CTEDocument

class atomate2.common.schemas.cte.CTEDocument(*, nsites=None, elements=None, nelements=None, composition=None, composition_reduced=None, formula_pretty=None, formula_anonymous=None, chemsys=None, volume=None, density=None, density_atomic=None, symmetry=None, structure=None, supercell_matrix=None, temperatures=None, mesh=None, elastic_tensor=None, min_frequency=None, tol_imaginary_modes=None, phonon_job_dir=None, results=None)

Bases: StructureMetadata

Thermal expansion from mode Grueneisen tensors and the elastic tensor.

Parameters:

• nsites (int | None)

• elements (list[Annotated[ElementTypeVar, BeforeValidator(func=~emmet.core.types.pymatgen_types.element_adapter.<lambda>, json_schema_input_type=PydanticUndefined), WrapSerializer(func=~emmet.core.types.pymatgen_types.element_adapter.<lambda>, return_type=str, when_used=always)]] | None)

• nelements (int | None)

• composition (Annotated[CompositionTypeVar, BeforeValidator(func=~emmet.core.types.pymatgen_types.composition_adapter.<lambda>, json_schema_input_type=PydanticUndefined), WrapSerializer(func=~emmet.core.types.pymatgen_types.composition_adapter.<lambda>, return_type=dict[str, float], when_used=always)] | None)

• composition_reduced (Annotated[CompositionTypeVar, BeforeValidator(func=~emmet.core.types.pymatgen_types.composition_adapter.<lambda>, json_schema_input_type=PydanticUndefined), WrapSerializer(func=~emmet.core.types.pymatgen_types.composition_adapter.<lambda>, return_type=dict[str, float], when_used=always)] | None)

• formula_pretty (str | None)

• formula_anonymous (str | None)

• chemsys (str | None)

• volume (float | None)

• density (float | None)

• density_atomic (float | None)

• symmetry (SymmetryData | None)

• structure (Structure | None)

• supercell_matrix (tuple[tuple[float, float, float], tuple[float, float, float], tuple[float, float, float]] | None)

• temperatures (list[float] | None)

• mesh (tuple[int, int, int] | None)

• elastic_tensor (tuple[tuple[float, float, float, float, float, float], tuple[float, float, float, float, float, float], tuple[float, float, float, float, float, float], tuple[float, float, float, float, float, float], tuple[float, float, float, float, float, float], tuple[float, float, float, float, float, float]] | None)

• min_frequency (float | None)

• tol_imaginary_modes (float | None)

• phonon_job_dir (str | None)

• results (list[CTEResult] | None)

classmethod from_force_constants(phonopy_yaml, force_constant_files, elastic_tensor, structure, temperatures, mesh, tol_imaginary_modes, min_frequency, symprec)

Compute the thermal expansion from second- and third-order force constants.

phono3py gives the frequencies and mode Grueneisen tensors on the q-point mesh. Only time reversal symmetry is used to reduce the mesh. The non-analytical term correction is applied to the dynamical matrix when the phonopy yaml file holds the Born charges and the dielectric tensor. Only the third-order force constants enter the strain derivative of the dynamical matrix. The results of each fit are written to gruneisen_<method>.hdf5 in the current directory.

Parameters:

• phonopy_yaml (str or Path) – phonopy.yaml of the pheasy fit, with the unit cell, the supercell matrix and the Born charges.

• force_constant_files (Mapping) – For each fit method, “cocktail” or “one-shot”, the files with the second- and third-order force constants.

• elastic_tensor (MatrixVoigt) – Elastic tensor in GPa and Voigt notation.

• structure (Structure) – Structure of the elastic calculation. Its lattice must match the unit cell in phonopy_yaml, so that both tensors are in the same frame.

• temperatures (Sequence[float]) – Temperatures in K, not negative.

• mesh (tuple[int, int, int] or float) – q-point mesh, or a q-point density used as kppa in pymatgen’s Kpoints.automatic_density for the unit cell.

• tol_imaginary_modes (float) – If a frequency on the mesh is below -tol_imaginary_modes in THz, a warning is raised and the thermal expansion of that fit is not computed.

• min_frequency (float) – Modes below this frequency in THz are left out.

• symprec (float) – Symmetry precision passed to phono3py.

Return type:

CTEDocument

model_config = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].