hylight.phonopy package

Submodules

hylight.phonopy.loader module

Module to load phonons frequencies and eigenvectors from phonopy output files.

It always uses PyYAML, but it may also need h5py to read hdf5 files.

class hylight.phonopy.loader.PPStruct(pops: list[int], lattice: ndarray, masses: list[float], atoms: list[str], ref: ndarray)

Bases: object

Crystal structure as described by phonopy.

atoms: list[str]
classmethod from_yaml_cell(cell: dict) → PPStruct

Create a PPStruct from a cell dictionary found in phonopy files.

lattice: ndarray
masses: list[float]
pops: list[int]
ref: ndarray
hylight.phonopy.loader.get_struct(phyaml: str) → PPStruct

Get a structure from the phonopy.yaml file.

hylight.phonopy.loader.load_phonons(dir_: str) → tuple[list[Mode], list[int], list[float]]

Load vibrational modes from phonopy output files.

This function takes the directory where the files are stored and tries to detect the right file to process.

See also

Parameters:

dir – directory containing phonopy output files

Returns:

(modes, frequencies, eigenvectors) tuple

hylight.phonopy.loader.load_phonons_bandsh5(bandh5: str, phyaml: str, op=<built-in function open>) → tuple[list[Mode], list[int], list[float]]

Load vibrational modes from phonopy HDF5 output files.

Parameters:

  • bandh5 – path to band.hdf5 or band.hdf5.gz file

  • op – (optional, open) open function, pass gzip.open() when dealing with compressed file.

Returns:

(modes, frequencies, eigenvectors) tuple

hylight.phonopy.loader.load_phonons_bandyaml(bandy: str) → tuple[list[Mode], list[int], list[float]]

Load vibrational modes from phonopy YAML output files.

Parameters:

bandy – path to band.yaml file

Returns:

(modes, frequencies, eigenvectors) tuple

hylight.phonopy.loader.load_phonons_qpointsh5(qph5: str, phyaml: str, op=<built-in function open>) → tuple[list[Mode], list[int], list[float]]

Load vibrational modes from phonopy HDF5 output files.

Parameters:

  • qph5 – path to qpoints.hdf5 or qpoints.hdf5.gz file

  • phyaml – path to phonopy.yaml file

  • op – (optional, open) open function, pass gzip.open() when dealing with compressed file.

Returns:

(modes, frequencies, eigenvectors) tuple

hylight.phonopy.loader.load_phonons_qpointsyaml(qpyaml: str, phyaml: str) → tuple[list[Mode], list[int], list[float]]

Load vibrational modes from phonopy YAML output files.

Parameters:

  • qpyaml – path to qpoints.yaml file

  • phyaml – path to phonopy.yaml file

Returns:

(modes, frequencies, eigenvectors) tuple

Module contents

phonopy related utils.