pymatgen.analysis.xas package

Package for analysis of X-ray Absorption Spectroscopy.

Submodules

pymatgen.analysis.xas.spectrum module

This module defines classes to represent all xas and stitching methods.

class XAS(x: Sequence, y: Sequence, structure: Structure, absorbing_element: str | Element, edge: str = 'K', spectrum_type: str = 'XANES', absorbing_index: int | None = None, zero_negative_intensity: bool = False)[source]

Bases: Spectrum

Basic XAS object.

Parameters:

  • x – A sequence of x-ray energies in eV

  • y – A sequence of mu(E)

  • structure (Structure) – Structure associated with the spectrum

  • absorbing_element (Element) – Element associated with the spectrum

  • edge (str) – Absorption edge associated with the spectrum

  • spectrum_type (str) – ‘XANES’ or ‘EXAFS’

  • absorbing_index (None or int) – If None, the spectrum is assumed to be a site-weighted spectrum, which is comparable to experimental one. Otherwise, it indicates that the absorbing_index for a site-wise spectrum.

x[source]

The sequence of energies.

Type:

Sequence[float]

y[source]

The sequence of mu(E).

Type:

Sequence[float]

absorbing_element[source]

The absorbing element of the spectrum.

Type:

str or .Element

edge[source]

The edge of the spectrum.

Type:

str

spectrum_type[source]

The type of the spectrum (XANES or EXAFS).

Type:

str

absorbing_index[source]

The absorbing index of the spectrum.

Type:

int

zero_negative_intensity[source]

Whether to set unphysical negative intensities to zero

Type:

bool

Initialize a spectrum object.

XLABEL = 'Energy'[source]
YLABEL = 'Intensity'[source]
stitch(other: XAS, num_samples: int = 500, mode: Literal['XAFS', 'L23'] = 'XAFS') → XAS[source]

Stitch XAS objects to get the full XAFS spectrum or L23 edge XANES spectrum depending on the mode.

  1. Use XAFS mode for stitching XANES and EXAFS with same absorption edge.

    The stitching will be performed based on wavenumber, k. for k <= 3, XAS(k) = XAS[XANES(k)] for 3 < k < max(xanes_k), will interpolate according to

    XAS(k)=f(k)*mu[XANES(k)]+(1-f(k))*mu[EXAFS(k)] where f(k)=cos^2((pi/2) (k-3)/(max(xanes_k)-3)

    for k > max(xanes_k), XAS(k) = XAS[EXAFS(k)]

  2. Use L23 mode for stitching L2 and L3 edge XANES for elements with

    atomic number <=30.

Parameters:

  • other – Another XAS object.

  • num_samples (int) – Number of samples for interpolation.

  • mode ("XAFS" | "L23") – Either XAFS mode for stitching XANES and EXAFS or L23 mode for stitching L2 and L3.

Returns:

The stitched spectrum.

Return type:

XAS object

site_weighted_spectrum(xas_list: list[XAS], num_samples: int = 500) → XAS[source]

Obtain site-weighted XAS object based on site multiplicity for each absorbing index and its corresponding site-wise spectrum.

Parameters:

  • xas_list ([XAS]) – List of XAS object to be weighted

  • num_samples (int) – Number of samples for interpolation

Returns:

The site-weighted spectrum

Return type:

XAS object