soprano.calculate.xrd.xrd

soprano.calculate.xrd.xrd#

Classes and functions for simulating X-ray diffraction spectroscopic results from structures.

Classes

`XRDCalculator`([lambdax, theta2_digits, ...])	A class implementing methods for XRD simulations, comparisons and fittings.
`XraySpectrum`(theta2, hkl, hkl_unique, invd, ...)	Create new instance of XraySpectrum(theta2, hkl, hkl_unique, invd, intensity, lambdax)
`XraySpectrumData`(theta2, intensity)	Create new instance of XraySpectrumData(theta2, intensity)

class soprano.calculate.xrd.xrd.XRDCalculator(lambdax=1.54056, theta2_digits=6, baseline=0.0, peak_func=None, peak_f_args=None)[source]#

Bases: object

A class implementing methods for XRD simulations, comparisons and fittings.

Initialize the XDRCalculator object’s main parameters

Args:

lambdax (Optional[float]): X-ray wavelength in Angstroms

(default is 1.54056 Ang)

theta2_digits (Optional[int]): Rounding within which

two theta angles (in degrees)
are considered to be equivalent
(default is 6 digits) when
calculating theoretical peaks

baseline (Optional[float]): baseline to use as starting point for

simulated spectra

peak_func (Optional[function<float, float, *kargs>

=> <np.ndarray>]): the function used to

simulate peaks. Should take
th2 as its first argument,
peak centre as its second,
and any number of optional
arguments. Returns a numpy
array containing the peak
shape. Should be able to
work with numpy arrays as
input

peak_f_args (Optional[list<float>]): optional arguments for

peak_func. If no peak_func
has been supplied by the
user, the first value will
be used as the Gaussian width

dataset_range(xpeaks, theta2_range=(None, None))[source]#

Restrict the given dataset (XraySpectrum or XraySpectrumData) to: only the values that lie within a certain theta2 range.

Args:

xpeaks (XraySpectrum or XraySpectrumData): the dataset to modify

theta2_range (tuple<int>): a tuple indicating minimum and maximum

of the desired theta2 range (degrees).

A value of None means no boundary

Returns:

xpeaks_restrict (XraySpectrum or XraySpectrumData): the restricted

dataset

Raises:

ValueError: if some of the values passed are invalid

exp_dataset(th2_axis, int_axis)[source]#: Build an experimental dataset as an XraySpectrumData object.

Args:

th2_axis (np.ndarray): array containing the values for 2*theta

int_axis (np.ndarray): array containing the values for intensity

Returns:

exp_spec (XraySpectrumData): named tuple containing the

experimental dataset

Raises:

ValueError: if some of the values passed are invalid

lebail_fit(xpeaks, exp_spec, rwp_tol=0.01, max_iter=100)[source]#: Perform a refining on an XraySpectrum object’s intensities based on experimental data with leBail’s method.

Args:

xpeaks (XraySpectrum): object containing the details of the XRD

peaks

exp_spec (XraySpectrumData): experimental data, dataset built

using xrd_exp_dataset

rwp_tol (Optional[float]): tolerance on the Rwp error value

between two iterations that stops the

calculation. Default is 1e-2

max_iter (Optional[int]): maximum number of iterations to perform

Returns:

xpeaks_scaled (XraySpectrum): a new XraySpectrum object, with

intensities properly scaled to match

the experimental data

simul_spec (np.ndarray): final simulated XRD spectrum

simul_peaks (np.ndarray): final simulated spectrum broken by peak

contribution along axis 1

rwp (float): the final value of Rwp (fitness of simulated to

experimental data)

Raises:

ValueError: if some of the arguments are invalid

property peak_f_args#: Additional arguments to be passed to peak_func

property peak_func#

The function used to build peaks in simulated spectra

Should be of form peak_func(theta2, peak_position, *peak_f_args)

powder_peaks(atoms=None, latt_abc=None, n=1, o='all')[source]#: Calculate the peaks (without intensities) of a powder XRD spectrum given either an Atoms object or the lattice in ABC form and the spacegroup indices to apply the selection rules

Args:

atoms (Optional[soprano.Atoms]): atoms object to gather lattice

and spacegroup information from

latt_abc (Optional[np.ndarray]): periodic lattice in ABC form,

Angstroms and radians

n (Optional[int]): International number of the required spacegroup

o (Optional[int]): Sub-option of the required spacegroup

Returns:

xpeaks (XraySpectrum): a named tuple containing the peaks

with theta2, corresponding hkl indices,

a unique hkl tuple for each peak,

inverse reciprocal lattice distances,

intensities and wavelength

Raises:

ValueError: if some of the arguments are invalid

set_peak_func(peak_func=None, peak_f_args=None)[source]#: Set a new peak_func for this XDRCalculator. If no new function is passed, reset the default Gaussian function.

Args:

peak_func (Optional[function<float, float, *kargs>

=> <np.ndarray>]): the function used to

simulate peaks. Should

take th2 as its first

argument, peak centre as

its second, and any

number of optional

arguments. Returns a

numpy array containing

the peak shape. Should

be able to work with

numpy arrays as input

peak_f_args (Optional[list<float>]): optional arguments for

peak_func. If no peak_func

has been supplied by the

user, the first value will

be used as the Gaussian

width

spec_simul(xpeaks, th2_axis)[source]#: Simulate an XRD spectrum given positions of peaks, intensities, baseline, and a peak function (a Gaussian by default).

Args:

xpeaks (XraySpectrum): object containing the details of the XRD

peaks

th2_axis (np.ndarray): theta2 axis points on which the

spectrum should be simulated

Returns:

simul_spec (XraySpectrumData): simulated XRD spectrum

simul_peaks (np.ndarray): simulated spectrum intensities broken by

peak contribution along axis 1

Raises:

ValueError: if some of the arguments are invalid

class soprano.calculate.xrd.xrd.XraySpectrum(theta2, hkl, hkl_unique, invd, intensity, lambdax)#

Bases: tuple

Create new instance of XraySpectrum(theta2, hkl, hkl_unique, invd, intensity, lambdax)

_asdict()#: Return a new dict which maps field names to their values.

classmethod _make(iterable)#: Make a new XraySpectrum object from a sequence or iterable

_replace(**kwds)#: Return a new XraySpectrum object replacing specified fields with new values

count(value, /)#: Return number of occurrences of value.

hkl#: Alias for field number 1

hkl_unique#: Alias for field number 2

index(value, start=0, stop=9223372036854775807, /)#

Return first index of value.

Raises ValueError if the value is not present.

intensity#: Alias for field number 4

invd#: Alias for field number 3

lambdax#: Alias for field number 5

theta2#: Alias for field number 0

class soprano.calculate.xrd.xrd.XraySpectrumData(theta2, intensity)#