def wavelength_must_be_known(
cls, value
): # pylint:disable=no-self-argument,no-self-use
"""We only allow for anode names for which we know the wavelength"""
if value not in list(WAVELENGTHS.keys()):
raise ValueError(
"Wavelength must be in {}".format(", ".join(list(WAVELENGTHS.keys())))
)
return value
def get_target_and_edge(cls, values: Dict):
print("Validations")
# Only do this if neither target not edge is defined
if "target" not in values and "edge" not in values:
print("Are we even getting here?")
try:
pymatgen_wavelength = next(
k
for k, v in WAVELENGTHS.items()
if np.allclose(values["wavelength"], v)
)
values["target"] = pymatgen_wavelength[:2]
values["edge"] = pymatgen_wavelength[2:]
except Exception:
return values
return values
def all_layouts(self):
# Main plot
graph = html.Div(
[
dcc.Graph(
figure=go.Figure(layout=XRayDiffractionComponent.empty_plot_style),
id=self.id("xrd-plot"),
config={"displayModeBar": False},
)
]
)
# Radiation source selector
rad_source = html.Div(
[
html.P("Radiation Source"),
dcc.Dropdown(
id=self.id("rad-source"),
options=[{"label": i, "value": i} for i in WAVELENGTHS.keys()],
value=self.initial_xrdcalculator_kwargs["wavelength"],
placeholder="Select a source...",
clearable=False,
),
],
style={"max-width": "200"},
)
# Shape factor input
shape_factor = html.Div(
[
html.P("Shape Factor, K "),
dcc.Input(
id=self.id("shape-factor"),
placeholder="0.94",
type="text",
value="0.94",
),
],
style={"max-width": "200"},
)
# Peak profile selector (Gaussian, Lorentzian, Voigt)
peak_profile = html.Div(
[
html.P("Peak Profile"),
dcc.Dropdown(
id=self.id("peak-profile"),
options=[
{"label": "Gaussian", "value": "G"},
{"label": "Lorentzian", "value": "L"},
{"label": "Voigt", "value": "V"},
],
value="G",
clearable=False,
),
],
style={"max-width": "200"},
)
# Crystallite size selector (via Scherrer Equation)
crystallite_size = html.Div(
[
html.P("Scherrer Crystallite Size (nm)"),
html.Div(
[
dcc.Slider(
id=self.id("crystallite-slider"),
marks={i: "{}".format(10 ** i) for i in range(-1, 3)},
min=-1,
max=2,
value=0,
step=0.01,
)
],
style={"max-width": "500"},
),
html.Div(
[], id=self.id("crystallite-input"), style={"padding-top": "20px"}
),
]
)
return {
"graph": graph,
"rad_source": rad_source,
"peak_profile": peak_profile,
"shape_factor": shape_factor,
"crystallite_size": crystallite_size,
}
def _sub_layouts(self):
state = {
"peak_profile": "G",
"shape_factor": 0.94,
"rad_source": "CuKa",
"x_axis": "twotheta",
"crystallite_size": 0.1,
}
# Main plot
graph = Loading([
dcc.Graph(
figure=go.Figure(
layout=XRayDiffractionComponent.empty_plot_style),
id=self.id("xrd-plot"),
config={
"displayModeBar": False, # or "hover",
"plotGlPixelRatio": 2,
"displaylogo": False,
# "modeBarButtons": [["toImage"]], # to only add an image download button
"toImageButtonOptions": {
"format": "png",
"filename": "xrd",
"scale": 4,
"width": 600,
"height": 400,
},
"editable": True,
},
responsive=True,
animate=False,
)
])
# Radiation source selector
rad_source = self.get_choice_input(
kwarg_label="rad_source",
state=state,
label="Radiation source",
help_str=
"This defines the wavelength of the incident X-ray radiation.",
options=[{
"label":
f'{name.replace("a", "α").replace("b", "β")} ({wavelength:.3f} Å)',
"value": name,
} for name, wavelength in WAVELENGTHS.items()],
style={"width": "10rem"},
)
# Shape factor input
shape_factor = self.get_numerical_input(
kwarg_label="shape_factor",
state=state,
label="Shape Factor",
help_str=
"""The peak profile determines what distribute characterizes the broadening of an XRD pattern.
Two extremes are Gaussian distributions, which are useful for peaks with more rounded tops (typically due to strain
broadening) and Lorentzian distributions, which are useful for peaks with sharper top (typically due to size
distributions and dislocations). In reality, peak shapes usually follow a Voigt distribution, which is a convolution of
Gaussian and Lorentzian peak shapes, with the contribution to both Gaussian and Lorentzian components sample and instrument
dependent. Here, both contributions are equally weighted if Voigt is chosen.""",
)
# Peak profile selector (Gaussian, Lorentzian, Voigt)
peak_profile = self.get_choice_input(
kwarg_label="peak_profile",
state=state,
label="Peak Profile",
help_str=
"""The shape factor K, also known as the “Scherrer constant” is a dimensionless
quantity to obtain an actual particle size from an apparent particle size determined from XRD. The discrepancy is
because the shape of an individual crystallite will change the resulting diffraction broadening. Commonly, a value
of 0.94 for isotropic crystals in a spherical shape is used. However, in practice K can vary from 0.62 to 2.08.""",
options=[
{
"label": "Gaussian",
"value": "G"
},
{
"label": "Lorentzian",
"value": "L"
},
{
"label": "Voigt",
"value": "V"
},
],
style={"width": "10rem"},
)
# 2Theta or Q for x-axis
x_axis_choice = html.Div(
[
self.get_choice_input(
kwarg_label="x_axis",
state=state,
label="Choice of 𝑥 axis",
help_str=
"Can choose between 2𝜃 or Q, where Q is the magnitude of the reciprocal lattice and "
"independent of radiation source.", # TODO: improve
options=[
{
"label": "2𝜃",
"value": "twotheta"
},
{
"label": "Q",
"value": "Q"
},
],
)
],
style={"display": "none"
}, # TODO: this is buggy! let's fix it before we share
)
# Crystallite size selector (via Scherrer Equation)
crystallite_size = self.get_slider_input(
kwarg_label="crystallite_size",
label="Scherrer crystallite size / nm",
state=state,
help_str=
"Simulate a real diffraction pattern by applying Scherrer broadening, which estimates the "
"full width at half maximum (FWHM) resulting from a finite, rather than infinite, crystallite "
"size.",
domain=[-1, 2],
step=0.01,
isLogScale=True)
static_image = self.get_figure_placeholder("xrd-plot")
return {
"x_axis": x_axis_choice,
"graph": graph,
"rad_source": rad_source,
"peak_profile": peak_profile,
"shape_factor": shape_factor,
"crystallite_size": crystallite_size,
"static_image": static_image,
}
def all_layouts(self):
# Main plot
graph = html.Div([
dcc.Graph(
figure=go.Figure(
layout=XRayDiffractionComponent.empty_plot_style),
id=self.id("xrd-plot"),
config={"displayModeBar": False},
)
])
# Radiation source selector
rad_source = html.Div([
html.P("Radiation Source"),
dcc.Dropdown(id=self.id("rad-source"),
options=[{
"label": i,
"value": i
} for i in WAVELENGTHS.keys()],
value="CuKa",
placeholder="Select a source...",
clearable=False)
],
style={'max-width': '200'})
# Shape factor input
shape_factor = html.Div([
html.P("Shape Factor, K "),
dcc.Input(id=self.id("shape-factor"),
placeholder='0.94',
type='text',
value='0.94')
],
style={'max-width': '200'})
# Peak profile selector (Gaussian, Lorentzian, Voigt)
peak_profile = html.Div([
html.P("Peak Profile"),
dcc.Dropdown(id=self.id("peak-profile"),
options=[{
"label": 'Gaussian',
"value": 'G'
}, {
"label": 'Lorentzian',
"value": 'L'
}, {
"label": 'Voigt',
"value": 'V'
}],
value="G",
clearable=False)
],
style={'max-width': '200'})
# Crystallite size selector (via Scherrer Equation)
crystallite_size = html.Div([
html.P("Scherrer Crystallite Size (nm)"),
html.Div([
dcc.Slider(id=self.id("crystallite-slider"),
marks={i: '{}'.format(10**i)
for i in range(-1, 3)},
min=-1,
max=2,
value=0,
step=0.01),
],
style={'max-width': '500'}),
html.Div([],
id=self.id("crystallite-input"),
style={"padding-top": "20px"})
])
return {
"graph": graph,
"rad_source": rad_source,
"peak_profile": peak_profile,
"shape_factor": shape_factor,
"crystallite_size": crystallite_size
}
from emmet.core.spectrum import SpectrumDoc
from emmet.core.structure import StructureMetadata
from emmet.core.symmetry import CrystalSystem, SymmetryData
from emmet.core.xrd import Edge, XRDDoc
@pytest.fixture
def structure():
test_latt = Lattice.cubic(3.0)
test_struc = Structure(lattice=test_latt,
species=["Fe"],
coords=[[0, 0, 0]])
return test_struc
@pytest.mark.parametrize("target", list(WAVELENGTHS.keys()))
def test_target_detection(structure, target):
doc = XRDDoc.from_structure(
structure=structure,
spectrum_id="test-1",
material_id="test-1",
wavelength=WAVELENGTHS[target],
)
target_element = Element(target[:2])
target_edge = Edge(target[2:])
assert doc.target == target_element
assert doc.edge == target_edge
@pytest.mark.parametrize("target", list(WAVELENGTHS.keys()))
class LatticeXRDCalculator(AbstractDiffractionPatternCalculator):
r"""
Computes the XRD pattern of a crystal structure.
This code is implemented by Shyue Ping Ong as part of UCSD's NANO106 -
Crystallography of Materials. The formalism for this code is based on
that given in Chapters 11 and 12 of Structure of Materials by Marc De
Graef and Michael E. McHenry. This takes into account the atomic
scattering factors and the Lorentz polarization factor, but not
the Debye-Waller (temperature) factor (for which data is typically not
available). Note that the multiplicity correction is not needed since
this code simply goes through all reciprocal points within the limiting
sphere, which includes all symmetrically equivalent facets. The algorithm
is as follows
1. Calculate reciprocal lattice of structure. Find all reciprocal points
within the limiting sphere given by :math:`\\frac{2}{\\lambda}`.
2. For each reciprocal point :math:`\\mathbf{g_{hkl}}` corresponding to
lattice plane :math:`(hkl)`, compute the Bragg condition
:math:`\\sin(\\theta) = \\frac{\\lambda}{2d_{hkl}}`
3. Compute the structure factor as the sum of the atomic scattering
factors. The atomic scattering factors are given by
.. math::
f(s) = Z - 41.78214 \\times s^2 \\times \\sum\\limits_{i=1}^n a_i \
\\exp(-b_is^2)
where :math:`s = \\frac{\\sin(\\theta)}{\\lambda}` and :math:`a_i`
and :math:`b_i` are the fitted parameters for each element. The
structure factor is then given by
.. math::
F_{hkl} = \\sum\\limits_{j=1}^N f_j \\exp(2\\pi i \\mathbf{g_{hkl}}
\\cdot \\mathbf{r})
4. The intensity is then given by the modulus square of the structure
factor.
.. math::
I_{hkl} = F_{hkl}F_{hkl}^*
5. Finally, the Lorentz polarization correction factor is applied. This
factor is given by:
.. math::
P(\\theta) = \\frac{1 + \\cos^2(2\\theta)}
{\\sin^2(\\theta)\\cos(\\theta)}
"""
# Tuple of available radiation keywords.
AVAILABLE_RADIATION = tuple(WAVELENGTHS.keys())
def __init__(self, wavelength="CuKa", symprec=0, debye_waller_factors=None):
"""
Initializes the XRD calculator with a given radiation.
Args:
wavelength (str/float): The wavelength can be specified as either a
float or a string. If it is a string, it must be one of the
supported definitions in the AVAILABLE_RADIATION class
variable, which provides useful commonly used wavelengths.
If it is a float, it is interpreted as a wavelength in
angstroms. Defaults to "CuKa", i.e, Cu K_alpha radiation.
symprec (float): Symmetry precision for structure refinement. If
set to 0, no refinement is done. Otherwise, refinement is
performed using spglib with provided precision.
debye_waller_factors ({element symbol: float}): Allows the
specification of Debye-Waller factors. Note that these
factors are temperature dependent.
"""
if isinstance(wavelength, float):
self.wavelength = wavelength
else:
self.radiation = wavelength
self.wavelength = WAVELENGTHS[wavelength]
self.symprec = symprec
self.debye_waller_factors = debye_waller_factors or {}
def get_pattern(self, structure, scaled=True, two_theta_range=(0, 90)):
"""
Calculates the diffraction pattern for a structure.
Args:
structure (Structure): Input structure
scaled (bool): Whether to return scaled intensities. The maximum
peak is set to a value of 100. Defaults to True. Use False if
you need the absolute values to combine XRD plots.
two_theta_range ([float of length 2]): Tuple for range of
two_thetas to calculate in degrees. Defaults to (0, 90). Set to
None if you want all diffracted beams within the limiting
sphere of radius 2 / wavelength.
Returns:
(XRDPattern)
"""
if self.symprec:
finder = SpacegroupAnalyzer(structure, symprec=self.symprec)
structure = finder.get_refined_structure()
wavelength = self.wavelength
latt = structure.lattice
is_hex = latt.is_hexagonal()
# Obtained from Bragg condition. Note that reciprocal lattice
# vector length is 1 / d_hkl.
min_r, max_r = (
(0, 2 / wavelength)
if two_theta_range is None
else [2 * sin(radians(t / 2)) / wavelength for t in two_theta_range]
)
# Obtain crystallographic reciprocal lattice points within range
recip_latt = latt.reciprocal_lattice_crystallographic
recip_pts = recip_latt.get_points_in_sphere([[0, 0, 0]], [0, 0, 0], max_r)
if min_r:
recip_pts = [pt for pt in recip_pts if pt[1] >= min_r]
peaks = {}
two_thetas = []
for hkl, g_hkl, ind, _ in sorted(
recip_pts, key=lambda i: (i[1], -i[0][0], -i[0][1], -i[0][2])
):
# Force miller indices to be integers.
hkl = [int(round(i)) for i in hkl]
if g_hkl != 0:
d_hkl = 1 / g_hkl
# Bragg condition
theta = asin(wavelength * g_hkl / 2)
two_theta = degrees(2 * theta)
if is_hex:
# Use Miller-Bravais indices for hexagonal lattices.
hkl = (hkl[0], hkl[1], -hkl[0] - hkl[1], hkl[2])
# Deal with floating point precision issues.
ind = np.where(
np.abs(np.subtract(two_thetas, two_theta))
< AbstractDiffractionPatternCalculator.TWO_THETA_TOL
)
if len(ind[0]) > 0:
peaks[two_thetas[ind[0][0]]][0] += 1.0
peaks[two_thetas[ind[0][0]]][1].append(tuple(hkl))
else:
peaks[two_theta] = [1.0, [tuple(hkl)], d_hkl]
two_thetas.append(two_theta)
x = []
y = []
hkls = []
d_hkls = []
for k in sorted(peaks.keys()):
v = peaks[k]
fam = get_unique_families(v[1])
x.append(k)
y.append(v[0])
hkls.append(
[{"hkl": hkl, "multiplicity": mult} for hkl, mult in fam.items()]
)
d_hkls.append(v[2])
xrd = DiffractionPattern(x, y, hkls, d_hkls)
return xrd
def _sub_layouts(self):
state = {
"mode": "powder",
"peak_profile": "G",
"shape_factor": 0.94,
"rad_source": "CuKa",
"x_axis": "twotheta",
"crystallite_size": 0.1,
}
# mode selector
mode = self.get_choice_input(
kwarg_label="mode",
state=state,
label="Mode",
help_str="""Select whether to generate a powder diffraction pattern
(a pattern averaged over all orientations of a polycrystalline material)
or a single crystal diffraction pattern (a diffraction pattern generated
from a single crystal structure.""",
options=[
{"value": "powder", "label": "Powder"},
{"value": "single", "label": "Single Crystal"},
],
)
# download
# Main plot
graph = Loading(
[
dcc.Graph(
figure=go.Figure(layout=XRayDiffractionComponent.empty_plot_style),
id=self.id("xrd-plot"),
config={
"displayModeBar": False, # or "hover",
"plotGlPixelRatio": 2,
"displaylogo": False,
# "modeBarButtons": [["toImage"]], # to only add an image download button
"toImageButtonOptions": {
"format": "png",
"filename": "xrd",
"scale": 4,
"width": 600,
"height": 400,
},
"editable": True,
},
responsive=True,
animate=False,
)
]
)
# Broaden peaks
broadening_toggle = ...
# Radiation source selector
rad_source = self.get_choice_input(
kwarg_label="rad_source",
state=state,
label="Radiation source",
help_str="...",
options=[
{"label": wav.replace("a", "α").replace("b", "β"), "value": wav}
for wav in WAVELENGTHS.keys()
],
)
# Shape factor input
shape_factor = self.get_numerical_input(
kwarg_label="shape_factor",
state=state,
label="Shape Factor",
help_str="""The peak profile determines what distribute characterizes the broadening of an XRD pattern.
Two extremes are Gaussian distributions, which are useful for peaks with more rounded tops (typically due to strain
broadening) and Lorentzian distributions, which are useful for peaks with sharper top (typically due to size
distributions and dislocations). In reality, peak shapes usually follow a Voigt distribution, which is a convolution of
Gaussian and Lorentzian peak shapes, with the contribution to both Gaussian and Lorentzian components sample and instrument
dependent. Here, both contributions are equally weighted if Voigt is chosen.""",
)
# Peak profile selector (Gaussian, Lorentzian, Voigt)
peak_profile = self.get_choice_input(
kwarg_label="peak_profile",
state=state,
label="Peak Profile",
help_str="""The shape factor K, also known as the “Scherrer constant” is a dimensionless
quantity to obtain an actual particle size from an apparent particle size determined from XRD. The discrepancy is
because the shape of an individual crystallite will change the resulting diffraction broadening. Commonly, a value
of 0.94 for isotropic crystals in a spherical shape is used. However, in practice K can vary from 0.62 to 2.08.""",
options=[
{"label": "Gaussian", "value": "G"},
{"label": "Lorentzian", "value": "L"},
{"label": "Voigt", "value": "V"},
],
)
# 2Theta or Q for x-axis
x_axis_choice = self.get_choice_input(
kwarg_label="x_axis",
state=state,
label="Choice of 𝑥 axis",
help_str="Can choose between 2Θ or Q, where Q is the magnitude of the reciprocal lattice and "
"independent of radiation source.", # TODO: improve
options=[
{"label": "2Θ", "value": "twotheta"},
{"label": "Q", "value": "Q"},
],
)
# Crystallite size selector (via Scherrer Equation)
crystallite_size = self.get_slider_input(
kwarg_label="crystallite_size",
label="Scherrer crystallite size / nm",
state=state,
help_str="...",
marks={i: "{}".format(10 ** i) for i in range(-1, 3)},
min=-1,
max=2,
step=0.01,
)
return {
"mode": mode,
"x_axis": x_axis_choice,
"graph": graph,
"rad_source": rad_source,
"peak_profile": peak_profile,
"shape_factor": shape_factor,
"crystallite_size": crystallite_size,
}