd, expected_xrd, rtol=tolerance)
# creates: saxs.png, xrd.png
from ase.utils.xrdebye import XrDebye
from ase.cluster.cubic import FaceCenteredCubic
import numpy as np
# create nanoparticle with approx. 2 nm diameter
atoms = FaceCenteredCubic('Ag', [(1, 0, 0), (1, 1, 0), (1, 1, 1)], [6, 8, 8],
4.09)
# setup for desired wavelength
xrd = XrDebye(atoms=atoms, wavelength=0.50523)
# calculate and plot diffraction pattern
xrd.calc_pattern(x=np.arange(15, 30, 0.1), mode='XRD')
xrd.plot_pattern('xrd.png')
# calculate and plot samll-angle scattering
xrd.calc_pattern(x=np.logspace(-2, -0.3, 50), mode='SAXS')
xrd.plot_pattern('saxs.png')