QpointFrequencies

The QpointFrequencies object contains precalculated phonon frequencies at certain q-points. This object does not contain eigenvectors, so allows some quantities such as a basic DOS or bandstructures to be calculated with lower memory requirements.

Reading From CASTEP

Phonon frequencies and eigenvectors can be read from a .phonon file using QpointFrequencies.from_castep.

from euphonic import QpointFrequencies

filename = 'quartz.phonon'
phonons = QpointFrequencies.from_castep(filename)

Reading From Phonopy

Using QpointFrequencies.from_phonopy Euphonic can read frequencies from Phonopy files with the following default names:

  • mesh.yaml/mesh.hdf5

  • qpoints.yaml/qpoints.hdf5

  • bands.yaml/bands.hdf5

The file to be read can be specified with the phonon_name argument. Some of these files do not include the crystal information, so it must be read from a phonopy.yaml file, which can be specified with the summary_name argument. A path can also be specified.

from euphonic import QpointFrequencies

phonons = QpointFrequencies.from_phonopy(path='NaCl', phonon_name='mesh.hdf5')

Docstring

class QpointFrequencies(crystal, qpts, frequencies, weights=None)

A class to read and store frequency data at q-points

Variables

  • crystal – Lattice and atom information

  • n_qpts – Number of q-points in the object

  • qpts – Shape (n_qpts, 3) float ndarray. Q-point coordinates, in fractional coordinates of the reciprocal lattice

  • frequencies – Shape (n_qpts, n_branches) float Quantity in energy units. Frequencies per q-point and mode

  • weights – Shape (n_qpts,) float ndarray. The weight for each q-point

__init__(crystal, qpts, frequencies, weights=None)
Parameters

  • crystal (Crystal) – Lattice and atom information

  • qpts (ndarray) – Shape (n_qpts, 3) float ndarray. Q-point coordinates

  • frequencies (Quantity) – Shape (n_qpts, n_branches) float Quantity in energy units. Frequencies per q-point and mode

  • weights (Optional[ndarray]) – Shape (n_qpts,) float ndarray. The weight for each q-point. If None, equal weights are assumed

calculate_dos(dos_bins, mode_widths=None, mode_widths_min=<Quantity(0.01, 'millielectron_volt')>)

Calculates a density of states

Parameters

  • dos_bins (Quantity) – Shape (n_e_bins + 1,) float Quantity in energy units. The energy bin edges to use for calculating the DOS

  • mode_widths (Optional[Quantity]) – Shape (n_qpts, n_branches) float Quantity in energy units. The broadening width for each mode at each q-point, for adaptive broadening

  • mode_widths_min (Quantity) – Scalar float Quantity in energy units. Sets a lower limit on the mode widths, as mode widths of zero will result in infinitely sharp peaks

Return type

Spectrum1D

Returns

dos – A spectrum containing the energy bins on the x-axis and dos on the y-axis

calculate_dos_map(dos_bins, mode_widths=None, mode_widths_min=<Quantity(0.01, 'millielectron_volt')>)

Produces a bandstructure-like plot, using the DOS at each q-point

Parameters

  • dos_bins (Quantity) – Shape (n_e_bins + 1,) float Quantity in energy units. The energy bin edges to use for calculating the DOS

  • mode_widths (Optional[Quantity]) – Shape (n_qpts, n_branches) float Quantity in energy units. The broadening width for each mode at each q-point, for adaptive broadening

  • mode_widths_min (Quantity) – Scalar float Quantity in energy units. Sets a lower limit on the mode widths, as mode widths of zero will result in infinitely sharp peaks

Return type

Spectrum2D

Returns

dos_map – A 2D spectrum containing the q-point bins on the x-axis, energy bins on the y-axis and DOS on the z-axis

get_dispersion()

Creates a set of 1-D bands from mode data

Bands follow the same q-point order as in the qpts array, with x-axis spacing corresponding to the absolute distances between q-points. Discontinuities will appear as large jumps on the x-axis.

Return type

Spectrum1DCollection

Returns

dispersion – A sequence of mode bands with a common x-axis

to_dict()

Convert to a dictionary. See QpointFrequencies.from_dict for details on keys/values

Return type

Dict[str, Any]

to_json_file(filename)

Write to a JSON file. JSON fields are equivalent to from_dict keys

Parameters

filename (str) – Name of the JSON file to write to

Return type

None

classmethod from_dict(d)

Convert a dictionary to a QpointFrequencies object

Parameters

d (Dict[str, Any]) –

A dictionary with the following keys/values:

  • ’crystal’: dict, see Crystal.from_dict

  • ’qpts’: (n_qpts, 3) float ndarray

  • ’frequencies’: (n_qpts, n_branches) float ndarray

  • ’frequencies_unit’: str

There are also the following optional keys:

  • ’weights’: (n_qpts,) float ndarray

Return type

~T

classmethod from_json_file(filename)

Read from a JSON file. See from_dict for required fields

Parameters

filename (str) – The file to read from

Return type

~T

classmethod from_castep(filename)

Reads precalculated phonon mode data from a CASTEP .phonon file

Parameters

filename (str) – The path and name of the .phonon file to read

Return type

~T

classmethod from_phonopy(path='.', phonon_name='band.yaml', phonon_format=None, summary_name='phonopy.yaml')

Reads precalculated phonon mode data from a Phonopy mesh/band/qpoints.yaml/hdf5 file. May also read from phonopy.yaml for structure information.

Parameters

  • path (str) – Path to directory containing the file(s)

  • phonon_name (str) – Name of Phonopy file including the frequencies

  • phonon_format (Optional[str]) – Format of the phonon_name file if it isn’t obvious from the phonon_name extension, one of {‘yaml’, ‘hdf5’}

  • summary_name (str) – Name of Phonopy summary file to read the crystal information from. Crystal information in the phonon_name file takes priority, but if it isn’t present, crystal information is read from summary_name instead

Return type

~T