aiida_phonopy.data.preprocess

Module defining the class for managing the frozen phonon structure.

Module Contents

Classes

PreProcessData

Class for pre-processing of frozen-phonon calculations.

Functions

_serialize(data)

Serialize the data for displacement dataset, in case it contains numpy.ndarray.

class aiida_phonopy.data.preprocess.PreProcessData(structure: aiida.orm.StructureData | None = None, phonopy_atoms: phonopy.structure.cells.PhonopyAtoms | None = None, supercell_matrix: list | None = None, primitive_matrix: list | None = None, symprec: float = 1e-05, is_symmetry: bool = True, distinguish_kinds: bool = True, **kwargs)

Bases: aiida_phonopy.data.raw.RawData

Class for pre-processing of frozen-phonon calculations.

This class is designed for handling the pre-process information regarding a frozen phonon calculation using Phonopy. These regard the unitcell structure, the supercell and primitive matrix, as well as other symmetry information.

property displacement_dataset: dict | list | None

Get the dispacement dataset in a readible format for phonopy.

If not set, None is returned.

property displacements: list | dict

Get the displacements to apply to the supercell.

Returns:

array with displacements; can be type-I or type-II (see phonopy.Phonopy.displacements())

property calcfunctions

Namespace to access the calcfunction utilities.

get_displacements() → list | dict

Get the displacements to apply to the supercell.

set_displacements(distance: float = 0.01, is_plusminus: str = 'auto', is_diagonal: bool = True, is_trigonal: bool = False, number_of_snapshots: int | None = None, random_seed: int | None = None, temperature: float | None = None, cutoff_frequency: float | None = None)

Set displacements for frozen phonon calculation.

Refer to phonopy.Phonopy.generate_displacements() for a complete description of the inputs.

Thus, in the PreProcessData value different from zero will raise an error.

Raises:

ValueError – if the inputs are not compatible with phonopy standards

_set_displacements(value: list | dict)

Put in the repository the displacement dataset in json format.

set_displacements_from_dataset(dataset: dict | list)

Set displacements for frozen phonon calculation from a dataset.

Useful if you want to set displacements from a previously random generated displacement dataset, or for setting dataset for self-consistent harmonic approximation.

Parameters:

dataset – dictionary or array like (numpy or list), compatible with phonopy

Raises:

ValueError – if the inputs are not compatible with phonopy standards

get_phonopy_instance(symmetrize_nac: bool = None, factor_nac: float | None = None, **kwargs)

Return a Phonopy object with the current values.

Parameters:

• symmetrize_nac (bool) – whether or not to symmetrize the nac parameters using point group symmetry; defaults to self.is_symmetry

• factor_nac (float) – factor for non-analytical corrections; defaults to Hartree*Bohr

• kwargs – for internal use to set the primitive cell

get_supercells_with_displacements() → dict[aiida.orm.StructureData]

Get the supercells with displacements for frozen phonon calculation.

Returns:

dictionary with StructureData nodes, None if the displacement dataset has not been set

generate_displacement_dataset(distance: float = 0.01, is_plusminus: str = 'auto', is_diagonal: bool = True, is_trigonal: bool = False, number_of_snapshots: int | None = None, random_seed: int | None = None, temperature: float | None = None, cutoff_frequency: float | None = None)

Return the displacement dataset for frozen phonon calculation.

Refer to phonopy.Phonopy.generate_displacements() for a complete description of the inputs.

Raises:

ValueError – if the inputs are not compatible with phonopy standards

static generate_preprocess_data(structure: aiida.orm.StructureData, displacement_generator: dict | None = None, supercell_matrix: list | None = None, primitive_matrix: list | None = None, symprec: float | None = None, is_symmetry: bool | None = None, distinguish_kinds: bool | None = None)

Return a complete stored PreProcessData node.

Parameters:

• structure (StructureData) – structure data node representing the unitcell

• displacement_generator (orm.Dict) – dictionary containing the info for generating the displacements, defaults to phonopy default (see phonopy doc)

• supercell_matrix (List, Optional) – supercell matrix, defaults to diag(1,1,1)

• primitive_matrix (List, Optional) – primitive matrix, defaults to “auto”

• symprec (Float, Optional) – symmetry precision on atoms, defaults to 1e-5

• is_symmetry (Bool, Optional) – if using space group symmetry, defaults to True

• distinguish_kinds (Bool, Optional) – if distinguish names of same specie by symmetry, defaults to True

Returns:

PreProcessData node

aiida_phonopy.data.preprocess._serialize(data: dict | list)

Serialize the data for displacement dataset, in case it contains numpy.ndarray.