phonon_lifetime.modes package

A collection of code for manipulating normal modes.

class phonon_lifetime.modes.CanonicalMode(*, omega: float, vector: ndarray[tuple[int, int], dtype[complex128]], system: S)

Bases: NormalMode, Generic

A normal mode in the canonical form, with vectors provided explicitly.

property omega: float

The frequency of the mode.

property system: S

The system that this normal mode belongs to.

property vector: ndarray[tuple[int, int], dtype[complex128]]

The vector of the mode, an (n_atoms, 3) array.

class phonon_lifetime.modes.NormalMode

Bases: ABC, Generic

Represents a normal mode of the system.

as_canonical() → CanonicalMode

Convert this mode to the canonical form.

abstract property omega: float

The frequency of the mode.

abstract property system: S

The system that this normal mode belongs to.

abstract property vector: ndarray[tuple[int, int], dtype[complex128]]

The vector of the mode, an (n_atoms, 3) array.

For a mode with multiple atoms in a primitive cell, the vector is ordered (n_primitive_atoms, n_repeats_x, n_repeats_y, n_repeats_z, 3).

class phonon_lifetime.modes.NormalModes

Bases: ABC, Generic

Represents all normal modes of a system.

as_canonical() → CanonicalModes

Convert this mode to the canonical form.

abstract property n_modes: int

The number of modes in the calculation.

abstract property omega: ndarray[tuple[int], dtype[floating]]

A np.array of frequencies for each mode.

abstract property system: S

The system that this normal mode belongs to.

property vectors: ndarray[tuple[int, int], dtype[complex128]]

The vector of the mode, an (n_modes, n_atoms * 3) array.

phonon_lifetime.modes.animate_mode_1d_x(mode: NormalMode, times: ndarray[Any, dtype[floating]] | None = None, idx: tuple[int, int] = (0, 0), *, ax: Axes | None = None) → tuple[Figure, Axes, ArtistAnimation]

phonon_lifetime.modes.animate_mode_xy(mode: NormalMode, times: ndarray[Any, dtype[floating]] | None = None, *, ax: Axes3D | None = None, bond_cutoff: float = inf, scale_bond_lines: bool = True, scale_displacement: float = 1.0) → tuple[Figure, Axes3D, ArtistAnimation]

phonon_lifetime.modes.animate_mode_xyz(mode: NormalMode, times: ndarray[Any, dtype[floating]] | None = None, *, ax: Axes3D | None = None, bond_cutoff: float = inf, scale_bond_lines: bool = True) → tuple[Figure, Axes3D, ArtistAnimation]

phonon_lifetime.modes.get_mode_displacement(mode: NormalMode, time: float = 0.0) → ndarray[Any, Any]

Get the displacement of the mode at a given time.

returns an array of displacements (n_atoms, 3) at the given time.

phonon_lifetime.modes.plot_mode_1d_x(mode: NormalMode, time: float = 0, idx: tuple[int, int] = (0, 0), *, ax: Axes | None = None) → tuple[Figure, Axes, Line2D]

phonon_lifetime.modes.plot_mode_xy(mode: NormalMode, time: float = 0, *, ax: Axes3D | None = None, bond_cutoff: float = inf, scale_bond_lines: bool = True, scale_displacement: float = 1.0) → tuple[Figure, Axes3D, tuple[PathCollection, Artist]]

phonon_lifetime.modes.plot_mode_xyz(mode: NormalMode, time: float = 0, *, ax: Axes3D | None = None, bond_cutoff: float = inf, scale_bond_lines: bool = True) → tuple[Figure, Axes3D, tuple[PathCollection, Artist]]

phonon_lifetime.modes.repeat_mode(mode: NormalMode[__annotationlib_name_1__], n_repeats: tuple[int, int, int]) → NormalMode[__annotationlib_name_2__]

Repeat a mode to create a new mode for a larger system.

phonon_lifetime.modes.repeat_modes(modes: NormalModes, n_repeats: tuple[int, int, int]) → NormalModes[RepeatSystem]

Repeat a set of modes to create new modes for a larger system.