Modulation#

class spgrep_modulation.modulation.Modulation(primitive_symmetry: Symmetry, supercell: Supercell, dynamical_matrix: DynamicalMatrix | DynamicalMatrixNAC, qpoint: NDArrayFloat, nac_q_direction: NDArrayFloat | None = None, factor: float = 15.633302300230191, degeneracy_tolerance: float = 0.0001, seed: int = 0)[source]#

Generate modulated cells based on dynamical matrix of phonon.

Generate modulated cells based on dynamical matrix of phonon.

Parameters

  • primitive_symmetry (phonopy.structure.symmetry.Symmetry) – phonopy’s Symmetry object for primitive cell

  • supercell (phonopy.structure.cells.Supercell) – phonopy’s supercell object to apply modulation

  • dynamical_matrix (phonopy.harmonic.dynamical_matrix.DynamicalMatrix) – phonopy’s dynamical matrix object

  • qpoint (array, (3, )) –

  • nac_q_direction – Used to calculate dynamical matrix around Gamma point if specified

  • factor (float) – Unit conversion

  • degeneracy_tolerance (float) – Absolute tolerance to groupby phonon frequencies in factor unit

  • seed (int) – Seed value for sampling modulation from degenerated modes

property dynamical_matrix: DynamicalMatrix | DynamicalMatrixNAC#

Return Phonopy’s dynamical matrix.

property primitive_symmetry: phonopy.structure.symmetry.Symmetry#

Return Phonopy’s symmetry for primitive cell.

property little_rotations: numpy.ndarray[Any, numpy.dtype[numpy.int32]]#

Return rotations of little group at qpoint.

property little_translations: numpy.ndarray[Any, numpy.dtype[numpy.float64]]#

Return translations of little group at qpoint.

property primitive: phonopy.structure.cells.Primitive#

Return Phonopy’s primitive cell.

property supercell: phonopy.structure.cells.Supercell#

Return Phonopy’s supercell without modulations.

property qpoint: numpy.ndarray[Any, numpy.dtype[numpy.float64]]#

Return qpoint.

property unit_conversion_factor: float#

Return unit conversion for frequencies.

property degeneracy_tolerance: float#

Return absolute tolerance to detect degenerated bands.

property eigenspaces: list[tuple[float, numpy.ndarray[Any, numpy.dtype[numpy.complex128]], numpy.ndarray[Any, numpy.dtype[numpy.complex128]]]]#

Return list of (eigenvalue, degenerated eigenvectors, irrep formed by the eigenvectors) of dynamical matrix.

  • eigenvalue: float

  • eigenvectors: array, (dim, num_atoms, 3)

  • irrep: array, (little_order, dim, dim)

get_modulated_supercell_and_modulation(frequency_index: int, amplitudes: list[float], arguments: list[float], return_cell: bool = True) → tuple[PhonopyAtoms, NDArrayComplex] | NDArrayComplex[source]#

Return modulated cell and modulation with given amplitudes and arguments.

Parameters

  • frequency_index (int) – Index of frequency with dim eivenvectors

  • amplitudes (list[float], (dim, )) –

  • arguments (list[float], (dim, )) – in radian

  • return_cell (bool = True) –

get_modulated_supercells(frequency_index: int, maximal_displacement: float = 0.11, max_size: int = 1) → list[phonopy.structure.atoms.PhonopyAtoms][source]#

Return modulated cells with randomly sampled arguments.

Parameters

  • frequency_index (int) – Index of considered eigenmodes in Modulation.eigenspaces

  • maximal_displacement (int) – Amplitude of modulation is chosen so that the maximal displacement in returned modulation is equal to maximal_displacement. Same unit as Modulation.primitive.cell.

  • max_size (int) – Number of returned modulated structures when degenerated eigenmodes are specified.

Returns

cells

Return type

list of PhonopyAtoms

get_high_symmetry_modulated_supercells(frequency_index: int, maximal_displacement: float = 0.11) → list[phonopy.structure.atoms.PhonopyAtoms][source]#

Return modulated cells corresponding to one-dimensional order-parameter directions of an isotropy subgroup.

Parameters

  • frequency_index (int) – Index of considered eigenmodes in Modulation.eigenspaces

  • maximal_displacement (int) – Amplitude of modulation is chosen so that the maximal displacement in returned modulation is equal to maximal_displacement. Same unit as Modulation.primitive.cell.

Returns

cells

Return type

list of PhonopyAtoms

Return Modulation class with supercell matrix.

eigvals_to_frequencies(eigvals: numpy.ndarray[Any, numpy.dtype[numpy.complex128]]) → numpy.ndarray[Any, numpy.dtype[numpy.float64]][source]#

Convert eigenvalue to frequency.

apply_modulation_to_supercell(modulation: numpy.ndarray[Any, numpy.dtype[numpy.complex128]]) → phonopy.structure.atoms.PhonopyAtoms[source]#

Apply modulation to supercell.