lineshape_tools.phonon
======================

.. py:module:: lineshape_tools.phonon

.. autoapi-nested-parse::

   Implements functionality for handling phonons.



Functions
---------

.. autoapisummary::

   lineshape_tools.phonon.get_ipr
   lineshape_tools.phonon.get_disp_vect
   lineshape_tools.phonon.get_dq_vect
   lineshape_tools.phonon.get_phonons


Module Contents
---------------

.. py:function:: get_ipr(U: numpy.ndarray) -> numpy.ndarray

   Evaluate the inverse participation ratio.

   :param U: matrix with phonon eigenvectors as columns (see np.linalg.eigh).
   :type U: np.ndarray


.. py:function:: get_disp_vect(atoms0: ase.atoms.Atoms, atoms1: ase.atoms.Atoms) -> numpy.ndarray

   Compute smallest displacement vector between two sets of atoms.

   :param atoms0: first set of atoms
   :type atoms0: Atoms
   :param atoms1: second set of atoms
   :type atoms1: Atoms

   :returns: 3N dimensional displacement vector in Å
   :rtype: np.ndarray


.. py:function:: get_dq_vect(atoms0: ase.atoms.Atoms, atoms1: ase.atoms.Atoms) -> numpy.ndarray

   Compute smallest mass-weighted displacement vector between two sets of atoms.

   :param atoms0: first set of atoms
   :type atoms0: Atoms
   :param atoms1: second set of atoms
   :type atoms1: Atoms

   :returns: 3N dimensional displacement vector in amu^{1/2} Å
   :rtype: np.ndarray


.. py:function:: get_phonons(dynmat: numpy.ndarray | pathlib.Path | str, acoustic_tol: float = 0.0005) -> tuple[numpy.ndarray, numpy.ndarray]

   Compute the phonon frequencies and eigenvectors from a dynamical matrix.

   :param dynmat: path to a dynamical matrix in .npz format or a np.ndarray
                  corresponding to a dynamical matrix (shape 3N x 3N).
   :type dynmat: np.ndarray | Path | str
   :param acoustic_tol: tolerance (in eV) to determine acoustic phonon modes.
   :type acoustic_tol: float

   :returns: phonon frequencies (in eV/amu/Ang^2).
             U (np.ndarray): matrix with phonon eigenvectors as columns (see np.linalg.eigh).
   :rtype: omega (np.ndarray)