phonon_lifetime.cell package

Package for manipulating and building a unit cell.

class phonon_lifetime.cell.PrimitiveCell(*, masses: ndarray[tuple[int], dtype[floating]], symbols: list[str] | None = None, vectors: ndarray[tuple[int, int], dtype[floating]], atom_fractions: ndarray[tuple[int, int], dtype[floating]])

Bases: UnitCell

Represents the primitive cell of a defect free system.

property atom_fractions: ndarray[tuple[int, int], dtype[floating]]

The positions of the atoms as a fraction of the primitive cell.

primitive_atom_positions[i] is the position (x, y, z) of the i’th atom in the primitive cell.

property masses: ndarray[tuple[int], dtype[floating]]

Mass of the atoms in the unit cell.

property symbols: list[str]

Symbols of the atoms in the unit cell.

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

The primitive cell vectors.

primitive_cell[i] is the vector (x, y, z) for the i’th lattice vector of the primitive cell.

class phonon_lifetime.cell.SuperCell(primitive_cell: C, n_repeats: tuple[int, int, int])

Bases: UnitCell, Generic

Represents the supercell of a system.

property atom_fractions: np.ndarray[__annotationlib_name_1__, np.dtype[np.floating]]

The positions of the atoms as a fraction of the primitive cell.

primitive_atom_positions[i] is the position (x, y, z) of the i’th atom in the primitive cell.

property masses: np.ndarray[__annotationlib_name_1__, np.dtype[np.floating]]

Mass of the atoms in the unit cell.

property n_repeats: tuple[int, int, int]

Get the number of repeats of the primitive cell in each direction.

property primitive_cell: C

Get the primitive cell of the system.

property symbols: list[str]

Symbols of the atoms in the unit cell.

property vectors: np.ndarray[__annotationlib_name_1__, np.dtype[np.floating]]

The primitive cell vectors.

primitive_cell[i] is the vector (x, y, z) for the i’th lattice vector of the primitive cell.

class phonon_lifetime.cell.UnitCell

Bases: ABC

Represents the unit cell of a system.

abstract property atom_fractions: np.ndarray[__annotationlib_name_1__, np.dtype[np.floating]]

The positions of the atoms as a fraction of the primitive cell.

primitive_atom_positions[i] is the position (x, y, z) of the i’th atom in the primitive cell.

abstract property masses: np.ndarray[__annotationlib_name_1__, np.dtype[np.floating]]

Mass of the atoms in the unit cell.

property n_atoms: int

Number of atoms in the cell.

abstract property symbols: list[str]

Symbols of the atoms in the unit cell.

abstract property vectors: np.ndarray[__annotationlib_name_1__, np.dtype[np.floating]]

The primitive cell vectors.

primitive_cell[i] is the vector (x, y, z) for the i’th lattice vector of the primitive cell.

phonon_lifetime.cell.as_ase_atoms(cell: UnitCell) → Atoms

Convert a UnitCell to an ASE Atoms object.

phonon_lifetime.cell.from_ase_atoms(atoms: Atoms) → PrimitiveCell

Convert an ASE Atoms object to a PrimitiveCell.

phonon_lifetime.cell.get_atom_positions(cell: UnitCell) → np.ndarray[__annotationlib_name_1__, np.dtype[np.floating]]

Get the positions of the atoms in the cell.

phonon_lifetime.cell.plot_xy(cell: UnitCell, displacement: ndarray[tuple[int, Literal[3]], dtype[floating]] | None = None, *, ax: Axes3D | None = None, bond_cutoff: float = inf) → tuple[Figure, Axes3D, tuple[PathCollection, Line3DCollection]]

phonon_lifetime.cell.plot_xyz(cell: UnitCell, displacement: ndarray[tuple[int, Literal[3]], dtype[floating]] | None = None, *, ax: Axes3D | None = None, bond_cutoff: float = inf) → tuple[Figure, Axes3D, tuple[PathCollection, Line3DCollection]]

Submodules

phonon_lifetime.cell.build module

type phonon_lifetime.cell.build.CubicStructure = Literal['simple', 'bcc', 'fcc']

phonon_lifetime.cell.build.cubic(*, mass: float, structure: CubicStructure, distance: float = 1.0) → PrimitiveCell

Build a simple cubic system.

phonon_lifetime.cell.build.from_primitive(*, mass: float, primitive_cell: np.ndarray[__annotationlib_name_1__, np.dtype[np.float64]]) → PrimitiveCell

Build a system with a primitive cell.

phonon_lifetime.cell.build.graphene(*, mass: float, distance: float = 2.46) → PrimitiveCell

Build a graphene system.