doped.gpaw module

Code to generate and parse GPAW defect calculations.

class doped.gpaw.GPAWDefectRelaxSet(defect_entry: DefectEntry | Structure, charge_state: int | None = None, gpaw_settings: dict[str, Any] | None = None, **kwargs)

Bases: object

Class for generating input files (Python scripts) for GPAW defect relaxation.

Parameters:

• defect_entry (DefectEntry, Structure) – doped/pymatgen DefectEntry or Structure object.

• charge_state (int) – Charge state of the defect. Overrides DefectEntry.charge_state.

• gpaw_settings (dict) – Dictionary of GPAW settings. Defaults used if not specified: - “mode”: {“name”: “pw”, “ecut”: 400} - “xc”: “PBE” - “kpts”: {“size”: (1, 1, 1), “gamma”: True} - “txt”: “gpaw_output.txt” - “spinpol”: True - “fmax”: 0.05 - “optimizer”: “BFGS”

• **kwargs – Additional keyword arguments.

write_input(output_path: str, filename: str = 'relax.py', make_dir_if_not_present: bool = True)

Writes the input files (structure and script) to a directory.

class doped.gpaw.GPAWDefectsParser(output_path: str = '.', bulk_path: str | None = None, dielectric: float | ndarray | None = None, subfolder: str | None = None)

Bases: object

Class for rapidly parsing multiple GPAW defect supercell calculations.

Parameters:

• output_path (str) – Path to directory containing defect folders.

• bulk_path (str) – Path to bulk reference folder.

• dielectric (float or matrix) – Dielectric constant for corrections.

• subfolder (str) – Optional subfolder within each defect folder.

parse_all() → dict[str, DefectEntry]

Parses all defect folders in output_path.

class doped.gpaw.GPAWParser(gpw_file: str)

Bases: object

Parser for GPAW calculations to interface with doped.

Note

The Kumagai (eFNV) finite-size charge correction is applied by default during parsing, as it is generally preferred. However, the standard Freysoldt (FNV) correction is also fully supported. If preferred, users can manually apply it to the parsed defects using: defect_entry.get_freysoldt_correction()

Parameters:

gpw_file (str) – Path to GPAW .gpw(.gz) file.

close()

Closes the underlying GPAW calculator.

get_computed_entry() → ComputedEntry

Returns a ComputedEntry for the calculation.

get_computed_structure_entry() → ComputedStructureEntry

Returns a ComputedStructureEntry for the calculation.

get_eigenvalue_properties() → tuple

Returns (band_gap, cbm, vbm, efermi).

get_locpot_dict() → dict[str, ndarray]

Returns planar-averaged potential dictionary.

get_site_potentials() → ndarray

Returns atomic site potentials.

doped.gpaw.get_gpaw_defect_entry(defect_path: str, bulk_path: str, dielectric: float | ndarray | None = None, charge_state: int = 0, bulk_parser: GPAWParser | None = None) → DefectEntry

Convenience function to create a DefectEntry from GPAW directories.

Assumes ‘relaxed.gpw(.gz)’ exists in both directories. # TODO: This should auto-detect the output file, with a name preference, as for VASP

doped.gpaw.get_gpaw_planar_averaged_potential(gpw_file: str) → dict[str, ndarray]

Extracts planar-averaged potential from a GPAW .gpw(.gz) file.

doped.gpaw.get_gpaw_site_potentials(gpw_file: str) → ndarray

Extracts atomic site potentials from a GPAW .gpw(.gz) file.