LobsterTaskDocument

class atomate2.lobster.schemas.LobsterTaskDocument(*, 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, dir_name, last_updated=<factory>, charges=None, lobsterout, lobsterin, lobsterpy_data=None, lobsterpy_text=None, calc_quality_summary=None, calc_quality_text=None, strongest_bonds=None, lobsterpy_data_cation_anion=None, lobsterpy_text_cation_anion=None, strongest_bonds_cation_anion=None, dos=None, lso_dos=None, madelung_energies=None, site_potentials=None, gross_populations=None, band_overlaps=None, cohp_data=None, coop_data=None, cobi_data=None, icohp_list=None, icoop_list=None, icobi_list=None, atomate2_version='0.0.1', **extra_data)[source]

Bases: StructureMetadata

Definition of LOBSTER task document.

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)

  • dir_name (str | Path)

  • last_updated (str)

  • charges (Charge | None)

  • lobsterout (LobsteroutModel)

  • lobsterin (LobsterinModel)

  • lobsterpy_data (CondensedBondingAnalysis | None)

  • lobsterpy_text (str | None)

  • calc_quality_summary (CalcQualitySummary | None)

  • calc_quality_text (str | None)

  • strongest_bonds (StrongestBonds | None)

  • lobsterpy_data_cation_anion (CondensedBondingAnalysis | None)

  • lobsterpy_text_cation_anion (str | None)

  • strongest_bonds_cation_anion (StrongestBonds | None)

  • dos (LobsterCompleteDos | None)

  • lso_dos (LobsterCompleteDos | None)

  • madelung_energies (MadelungEnergies | None)

  • site_potentials (SitePotential | None)

  • gross_populations (Grosspop | None)

  • band_overlaps (Bandoverlaps | None)

  • cohp_data (CompleteCohp | None)

  • coop_data (CompleteCohp | None)

  • cobi_data (CompleteCohp | None)

  • icohp_list (Icohplist | None)

  • icoop_list (Icohplist | None)

  • icobi_list (Icohplist | None)

  • atomate2_version (str)

  • extra_data (Any)

classmethod from_directory(dir_name, additional_fields=None, add_coxxcar_to_task_document=False, analyze_outputs=True, calc_quality_kwargs=None, lobsterpy_kwargs=None, plot_kwargs=None, store_lso_dos=False, save_cohp_plots=True, save_cba_jsons=True, save_computational_data_jsons=False)[source]

Create a task document from a directory containing LOBSTER files.

Parameters:

  • dir_name (path or str.) – The path to the folder containing the calculation outputs.

  • additional_fields (dict.) – Dictionary of additional fields to add to output document.

  • add_coxxcar_to_task_document (bool.) – Bool to indicate whether to add COHPCAR, COOPCAR, COBICAR data objects to the task document.

  • analyze_outputs (bool.) – If True, will enable lobsterpy analysis.

  • calc_quality_kwargs (dict.) – kwargs to change calc quality summary options in lobsterpy.

  • lobsterpy_kwargs (dict.) – kwargs to change default lobsterpy automatic analysis parameters.

  • plot_kwargs (dict.) – kwargs to change plotting options in lobsterpy.

  • store_lso_dos (bool.) – Whether to store the LSO DOS.

  • save_cohp_plots (bool.) – Bool to indicate whether automatic cohp plots and jsons from lobsterpy will be generated.

  • save_cba_jsons (bool.) – Bool to indicate whether condensed bonding analysis jsons should be saved, consists of outputs from lobsterpy analysis, calculation quality summary, lobster dos, charges and madelung energies

  • save_computational_data_jsons (bool.) – Bool to indicate whether computational data jsons should be saved

Returns:

A task document for the lobster calculation.

Return type:

LobsterTaskDocument

model_config = {'extra': 'allow'}

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