Source code for pymatgen.analysis.xas.spectrum

# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.

from pymatgen.core.spectrum import Spectrum
import numpy as np

"""
This module defines classes to represent all xas
"""

__author__ = "Chen Zheng"
__copyright__ = "Copyright 2012, The Materials Project"
__version__ = "2.0"
__maintainer__ = "Chen Zheng"
__email__ = "chz022@ucsd.edu"
__date__ = "Aug 9, 2017"


class XANES(Spectrum):
    """
    Basic XANES object.

    Args:
        x: A sequence of x-ray energies in eV
        y: A sequence of mu(E)
        structure (Structure): Structure associated with the XANES.
        absorption_specie (Specie): Specie associated with the XANES.
        edge (str):

    .. attribute: x
        The sequence of energies

    .. attribute: y
        The sequence of mu(E)

    .. attribute: absorption_specie
        The absorption_species of the spectrum

    .. attribute: edge
        The edge of XANES spectrum
    """
    XLABEL = 'Energy'
    YLABEL = 'Intensity'

    def __init__(self, x, y, structure, absorption_specie, edge):
        super(XANES, self).__init__(x, y, structure, absorption_specie, edge)
        self.structure = structure
        self.absorption_specie = absorption_specie
        self.edge = edge
        self.e0 = self.x[np.argmax(np.gradient(self.y) / np.gradient(self.x))]

    def __str__(self):
        return "%s %s Edge for %s: %s" % (
            self.absorption_specie, self.edge,
            self.structure.composition.reduced_formula,
            super(XANES, self).__str__()
        )