lineshape_tools.phonon

Implements functionality for handling phonons.

Functions

get_ipr(→ numpy.ndarray)	Evaluate the inverse participation ratio.
get_disp_vect(→ numpy.ndarray)	Compute smallest displacement vector between two sets of atoms.
get_dq_vect(→ numpy.ndarray)	Compute smallest mass-weighted displacement vector between two sets of atoms.
get_phonons(→ tuple[numpy.ndarray, numpy.ndarray])	Compute the phonon frequencies and eigenvectors from a dynamical matrix.

Module Contents

lineshape_tools.phonon.get_ipr(U: numpy.ndarray) → numpy.ndarray

Evaluate the inverse participation ratio.

Parameters:

U (np.ndarray) – matrix with phonon eigenvectors as columns (see np.linalg.eigh).

lineshape_tools.phonon.get_disp_vect(atoms0: ase.atoms.Atoms, atoms1: ase.atoms.Atoms) → numpy.ndarray

Compute smallest displacement vector between two sets of atoms.

Parameters:

• atoms0 (Atoms) – first set of atoms

• atoms1 (Atoms) – second set of atoms

Returns:

3N dimensional displacement vector in Å

Return type:

np.ndarray

lineshape_tools.phonon.get_dq_vect(atoms0: ase.atoms.Atoms, atoms1: ase.atoms.Atoms) → numpy.ndarray

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

Parameters:

• atoms0 (Atoms) – first set of atoms

• atoms1 (Atoms) – second set of atoms

Returns:

3N dimensional displacement vector in amu^{1/2} Å

Return type:

np.ndarray

lineshape_tools.phonon.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.

Parameters:

• dynmat (np.ndarray | Path | str) – path to a dynamical matrix in .npz format or a np.ndarray corresponding to a dynamical matrix (shape 3N x 3N).

• acoustic_tol (float) – tolerance (in eV) to determine acoustic phonon modes.

Returns:

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

Return type:

omega (np.ndarray)