pymatgen.io.lobster.future package
Modules for input and output to and from LOBSTER.
This package provides classes and utilities for reading and writing LOBSTER input and output files.
- class BWDF(filename: PathLike | None = None, process_immediately: bool = True, lobster_version: str | None = None)[source]
Bases:
LobsterFileParser for BWDF.lobster/BWDFCOHP.lobster files.
- Parameters:
filename (PathLike) – The BWDF file from LOBSTER, typically “BWDF.lobster” or “BWDFCOHP.lobster”.
- classmethod from_dict(d: dict[str, Any]) Self[source]
Deserialize object from dictionary produced by as_dict.
- Parameters:
d (dict[str, Any]) – Dictionary representation of the object.
- Returns:
Deserialized BWDF object.
- Return type:
Self
- class BandOverlaps(filename: PathLike | None = None, process_immediately: bool = True, lobster_version: str | None = None)[source]
Bases:
LobsterFileParser for bandOverlaps.lobster files.
Parses band overlap information produced by LOBSTER and stores it in a structured dictionary keyed by spin. See the
LobsterBandOverlapstype for details.- band_overlaps[source]
“k_points”, “max_deviations”, and “matrices” holding the corresponding data. - “k_points” (list[list[float]]): List of k-point coordinates. - “max_deviations” (list[float]): List of maximal deviations for each k-point. - “matrices” (list[np.ndarray]): List of overlap matrices for each k-point.
each holding data for each spin channel.
- Type:
dict[Spin, dict]
Initialize a LobsterFile instance.
- Parameters:
filename (PathLike | None) – Path to the file. If None, uses the default filename.
process_immediately (bool) – Whether to process the file immediately upon initialization. Defaults to True.
lobster_version (str | None) – LOBSTER version string to use for parsing. If None, attempts to detect
default. (from file or falls back to)
- classmethod from_dict(d: dict[str, Any]) Self[source]
Reconstruct a BandOverlaps instance from a dictionary.
- Parameters:
d (dict[str, Any]) – Dictionary representation of a BandOverlaps instance.
- Returns:
Reconstructed instance.
- Return type:
- classmethod get_default_filename() str[source]
Get the default filename for the BandOverlaps class.
- Returns:
Default filename.
- Return type:
str
- has_good_quality_check_occupied_bands(number_occ_bands_spin_up: int, number_occ_bands_spin_down: int | None = None, spin_polarized: bool = False, limit_deviation: float = 0.1) bool[source]
Check if deviation from the ideal overlap for occupied bands is acceptable.
- Parameters:
number_occ_bands_spin_up (int) – Number of occupied bands for spin up.
number_occ_bands_spin_down (int | None) – Number of occupied bands for spin down. Required if spin_polarized is True.
spin_polarized (bool) – Whether the calculation is spin-polarized.
limit_deviation (float) – Acceptable absolute tolerance for deviations.
- Raises:
ValueError – If number_occ_bands_spin_down is not specified for spin-polarized calculations.
- Returns:
True if all occupied-band submatrices are close to identity within the tolerance.
- Return type:
bool
- has_good_quality_max_deviation(limit_max_deviation: float = 0.1) bool[source]
Check if the maxDeviation values are within a given limit.
- Parameters:
limit_max_deviation (float) – Upper limit for acceptable max_deviation.
- Returns:
True if all recorded max_deviation values are <= limit_max_deviation.
- Return type:
bool
- parse_file(spin_numbers: list[int]) None[source]
Read all lines of the file and populate self.band_overlaps.
- Parameters:
spin_numbers (list[int]) – Two integers indicating the spin numbering used in the file (e.g., [0, 1] for legacy or [1, 2] for newer versions).
- Raises:
ValueError – If no data is found for a key in the bandOverlaps file.
- parse_file_v3_2_legacy() None[source]
Parse bandOverlaps.lobster file for LOBSTER versions ≤3.2.
Uses legacy spin numbering [0, 1] for parsing.
- class CHARGE(filename: PathLike | None = None, process_immediately: bool = True, lobster_version: str | None = None)[source]
Bases:
LobsterFileParser for CHARGE.lobster and CHARGE.LCFO.lobster files.
Initialize a LobsterFile instance.
- Parameters:
filename (PathLike | None) – Path to the file. If None, uses the default filename.
process_immediately (bool) – Whether to process the file immediately upon initialization. Defaults to True.
lobster_version (str | None) – LOBSTER version string to use for parsing. If None, attempts to detect
default. (from file or falls back to)
- classmethod get_default_filename() str[source]
Get the default filename for CHARGE files.
- Returns:
Default filename for the CHARGE file, depending on LCFO mode.
- Return type:
str
- class CHARGE_LCFO(filename: PathLike | None = None, process_immediately: bool = True, lobster_version: str | None = None)[source]
Bases:
CHARGEParser for CHARGE.LCFO.lobster files.
Initialize a LobsterFile instance.
- Parameters:
filename (PathLike | None) – Path to the file. If None, uses the default filename.
process_immediately (bool) – Whether to process the file immediately upon initialization. Defaults to True.
lobster_version (str | None) – LOBSTER version string to use for parsing. If None, attempts to detect
default. (from file or falls back to)
- class COBICAR(filename: PathLike | None = None, process_immediately: bool = True, lobster_version: str | None = None)[source]
Bases:
COXXCARReader for COBICAR.lobster files.
Initialize a LobsterFile instance.
- Parameters:
filename (PathLike | None) – Path to the file. If None, uses the default filename.
process_immediately (bool) – Whether to process the file immediately upon initialization. Defaults to True.
lobster_version (str | None) – LOBSTER version string to use for parsing. If None, attempts to detect
default. (from file or falls back to)
- class COBICAR_LCFO(filename: PathLike | None = None, process_immediately: bool = True, lobster_version: str | None = None)[source]
Bases:
COBICARReader for COBICAR.LCFO.lobster files.
Initialize a LobsterFile instance.
- Parameters:
filename (PathLike | None) – Path to the file. If None, uses the default filename.
process_immediately (bool) – Whether to process the file immediately upon initialization. Defaults to True.
lobster_version (str | None) – LOBSTER version string to use for parsing. If None, attempts to detect
default. (from file or falls back to)
- class COHPCAR(filename: PathLike | None = None, process_immediately: bool = True, lobster_version: str | None = None)[source]
Bases:
COXXCARReader for COHPCAR.lobster files.
Initialize a LobsterFile instance.
- Parameters:
filename (PathLike | None) – Path to the file. If None, uses the default filename.
process_immediately (bool) – Whether to process the file immediately upon initialization. Defaults to True.
lobster_version (str | None) – LOBSTER version string to use for parsing. If None, attempts to detect
default. (from file or falls back to)
- class COHPCAR_LCFO(filename: PathLike | None = None, process_immediately: bool = True, lobster_version: str | None = None)[source]
Bases:
COHPCARReader for COHPCAR.LCFO.lobster files.
Initialize a LobsterFile instance.
- Parameters:
filename (PathLike | None) – Path to the file. If None, uses the default filename.
process_immediately (bool) – Whether to process the file immediately upon initialization. Defaults to True.
lobster_version (str | None) – LOBSTER version string to use for parsing. If None, attempts to detect
default. (from file or falls back to)
- class COOPCAR(filename: PathLike | None = None, process_immediately: bool = True, lobster_version: str | None = None)[source]
Bases:
COXXCARReader for COOPCAR.lobster files.
Initialize a LobsterFile instance.
- Parameters:
filename (PathLike | None) – Path to the file. If None, uses the default filename.
process_immediately (bool) – Whether to process the file immediately upon initialization. Defaults to True.
lobster_version (str | None) – LOBSTER version string to use for parsing. If None, attempts to detect
default. (from file or falls back to)
- class DOSCAR(filename: PathLike | None = None, process_immediately: bool = True, lobster_version: str | None = None)[source]
Bases:
LobsterFileRepresents LOBSTER’s projected DOS and local projected DOS.
This class parses and stores data from the DOSCAR file generated by LOBSTER, which contains information about the total and projected density of states (DOS) for a quantum-chemical calculation performed with VASP.
- pdos[source]
Projected DOS data. Access as pdos[atomindex][‘orbitalstring’][Spin.up/Spin.down].
- Type:
list[dict[str, dict[Spin, np.ndarray]]]
- energies[source]
Energies at which the DOS was calculated (in eV, relative to Efermi).
- Type:
np.ndarray
- itdensities[source]
Integrated total density arrays for each spin channel.
- Type:
dict[Spin, np.ndarray]
Initialize a DOSCAR object.
- Parameters:
filename (PathLike | None) – Path to the DOSCAR file, typically “DOSCAR.lobster”.
process_immediately (bool) – Whether to process the file immediately upon initialization.
lobster_version (str | None) – LOBSTER version string to use for parsing. If None, attempts to detect
- Raises:
ValueError – If neither structure_file nor structure is provided.
- property energies: NDArray[floating][source]
Energies at which the DOS was calculated (in eV, relative to efermi).
- classmethod get_default_filename() str[source]
Get the default filename for the DOSCAR.
- Returns:
Default filename string. “DOSCAR.lobster” for regular DOSCAR, “DOSCAR.LCFO.lobster” for LCFO analysis.
- Return type:
str
- property is_spin_polarized: bool[source]
Whether the system is spin polarized.
- Returns:
True if the system is spin polarized, False otherwise.
- Return type:
bool
- process() None[source]
Process the DOSCAR file and extract DOS data.
Parses the DOSCAR file to extract total DOS, projected DOS, energies, and integrated densities. Sets the appropriate attributes based on whether the calculation is spin-polarized.
- Raises:
ValueError – If the DOSCAR file format is invalid or spin polarization cannot be determined.
- class DOSCAR_LCFO(filename: PathLike | None = None, process_immediately: bool = True, lobster_version: str | None = None)[source]
Bases:
DOSCARRepresents LOBSTER’s projected DOS and local projected DOS for LCFO analysis.
This class handles DOSCAR files generated from LCFO analysis, which have a different format than regular DOSCAR files.
Initialize a DOSCAR object.
- Parameters:
filename (PathLike | None) – Path to the DOSCAR file, typically “DOSCAR.lobster”.
process_immediately (bool) – Whether to process the file immediately upon initialization.
lobster_version (str | None) – LOBSTER version string to use for parsing. If None, attempts to detect
- Raises:
ValueError – If neither structure_file nor structure is provided.
- class Fatband(filename: PathLike, process_immediately: bool = True, lobster_version: str | None = None)[source]
Bases:
LobsterFileParser for a single FATBAND_*.lobster file.
- Parses a single FATBAND file and stores:
center (str): Central atom/species label parsed from filename. orbital (str): Orbital descriptor parsed from filename. nbands (int): Number of bands in the FATBAND file. fatband (LobsterFatband): Parsed fatband data dictionary. Please see
LobsterFatbandfor details.
The parsed data is available in the fatband attribute after parse_file().
Initialize a Fatband parser.
- Parameters:
filename (PathLike) – Path to the FATBAND file to parse.
process_immediately (bool) – If True, parse the file during initialization.
lobster_version (str | None) – LOBSTER version string to use for parsing. If None, attempts to detect
default. (from file or falls back to)
- Raises:
ValueError – If the orbital name cannot be parsed from the filename.
- classmethod from_dict(d: dict[str, Any]) Self[source]
Reconstruct a Fatband instance from a dictionary.
- Parameters:
d (dict[str, Any]) – Dictionary representation of a Fatband instance.
- Returns:
Reconstructed instance.
- Return type:
- class Fatbands(directory: PathLike = '.', structure: IStructure | None = None, kpoints_file: PathLike = 'KPOINTS', vasprun_file: PathLike = 'vasprun.xml', process_immediately: bool = True, lobster_version: str | None = None)[source]
Bases:
MSONableReader for multiple FATBAND_*.lobster files in a directory.
Collects FATBAND files, reads VASP outputs for the Fermi level and kpoints, and aggregates per-file parsed data.
Initialize the Fatbands reader.
- Parameters:
directory (PathLike) – Path to directory containing FATBAND files.
structure (IStructure | None) – Structure object. If None, POSCAR.lobster is read from directory.
kpoints_file (PathLike) – Name of the KPOINTS file to be read in the directory.
vasprun_file (PathLike) – Name of the vasprun.xml file to be read in the directory.
process_immediately (bool) – If True, process FATBAND files immediately after initialization.
lobster_version (str | None) – Optional LOBSTER version string. If None, the default LOBSTER_VERSION is used.
- Raises:
FileNotFoundError – If required files are missing in the directory.
ValueError – If no FATBAND files are found or KPOINTS file lacks weights.
- as_dict() dict[str, Any][source]
Serializes the LobsterFile object to a dictionary. Spin keys in dictionaries are converted to strings for JSON compatibility.
- Returns:
Dictionary with keys “@module”, “@class”, “@version”, and all attributes of the object.
- Return type:
dict[str, Any]
- fatbands: list[LobsterFatband][source]
- property has_spin: bool[source]
Indicates whether the file could contain spin-polarized data.
- Returns:
True if this file type supports spin, False otherwise.
- Return type:
bool
- class GROSSPOP(filename: PathLike | None = None, process_immediately: bool = True, lobster_version: str | None = None)[source]
Bases:
LobsterFileParser for GROSSPOP.lobster and GROSSPOP.LCFO.lobster files.
Initialize a LobsterFile instance.
- Parameters:
filename (PathLike | None) – Path to the file. If None, uses the default filename.
process_immediately (bool) – Whether to process the file immediately upon initialization. Defaults to True.
lobster_version (str | None) – LOBSTER version string to use for parsing. If None, attempts to detect
default. (from file or falls back to)
- classmethod get_default_filename() str[source]
Get the default filename for GROSSPOP files.
- Returns:
Default filename for the GROSSPOP file, depending on LCFO mode.
- Return type:
str
- class GROSSPOP_LCFO(filename: PathLike | None = None, process_immediately: bool = True, lobster_version: str | None = None)[source]
Bases:
GROSSPOPParser for GROSSPOP.LCFO.lobster files.
Initialize a LobsterFile instance.
- Parameters:
filename (PathLike | None) – Path to the file. If None, uses the default filename.
process_immediately (bool) – Whether to process the file immediately upon initialization. Defaults to True.
lobster_version (str | None) – LOBSTER version string to use for parsing. If None, attempts to detect
default. (from file or falls back to)
- class ICOBILIST(filename: PathLike | None = None, process_immediately: bool = True, lobster_version: str | None = None)[source]
Bases:
ICOXXLISTReader for ICOBILIST.lobster files.
Initialize a LobsterFile instance.
- Parameters:
filename (PathLike | None) – Path to the file. If None, uses the default filename.
process_immediately (bool) – Whether to process the file immediately upon initialization. Defaults to True.
lobster_version (str | None) – LOBSTER version string to use for parsing. If None, attempts to detect
default. (from file or falls back to)
- class ICOBILIST_LCFO(filename: PathLike | None = None, process_immediately: bool = True, lobster_version: str | None = None)[source]
Bases:
ICOBILISTReader for ICOBILIST.LCFO.lobster files.
Initialize a LobsterFile instance.
- Parameters:
filename (PathLike | None) – Path to the file. If None, uses the default filename.
process_immediately (bool) – Whether to process the file immediately upon initialization. Defaults to True.
lobster_version (str | None) – LOBSTER version string to use for parsing. If None, attempts to detect
default. (from file or falls back to)
- class ICOHPLIST(filename: PathLike | None = None, process_immediately: bool = True, lobster_version: str | None = None)[source]
Bases:
ICOXXLISTReader for ICOHPLIST.lobster files.
Initialize a LobsterFile instance.
- Parameters:
filename (PathLike | None) – Path to the file. If None, uses the default filename.
process_immediately (bool) – Whether to process the file immediately upon initialization. Defaults to True.
lobster_version (str | None) – LOBSTER version string to use for parsing. If None, attempts to detect
default. (from file or falls back to)
- class ICOHPLIST_LCFO(filename: PathLike | None = None, process_immediately: bool = True, lobster_version: str | None = None)[source]
Bases:
ICOHPLISTReader for ICOHPLIST.LCFO.lobster files.
Initialize a LobsterFile instance.
- Parameters:
filename (PathLike | None) – Path to the file. If None, uses the default filename.
process_immediately (bool) – Whether to process the file immediately upon initialization. Defaults to True.
lobster_version (str | None) – LOBSTER version string to use for parsing. If None, attempts to detect
default. (from file or falls back to)
- class ICOOPLIST(filename: PathLike | None = None, process_immediately: bool = True, lobster_version: str | None = None)[source]
Bases:
ICOXXLISTReader for ICOOPLIST.lobster files.
Initialize a LobsterFile instance.
- Parameters:
filename (PathLike | None) – Path to the file. If None, uses the default filename.
process_immediately (bool) – Whether to process the file immediately upon initialization. Defaults to True.
lobster_version (str | None) – LOBSTER version string to use for parsing. If None, attempts to detect
default. (from file or falls back to)
- class ICOXXLIST(filename: PathLike | None = None, process_immediately: bool = True, lobster_version: str | None = None)[source]
Bases:
LobsterInteractionsHolderReader for ICOXX data files (ICOHPLIST, ICOOPLIST, ICOBILIST).
Parses interaction data from ICOXXLIST files, including spin-resolved values.
- interactions[source]
List of parsed interactions.
- Type:
list[LobsterInteractionData]
Initialize a LobsterFile instance.
- Parameters:
filename (PathLike | None) – Path to the file. If None, uses the default filename.
process_immediately (bool) – Whether to process the file immediately upon initialization. Defaults to True.
lobster_version (str | None) – LOBSTER version string to use for parsing. If None, attempts to detect
default. (from file or falls back to)
- get_data_by_properties(indices: list[int] | None = None, centers: list[str] | None = None, cells: list[list[int]] | None = None, orbitals: list[str] | None = None, length: tuple[float, float] | None = None, spins: list[Literal[1, -1]] | None = None) NDArray[np.floating][source]
Get the data for bonds matching specified properties.
- Parameters:
indices (list[int] | None) – Indices of bonds to retrieve.
centers (list[str] | None) – Centers of bonds to retrieve.
cells (list[list[int]] | None) – Cells of bonds to retrieve.
orbitals (list[str] | None) – Orbitals of bonds to retrieve.
length (tuple[float, float] | None) – Length range to filter.
spins (list[Spin] | None) – Spins to retrieve.
- Returns:
Array of data for specified bonds.
- Return type:
NDArray[np.floating]
- interactions_regex: ClassVar[str] = '(?i)\\s*(\\d+)\\s+(\\S+\\s+\\S+)\\s+(\\d+\\.\\d+)\\s+(\\-?\\d+\\s+\\-?\\d+\\s+\\-?\\d+)?\\s+(\\-?\\d+\\.\\d+)(?:\\s+(\\-?\\d+\\.\\d+))?'[source]
- parse_file() None[source]
Parse ICOXXLIST file using modern format (versions ≥5.1).
Extracts interaction data, including spin-resolved values, and populates the interactions, spins, and data attributes.
- Raises:
ValueError – If the file contains invalid spin values or cannot parse interaction lines.
- parse_file_legacy() None[source]
Parse ICOXXLIST file using legacy format (versions ≤5.1).
Extracts interaction data, including spin-resolved values, and populates the interactions, spins, and data attributes.
- Raises:
ValueError – If the file contains invalid spin values or cannot parse interaction lines.
- class LobsterIn(settingsdict: dict)[source]
Bases:
UserDict,MSONableHandles and generates lobsterin files for LOBSTER calculations.
This class provides methods to create, modify, and write lobsterin files, which are input files for the LOBSTER program. It also includes utilities for generating related files such as INCAR, KPOINTS, and POSCAR, and for comparing different lobsterin configurations.
Reminder: LOBSTER input keywords are not case-sensitive.
- AVAILABLE_KEYWORDS[source]
All known keywords mapped to their canonical forms.
- Type:
ClassVar[dict[str, str]]
Initializes a LobsterIn object with the given settings.
- Parameters:
settingsdict (dict) – Dictionary of settings to initialize the LobsterIn object.
- Raises:
KeyError – If there are duplicate keywords (case-insensitive).
- AVAILABLE_KEYWORDS: ClassVar[dict[str, str]] = {'autorotate': 'autoRotate', 'bandwisespilling': 'bandwiseSpilling', 'basisfunctions': 'basisfunctions', 'basisrotation': 'basisRotation', 'basisset': 'basisSet', 'bwdf': 'BWDF', 'bwdfcohp': 'BWDFCOHP', 'cobibetween': 'cobiBetween', 'cohpbetween': 'cohpbetween', 'cohpendenergy': 'COHPendEnergy', 'cohpgenerator': 'cohpGenerator', 'cohpstartenergy': 'COHPstartEnergy', 'cohpsteps': 'COHPSteps', 'createfatband': 'createFatband', 'customstoforatom': 'customSTOforAtom', 'densityofenergy': 'DensityOfEnergy', 'donotignoreexcessivebands': 'doNotIgnoreExcessiveBands', 'donotorthogonalizebasis': 'doNotOrthogonalizeBasis', 'donotuseabsolutespilling': 'doNotUseAbsoluteSpilling', 'ewaldsum': 'EwaldSum', 'forceenergyrange': 'forceEnergyRange', 'forcev1hmatrix': 'forceV1HMatrix', 'gaussiansmearingwidth': 'gaussianSmearingWidth', 'gridbufferforprinting': 'gridBufferForPrinting', 'griddensityforprinting': 'gridDensityForPrinting', 'kpointwisespilling': 'kpointwiseSpilling', 'kspacecohp': 'kSpaceCOHP', 'loadprojectionfromfile': 'loadProjectionFromFile', 'lsodos': 'LSODOS', 'nofftforvisualization': 'noFFTforVisualization', 'nomemorymappedfiles': 'noMemoryMappedFiles', 'onlyreadvasprun.xml': 'onlyReadVasprun.xml', 'printlcaorealspacewavefunction': 'printLCAORealSpaceWavefunction', 'printlmosonatoms': 'printLmosOnAtoms', 'printlmosonatomswriteatomicdensities': 'printLmosOnAtomswriteAtomicDensities', 'printmofeatomwise': 'printMofeAtomWise', 'printmofemoleculewise': 'printMofeMoleculeWise', 'printpawrealspacewavefunction': 'printPAWRealSpaceWavefunction', 'printtotalspilling': 'printTotalSpilling', 'realspacehamiltonian': 'realspaceHamiltonian', 'realspaceoverlap': 'realspaceOverlap', 'rmsp': 'RMSp', 'saveprojectiontofile': 'saveProjectionToFile', 'skipcar': 'skipCar', 'skipcobi': 'skipcobi', 'skipcohp': 'skipcohp', 'skipcoop': 'skipcoop', 'skipdos': 'skipdos', 'skipgrosspopulation': 'skipGrossPopulation', 'skipmadelungenergy': 'skipMadelungEnergy', 'skipmofe': 'skipMOFE', 'skipmolecularorbitals': 'skipMolecularOrbitals', 'skippaworthonormalitytest': 'skipPAWOrthonormalityTest', 'skippopulationanalysis': 'skipPopulationAnalysis', 'skipprojection': 'skipProjection', 'skipreorthonormalization': 'skipReOrthonormalization', 'usedecimalplaces': 'useDecimalPlaces', 'useoriginaltetrahedronmethod': 'useOriginalTetrahedronMethod', 'userecommendedbasisfunctions': 'userecommendedbasisfunctions', 'writeatomicorbitals': 'writeAtomicOrbitals', 'writebasisfunctions': 'writeBasisFunctions', 'writematricestofile': 'writeMatricesToFile'}[source]
- BOOLEAN_KEYWORDS: ClassVar[dict[str, str]] = {'autorotate': 'autoRotate', 'bandwisespilling': 'bandwiseSpilling', 'bwdf': 'BWDF', 'bwdfcohp': 'BWDFCOHP', 'densityofenergy': 'DensityOfEnergy', 'donotignoreexcessivebands': 'doNotIgnoreExcessiveBands', 'donotorthogonalizebasis': 'doNotOrthogonalizeBasis', 'donotuseabsolutespilling': 'doNotUseAbsoluteSpilling', 'forceenergyrange': 'forceEnergyRange', 'forcev1hmatrix': 'forceV1HMatrix', 'kpointwisespilling': 'kpointwiseSpilling', 'loadprojectionfromfile': 'loadProjectionFromFile', 'lsodos': 'LSODOS', 'nofftforvisualization': 'noFFTforVisualization', 'nomemorymappedfiles': 'noMemoryMappedFiles', 'onlyreadvasprun.xml': 'onlyReadVasprun.xml', 'printlmosonatoms': 'printLmosOnAtoms', 'printmofeatomwise': 'printMofeAtomWise', 'printmofemoleculewise': 'printMofeMoleculeWise', 'printtotalspilling': 'printTotalSpilling', 'rmsp': 'RMSp', 'saveprojectiontofile': 'saveProjectionToFile', 'skipcar': 'skipCar', 'skipcobi': 'skipcobi', 'skipcohp': 'skipcohp', 'skipcoop': 'skipcoop', 'skipdos': 'skipdos', 'skipgrosspopulation': 'skipGrossPopulation', 'skipmadelungenergy': 'skipMadelungEnergy', 'skipmofe': 'skipMOFE', 'skipmolecularorbitals': 'skipMolecularOrbitals', 'skippaworthonormalitytest': 'skipPAWOrthonormalityTest', 'skippopulationanalysis': 'skipPopulationAnalysis', 'skipprojection': 'skipProjection', 'skipreorthonormalization': 'skipReOrthonormalization', 'useoriginaltetrahedronmethod': 'useOriginalTetrahedronMethod', 'userecommendedbasisfunctions': 'userecommendedbasisfunctions', 'writeatomicorbitals': 'writeAtomicOrbitals', 'writebasisfunctions': 'writeBasisFunctions', 'writematricestofile': 'writeMatricesToFile'}[source]
- FLOAT_KEYWORDS: ClassVar[dict[str, str]] = {'basisrotation': 'basisRotation', 'cohpendenergy': 'COHPendEnergy', 'cohpstartenergy': 'COHPstartEnergy', 'cohpsteps': 'COHPSteps', 'gaussiansmearingwidth': 'gaussianSmearingWidth', 'gridbufferforprinting': 'gridBufferForPrinting', 'griddensityforprinting': 'gridDensityForPrinting', 'usedecimalplaces': 'useDecimalPlaces'}[source]
- LIST_KEYWORDS: ClassVar[dict[str, str]] = {'basisfunctions': 'basisfunctions', 'cobibetween': 'cobiBetween', 'cohpbetween': 'cohpbetween', 'createfatband': 'createFatband', 'customstoforatom': 'customSTOforAtom', 'printlmosonatomswriteatomicdensities': 'printLmosOnAtomswriteAtomicDensities'}[source]
- STRING_KEYWORDS: ClassVar[dict[str, str]] = {'basisset': 'basisSet', 'cohpgenerator': 'cohpGenerator', 'ewaldsum': 'EwaldSum', 'kspacecohp': 'kSpaceCOHP', 'printlcaorealspacewavefunction': 'printLCAORealSpaceWavefunction', 'printpawrealspacewavefunction': 'printPAWRealSpaceWavefunction', 'realspacehamiltonian': 'realspaceHamiltonian', 'realspaceoverlap': 'realspaceOverlap'}[source]
- as_dict() dict[source]
Converts the LobsterIn object to a dictionary.
- Returns:
A dictionary representation of the LobsterIn object.
- Return type:
dict
- diff(other: Self) dict[str, dict[str, Any]][source]
Compares two LobsterIn objects and identifies differences.
- Parameters:
other (LobsterIn) – The other LobsterIn object to compare.
- Returns:
- A dictionary with keys “Same” and “Different”,
containing the same and differing parameters, respectively.
- Return type:
dict[str, dict[str, Any]]
- classmethod from_dict(dct: dict) Self[source]
Creates a LobsterIn object from a dictionary.
- Parameters:
dct (dict) – A dictionary representation of a LobsterIn object.
- Returns:
The created LobsterIn object.
- Return type:
- classmethod from_file(lobsterin: PathLike) Self[source]
Creates a LobsterIn object from a lobsterin file.
- Parameters:
lobsterin (PathLike) – Path to the lobsterin file.
- Returns:
The created LobsterIn object.
- Return type:
- Raises:
RuntimeError – If the lobsterin file contains no data.
ValueError – If invalid keywords are found or if there are duplicate keywords.
- static get_all_possible_basis_functions(structure: Structure | IStructure, potcar_symbols: list[str], address_basis_file_min: PathLike | None = None, address_basis_file_max: PathLike | None = None) list[dict][source]
- Parameters:
structure – Structure object
potcar_symbols – list of the potcar symbols
address_basis_file_min – path to file with the minimum required basis by the POTCAR
address_basis_file_max – path to file with the largest possible basis of the POTCAR.
- Returns:
- Can be used to create new Lobsterin objects in
standard_calculations_from_vasp_files as dict_for_basis
- Return type:
list[dict]
- static get_basis(structure: Structure | IStructure, potcar_symbols: list[str], address_basis_file: PathLike | None = None) list[str][source]
Retrieves basis functions for the given structure and POTCAR symbols.
- Parameters:
structure (Structure | IStructure) – The structure object.
potcar_symbols (list[str]) – List of POTCAR symbols.
address_basis_file (PathLike | None) – Path to the basis file. Defaults to None.
- Returns:
List of basis functions.
- Return type:
list[str]
- Raises:
ValueError – If the POSCAR does not match the POTCAR or if basis information is missing.
- classmethod standard_calculations_from_vasp_files(POSCAR_input: PathLike = 'POSCAR', INCAR_input: PathLike = 'INCAR', POTCAR_input: PathLike | None = None, Vasprun_output: PathLike = 'vasprun.xml', dict_for_basis: dict | None = None, option: str = 'standard') Self[source]
Generate lobsterin with standard settings.
- Parameters:
POSCAR_input (PathLike) – path to POSCAR
INCAR_input (PathLike) – path to INCAR
POTCAR_input (PathLike) – path to POTCAR
Vasprun_output (PathLike) – path to vasprun.xml
dict_for_basis (dict) – can be provided: it should look the following: dict_for_basis={“Fe”:’3p 3d 4s 4f’, “C”: ‘2s 2p’} and will overwrite all settings from POTCAR_input
option (str) – ‘standard’ will start a normal LOBSTER run where COHPs, COOPs, DOS, CHARGE etc. will be calculated ‘standard_with_energy_range_from_vasprun’ will start a normal LOBSTER run for entire energy range of VASP static run. vasprun.xml file needs to be in current directory. ‘standard_from_projection’ will start a normal LOBSTER run from a projection ‘standard_with_fatband’ will do a fatband calculation, run over all orbitals ‘onlyprojection’ will only do a projection ‘onlydos’ will only calculate a projected dos ‘onlycohp’ will only calculate cohp ‘onlycoop’ will only calculate coop ‘onlycohpcoop’ will only calculate cohp and coop
- Returns:
Lobsterin with standard settings
- write_INCAR(incar_input: PathLike = 'INCAR', incar_output: PathLike = 'INCAR.lobster', poscar_input: PathLike = 'POSCAR', isym: Literal[-1, 0] = 0, further_settings: dict | None = None) None[source]
Writes a modified INCAR file for LOBSTER calculations.
- Parameters:
incar_input (PathLike) – Path to the input INCAR file.
incar_output (PathLike) – Path to the output INCAR file.
poscar_input (PathLike) – Path to the input POSCAR file.
isym (Literal[-1, 0]) – ISYM value to set. Defaults to 0.
further_settings (dict | None) – Additional settings to include in the INCAR file.
- Raises:
ValueError – If isym is not -1 or 0.
- static write_KPOINTS(POSCAR_input: PathLike = 'POSCAR', KPOINTS_output: PathLike = 'KPOINTS.lobster', reciprocal_density: int = 100, isym: Literal[-1, 0] = 0, from_grid: bool = False, input_grid: tuple[int, int, int] = (5, 5, 5), line_mode: bool = True, kpoints_line_density: int = 20, symprec: float = 0.01) None[source]
Write a gamma-centered KPOINTS file for LOBSTER.
- Parameters:
POSCAR_input (PathLike) – path to POSCAR
KPOINTS_output (PathLike) – path to output KPOINTS
reciprocal_density (int) – Grid density
isym (-1 | 0) – ISYM value.
from_grid (bool) – If True KPOINTS will be generated with the help of a grid given in input_grid. Otherwise, they will be generated from the reciprocal_density
input_grid (tuple) – grid to generate the KPOINTS file
line_mode (bool) – If True, band structure will be generated
kpoints_line_density (int) – density of the lines in the band structure
symprec (float) – precision to determine symmetry
- static write_POSCAR_with_standard_primitive(POSCAR_input: PathLike = 'POSCAR', POSCAR_output: PathLike = 'POSCAR.lobster', symprec: float = 0.01) None[source]
Writes a POSCAR file with the standard primitive cell.
- Parameters:
POSCAR_input (PathLike) – Path to the input POSCAR file.
POSCAR_output (PathLike) – Path to the output POSCAR file.
symprec (float) – Precision for symmetry determination. Defaults to 0.01.
- write_lobsterin(path: PathLike = 'lobsterin', overwritedict: dict | None = None) None[source]
Writes the LobsterIn object to a lobsterin file.
- Parameters:
path (PathLike) – The output file path. Defaults to “lobsterin”.
overwritedict (dict | None) – A dictionary of settings to overwrite before writing.
- class LobsterMatrices(filename: PathLike | None = None, matrix_type: str | None = None, efermi: float | None = None, process_immediately: bool = True, lobster_version: str | None = None)[source]
Bases:
LobsterFileParser for LOBSTER matrix files.
Initialize LOBSTER matrices parser.
- Parameters:
filename – Path to the matrix file
matrix_type – Type of matrix. If None, inferred from filename
efermi – Fermi level in eV (required for Hamilton matrices)
process_immediately – Whether to parse the file immediately
- as_dict() dict[str, Any][source]
Serialize object to a dictionary.
- Returns:
Dictionary representation of the object.
- Return type:
dict[str, Any]
- classmethod get_default_filename() str[source]
Get the default filename for the LobsterMatrices class.
- Returns:
Default filename.
- Return type:
str
- get_matrix_type() str[source]
Infer matrix type from filename.
- Returns:
Matrix type.
- Return type:
str
- get_onsite_values(center: str | None = None, orbital: str | None = None) dict | float | floating[source]
Get onsite values for specific centers/orbitals.
- Parameters:
center (str | None) – Specific center or None for all.
orbital (str | None) – Specific orbital or None for all.
- Returns:
Dict of values or single value if both specified.
- Return type:
dict | float | floating
- class LobsterOut(filename: PathLike | None = None, process_immediately: bool = True, lobster_version: str | None = None)[source]
Bases:
LobsterFileParser for lobsterout file from LOBSTER.
This class reads the lobsterout file and extracts information about basis functions, spillings, warnings, timing, and file presence. It supports parsing for different LOBSTER versions and provides attributes to access the parsed data.
- has_madelung[source]
Whether SitePotentials.lobster and MadelungEnergies.lobster are present.
- Type:
bool
- is_restart_from_projection[source]
Whether calculation was restarted from a projection file.
- Type:
bool
Initialize a LobsterFile instance.
- Parameters:
filename (PathLike | None) – Path to the file. If None, uses the default filename.
process_immediately (bool) – Whether to process the file immediately upon initialization. Defaults to True.
lobster_version (str | None) – LOBSTER version string to use for parsing. If None, attempts to detect
default. (from file or falls back to)
- classmethod get_default_filename() str[source]
Get the default filename for LobsterOut.
- Returns:
The default filename.
- Return type:
str
- static get_lobster_version(lines: list[str]) str[source]
Get the LOBSTER version from the lobsterout lines.
- Parameters:
lines (list[str]) – Lines of the lobsterout file.
- Returns:
The LOBSTER version.
- Return type:
str
- Raises:
RuntimeError – If the version line is not found.
- class MadelungEnergies(filename: PathLike | None = None, process_immediately: bool = True, lobster_version: str | None = None)[source]
Bases:
LobsterFileParser for MadelungEnergies.lobster files.
Initialize a LobsterFile instance.
- Parameters:
filename (PathLike | None) – Path to the file. If None, uses the default filename.
process_immediately (bool) – Whether to process the file immediately upon initialization. Defaults to True.
lobster_version (str | None) – LOBSTER version string to use for parsing. If None, attempts to detect
default. (from file or falls back to)
- classmethod get_default_filename() str[source]
Get the default filename for MadelungEnergies.
- Returns:
Default filename.
- Return type:
str
- class NcICOBILIST(filename: PathLike | None = None, process_immediately: bool = True, lobster_version: str | None = None)[source]
Bases:
LobsterInteractionsHolderReader for NcICOBILIST.lobster files.
Parses non-conventional ICOBI interaction data.
Initialize a LobsterFile instance.
- Parameters:
filename (PathLike | None) – Path to the file. If None, uses the default filename.
process_immediately (bool) – Whether to process the file immediately upon initialization. Defaults to True.
lobster_version (str | None) – LOBSTER version string to use for parsing. If None, attempts to detect
default. (from file or falls back to)
- get_data_by_properties(indices: list[int] | None = None, centers: list[str] | None = None, cells: list[list[int]] | None = None, orbitals: list[str] | None = None, length: tuple[float, float] | None = None, spins: list[Literal[1, -1]] | None = None) NDArray[np.floating][source]
Get the data for bonds matching specified properties.
- Parameters:
indices (list[int] | None) – Indices of bonds to retrieve.
centers (list[str] | None) – Centers of bonds to retrieve.
cells (list[list[int]] | None) – Cells of bonds to retrieve.
orbitals (list[str] | None) – Orbitals of bonds to retrieve.
length (tuple[float, float] | None) – Length range to filter.
spins (list[Spin] | None) – Spins to retrieve.
- Returns:
Array of data for specified bonds.
- Return type:
NDArray[np.floating]
- interactions_regex: ClassVar[str] = '(?i)([a-z]+\\d*(?:\\_\\d+)?)(?:\\[(\\-?\\d+\\s+\\-?\\d+\\s+\\-?\\d+)\\])?(?:\\[([^]\\s]*)\\])?(?:\\(([^)]*)\\))?'[source]
- parse_file() None[source]
Parse the NcICOBILIST file.
Extracts interaction data, including spin-resolved values, and populates the interactions, spins, and data attributes.
- Raises:
ValueError – If the file contains invalid spin values or cannot parse interaction lines.
- class POLARIZATION(filename: PathLike | None = None, process_immediately: bool = True, lobster_version: str | None = None)[source]
Bases:
LobsterFileParser for POLARIZATION.lobster file.
Initialize a LobsterFile instance.
- Parameters:
filename (PathLike | None) – Path to the file. If None, uses the default filename.
process_immediately (bool) – Whether to process the file immediately upon initialization. Defaults to True.
lobster_version (str | None) – LOBSTER version string to use for parsing. If None, attempts to detect
default. (from file or falls back to)
- class SitePotentials(filename: PathLike | None = None, process_immediately: bool = True, lobster_version: str | None = None)[source]
Bases:
LobsterFileParser for SitePotentials.lobster files.
Initialize a LobsterFile instance.
- Parameters:
filename (PathLike | None) – Path to the file. If None, uses the default filename.
process_immediately (bool) – Whether to process the file immediately upon initialization. Defaults to True.
lobster_version (str | None) – LOBSTER version string to use for parsing. If None, attempts to detect
default. (from file or falls back to)
- classmethod get_default_filename() str[source]
Get the default filename for SitePotentials.
- Returns:
Default filename.
- Return type:
str
- class Wavefunction(filename: PathLike, structure: Structure, process_immediately: bool = True, lobster_version: str | None = None)[source]
Bases:
LobsterFileParser for wave function files from LOBSTER.
Reads wave function files and creates VolumetricData objects.
Initialize the Wavefunction parser.
- Parameters:
filename (PathLike) – The wavecar file from LOBSTER.
structure (Structure) – The Structure object.
process_immediately (bool) – Whether to parse the file immediately. Defaults to True.
- get_volumetricdata_density() VolumetricData[source]
Get VolumetricData object for the density part of the wave function.
- Returns:
Density volumetric data.
- Return type:
- get_volumetricdata_imaginary() VolumetricData[source]
Get VolumetricData object for the imaginary part of the wave function.
- Returns:
Imaginary part volumetric data.
- Return type:
- get_volumetricdata_real() VolumetricData[source]
Get VolumetricData object for the real part of the wave function.
- Returns:
Real part volumetric data.
- Return type:
- parse_file() None[source]
Parse wave function file.
Reads the wave function file and extracts grid, points, real and imaginary parts, and distances.
- Raises:
ValueError – If the number of real or imaginary parts does not match the expected grid size.
- set_volumetric_data(grid: tuple[int, int, int], structure: Structure) None[source]
Create VolumetricData instances for real, imaginary, and density parts.
- Parameters:
grid (tuple[int, int, int]) – Grid on which wavefunction was calculated.
structure (Structure) – Structure object.
- Raises:
ValueError – If the wavefunction file does not contain all relevant points.
- write_file(filename: PathLike = 'WAVECAR.vasp', part: Literal['real', 'imaginary', 'density'] = 'real') None[source]
Save the wave function in a file readable by VESTA.
- Parameters:
filename (PathLike) – Output file name. Defaults to “WAVECAR.vasp”.
part (Literal["real", "imaginary", "density"]) – Which part to save. Defaults to “real”.
- Raises:
ValueError – If the specified part is not “real”, “imaginary”, or “density”.
Subpackages
- pymatgen.io.lobster.future.outputs package
BWDFBWDFCOHPBandOverlapsBandOverlaps.band_overlapsBandOverlaps.from_dict()BandOverlaps.get_default_filename()BandOverlaps.has_good_quality_check_occupied_bands()BandOverlaps.has_good_quality_max_deviation()BandOverlaps.parse_file()BandOverlaps.parse_file_v3_2_legacy()BandOverlaps.parse_file_v4_0()BandOverlaps.version_processors
CHARGECHARGE_LCFOCOBICARCOBICAR_LCFOCOHPCARCOHPCAR_LCFOCOOPCARCOXXCARCOXXCAR.filenameCOXXCAR.num_bondsCOXXCAR.num_dataCOXXCAR.efermiCOXXCAR.spinsCOXXCAR.interactionsCOXXCAR.dataCOXXCAR.coxxcar_typeCOXXCAR.energiesCOXXCAR.get_data_by_properties()COXXCAR.get_data_indices_by_properties()COXXCAR.interaction_indices_to_data_indices_mapping()COXXCAR.interactions_regexCOXXCAR.parse_bonds()COXXCAR.parse_data()COXXCAR.parse_file()COXXCAR.parse_header()COXXCAR.process_data_into_interactions()COXXCAR.version_processors
DOSCARDOSCAR.completedosDOSCAR.pdosDOSCAR.tdosDOSCAR.energiesDOSCAR.tdensitiesDOSCAR.itdensitiesDOSCAR.is_spin_polarizedDOSCAR.efermiDOSCAR.energiesDOSCAR.get_default_filename()DOSCAR.integrated_total_dosDOSCAR.is_lcfoDOSCAR.is_spin_polarizedDOSCAR.process()DOSCAR.projected_dosDOSCAR.total_dosDOSCAR.version_processors
DOSCAR_LCFOFatbandFatbandsGROSSPOPGROSSPOP_LCFOICOBILISTICOBILIST_LCFOICOHPLISTICOHPLIST_LCFOICOOPLISTICOXXLISTICOXXLIST.interactionsICOXXLIST.spinsICOXXLIST.dataICOXXLIST.icoxxlist_typeICOXXLIST.is_lcfoICOXXLIST.get_data_by_properties()ICOXXLIST.icoxxlist_typeICOXXLIST.interactions_regexICOXXLIST.parse_file()ICOXXLIST.parse_file_legacy()ICOXXLIST.process_data_into_interactions()ICOXXLIST.version_processors
LobsterMatricesLobsterMatrices.matrix_typeLobsterMatrices.centersLobsterMatrices.orbitalsLobsterMatrices.matricesLobsterMatrices.efermiLobsterMatrices.as_dict()LobsterMatrices.centersLobsterMatrices.from_dict()LobsterMatrices.get_default_filename()LobsterMatrices.get_matrix_type()LobsterMatrices.get_onsite_values()LobsterMatrices.matricesLobsterMatrices.matrix_typesLobsterMatrices.orbitalsLobsterMatrices.parse_file()LobsterMatrices.version_processors
LobsterOutLobsterOut.basis_functionsLobsterOut.basis_typeLobsterOut.charge_spillingLobsterOut.dft_programLobsterOut.elementsLobsterOut.has_chargeLobsterOut.has_cohpcarLobsterOut.has_madelungLobsterOut.has_coopcarLobsterOut.has_cobicarLobsterOut.has_doscarLobsterOut.has_doscar_lsoLobsterOut.has_projectionLobsterOut.has_bandoverlapsLobsterOut.has_density_of_energiesLobsterOut.has_fatbandsLobsterOut.has_grosspopulationLobsterOut.has_polarizationLobsterOut.info_linesLobsterOut.info_orthonormalizationLobsterOut.is_restart_from_projectionLobsterOut.lobster_versionLobsterOut.number_of_spinsLobsterOut.number_of_threadsLobsterOut.timingLobsterOut.total_spillingLobsterOut.warning_linesLobsterOut.get_default_filename()LobsterOut.get_lobster_version()LobsterOut.process()LobsterOut.version_processors
MadelungEnergiesNcICOBILISTPOLARIZATIONSitePotentialsSitePotentials.centersSitePotentials.site_potentials_mullikenSitePotentials.site_potentials_loewdinSitePotentials.madelung_energies_mullikenSitePotentials.madelung_energies_loewdinSitePotentials.ewald_splittingSitePotentials.get_default_filename()SitePotentials.parse_file()SitePotentials.version_processors
WavefunctionWavefunction.gridWavefunction.pointsWavefunction.realsWavefunction.imaginariesWavefunction.distancesWavefunction.structureWavefunction.from_dict()Wavefunction.get_volumetricdata_density()Wavefunction.get_volumetricdata_imaginary()Wavefunction.get_volumetricdata_real()Wavefunction.parse_file()Wavefunction.set_volumetric_data()Wavefunction.version_processorsWavefunction.write_file()
- Submodules
- pymatgen.io.lobster.future.outputs.bands module
BandOverlapsBandOverlaps.band_overlapsBandOverlaps.from_dict()BandOverlaps.get_default_filename()BandOverlaps.has_good_quality_check_occupied_bands()BandOverlaps.has_good_quality_max_deviation()BandOverlaps.parse_file()BandOverlaps.parse_file_v3_2_legacy()BandOverlaps.parse_file_v4_0()BandOverlaps.version_processors
FatbandFatbands
- pymatgen.io.lobster.future.outputs.coxxcar module
COBICARCOBICAR_LCFOCOHPCARCOHPCAR_LCFOCOOPCARCOXXCARCOXXCAR.filenameCOXXCAR.num_bondsCOXXCAR.num_dataCOXXCAR.efermiCOXXCAR.spinsCOXXCAR.interactionsCOXXCAR.dataCOXXCAR.coxxcar_typeCOXXCAR.energiesCOXXCAR.get_data_by_properties()COXXCAR.get_data_indices_by_properties()COXXCAR.interaction_indices_to_data_indices_mapping()COXXCAR.interactions_regexCOXXCAR.parse_bonds()COXXCAR.parse_data()COXXCAR.parse_file()COXXCAR.parse_header()COXXCAR.process_data_into_interactions()COXXCAR.version_processors
- pymatgen.io.lobster.future.outputs.doscar module
DOSCARDOSCAR.completedosDOSCAR.pdosDOSCAR.tdosDOSCAR.energiesDOSCAR.tdensitiesDOSCAR.itdensitiesDOSCAR.is_spin_polarizedDOSCAR.efermiDOSCAR.energiesDOSCAR.get_default_filename()DOSCAR.integrated_total_dosDOSCAR.is_lcfoDOSCAR.is_spin_polarizedDOSCAR.process()DOSCAR.projected_dosDOSCAR.total_dosDOSCAR.version_processors
DOSCAR_LCFO
- pymatgen.io.lobster.future.outputs.icoxxlist module
ICOBILISTICOBILIST_LCFOICOHPLISTICOHPLIST_LCFOICOOPLISTICOXXLISTICOXXLIST.interactionsICOXXLIST.spinsICOXXLIST.dataICOXXLIST.icoxxlist_typeICOXXLIST.is_lcfoICOXXLIST.get_data_by_properties()ICOXXLIST.icoxxlist_typeICOXXLIST.interactions_regexICOXXLIST.parse_file()ICOXXLIST.parse_file_legacy()ICOXXLIST.process_data_into_interactions()ICOXXLIST.version_processors
NcICOBILIST
- pymatgen.io.lobster.future.outputs.lobsterout module
LobsterOutLobsterOut.basis_functionsLobsterOut.basis_typeLobsterOut.charge_spillingLobsterOut.dft_programLobsterOut.elementsLobsterOut.has_chargeLobsterOut.has_cohpcarLobsterOut.has_madelungLobsterOut.has_coopcarLobsterOut.has_cobicarLobsterOut.has_doscarLobsterOut.has_doscar_lsoLobsterOut.has_projectionLobsterOut.has_bandoverlapsLobsterOut.has_density_of_energiesLobsterOut.has_fatbandsLobsterOut.has_grosspopulationLobsterOut.has_polarizationLobsterOut.info_linesLobsterOut.info_orthonormalizationLobsterOut.is_restart_from_projectionLobsterOut.lobster_versionLobsterOut.number_of_spinsLobsterOut.number_of_threadsLobsterOut.timingLobsterOut.total_spillingLobsterOut.warning_linesLobsterOut.get_default_filename()LobsterOut.get_lobster_version()LobsterOut.process()LobsterOut.version_processors
- pymatgen.io.lobster.future.outputs.misc module
BWDFBWDFCOHPLobsterMatricesLobsterMatrices.matrix_typeLobsterMatrices.centersLobsterMatrices.orbitalsLobsterMatrices.matricesLobsterMatrices.efermiLobsterMatrices.as_dict()LobsterMatrices.centersLobsterMatrices.from_dict()LobsterMatrices.get_default_filename()LobsterMatrices.get_matrix_type()LobsterMatrices.get_onsite_values()LobsterMatrices.matricesLobsterMatrices.matrix_typesLobsterMatrices.orbitalsLobsterMatrices.parse_file()LobsterMatrices.version_processors
MadelungEnergiesPOLARIZATIONSitePotentialsSitePotentials.centersSitePotentials.site_potentials_mullikenSitePotentials.site_potentials_loewdinSitePotentials.madelung_energies_mullikenSitePotentials.madelung_energies_loewdinSitePotentials.ewald_splittingSitePotentials.get_default_filename()SitePotentials.parse_file()SitePotentials.version_processors
WavefunctionWavefunction.gridWavefunction.pointsWavefunction.realsWavefunction.imaginariesWavefunction.distancesWavefunction.structureWavefunction.from_dict()Wavefunction.get_volumetricdata_density()Wavefunction.get_volumetricdata_imaginary()Wavefunction.get_volumetricdata_real()Wavefunction.parse_file()Wavefunction.set_volumetric_data()Wavefunction.version_processorsWavefunction.write_file()
get_orb_from_str()
- pymatgen.io.lobster.future.outputs.populations module
Submodules
pymatgen.io.lobster.future.constants module
Constants for LOBSTER input and output parsing.
pymatgen.io.lobster.future.core module
- class LobsterFile(filename: PathLike | None = None, process_immediately: bool = True, lobster_version: str | None = None)[source]
Bases:
MSONableRepresentation of a LOBSTER file.
This class provides a framework for parsing and processing LOBSTER output files. It supports version-specific processing through a registry of version processors.
- lobster_version[source]
Version string parsed from the file or the default LOBSTER_VERSION.
- Type:
str
- version_processors[source]
Registry of version processors.
- Type:
ClassVar[dict[tuple[str, str | None], Callable]]
- spins[source]
List of Spin objects if the file contains spin-polarized data, else None.
- Type:
list[Spin] | None
Initialize a LobsterFile instance.
- Parameters:
filename (PathLike | None) – Path to the file. If None, uses the default filename.
process_immediately (bool) – Whether to process the file immediately upon initialization. Defaults to True.
lobster_version (str | None) – LOBSTER version string to use for parsing. If None, attempts to detect
default. (from file or falls back to)
- as_dict() dict[str, Any][source]
Serializes the LobsterFile object to a dictionary. Spin keys in dictionaries are converted to strings for JSON compatibility.
- Returns:
Dictionary with keys “@module”, “@class”, “@version”, and all attributes of the object.
- Return type:
dict[str, Any]
- static check_version(actual: str, minimum: str, maximum: str | None) bool[source]
Checks whether a version string falls within a min/max inclusive range.
- Parameters:
actual (str) – Version string to check (e.g., “1.2.3”).
minimum (str) – Minimum acceptable version string (exclusive).
maximum (str | None) – Maximum acceptable version string (exclusive) or None for no upper bound.
- Returns:
True if actual is > minimum and < maximum (if provided), otherwise False.
- Return type:
bool
- classmethod from_dict(d: dict[str, Any]) Self[source]
Deserializes a LobsterFile object from a dictionary. Spin keys in dictionaries are restored from strings.
- Parameters:
d (dict[str, Any]) – Dictionary produced by as_dict or similar serialization.
- Returns:
Instance of LobsterFile with attributes populated from the dictionary.
- Return type:
- abstractmethod classmethod get_default_filename() str[source]
Returns the default filename for this LobsterFile subclass.
- Returns:
The default filename.
- Return type:
str
- get_file_version() str | None[source]
Retrieves the file version. Override in subclasses to extract version from file content if possible.
- Returns:
Version string (e.g., “1.2.3”) if found, else None.
- Return type:
str | None
- property has_spin: bool[source]
Indicates whether the file could contain spin-polarized data.
- Returns:
True if this file type supports spin, False otherwise.
- Return type:
bool
- property is_spin_polarized: bool[source]
Indicates whether the file contains spin-polarized data.
- Returns:
True if multiple spins are present, False otherwise.
- Return type:
bool
- iterate_lines() Generator[str][source]
Iterates over lines in the file, yielding each line as a string.
- Yields:
str – Each line in the file, stripped of whitespace.
- property lines: list[str][source]
Returns all lines from the file as a list of strings.
- Returns:
Lines from the file.
- Return type:
list[str]
- Raises:
ValueError – If the file is empty.
- process() None[source]
Processes the file using the appropriate version processor.
Selects the best matching version processor from the version_processors registry and invokes it.
- Raises:
ValueError – If no processor matches the file version.
RuntimeError – If the selected processor raises an exception.
- class LobsterInteractionsHolder(filename: PathLike | None = None, process_immediately: bool = True, lobster_version: str | None = None)[source]
Bases:
LobsterFileContainer for LOBSTER interaction data. This class holds interaction metadata. It provides methods for filtering and retrieving interaction data based on various criteria.
- interactions[source]
List of interaction metadata dicts.
- Type:
list[LobsterInteractionData]
Initialize a LobsterFile instance.
- Parameters:
filename (PathLike | None) – Path to the file. If None, uses the default filename.
process_immediately (bool) – Whether to process the file immediately upon initialization. Defaults to True.
lobster_version (str | None) – LOBSTER version string to use for parsing. If None, attempts to detect
default. (from file or falls back to)
- classmethod from_dict(d: dict[str, Any]) Self[source]
Deserialize object from dictionary produced by as_dict.
- Parameters:
d (dict) – Dictionary produced by as_dict.
- Returns:
Reconstructed instance.
- Return type:
- get_interaction_indices_by_properties(indices: list[int] | None = None, centers: list[str] | None = None, cells: list[list[int]] | None = None, orbitals: list[str] | None = None, length: tuple[float, float] | None = None) list[int][source]
Returns indices of interactions that match provided property filters.
- Parameters:
indices (list[int] | None) – Optional sequence of interaction indices to match.
centers (list[str] | None) – Optional sequence of center name substrings; interaction must contain each
times. (orbital substring the required number of)
cells (list[list[int]] | None) – Optional sequence of cell vectors to match against interaction cells.
orbitals (list[str] | None) – Optional sequence of orbital name substrings; interaction must contain each
times.
length (tuple[float, float] | None) – Optional (min, max) tuple to filter interactions by length inclusive.
- Returns:
Sorted list of interaction indices that match all supplied filters. If no filters are supplied, returns an empty list.
- Return type:
list[int]
- get_interactions_by_properties(indices: list[int] | None = None, centers: list[str] | None = None, cells: list[list[int]] | None = None, orbitals: list[str] | None = None, length: tuple[float, float] | None = None) list[LobsterInteractionData][source]
Return interaction metadata dicts that match the provided filters.
- Parameters:
indices (list[int] | None) – Interaction indices to filter.
centers (list[str] | None) – Atom centers to filter.
cells (list[list[int]] | None) – Unit cell indices to filter.
orbitals (list[str] | None) – Orbitals to filter.
length (tuple[float, float] | None) – Length range to filter.
- Returns:
List of interaction dictionaries matching the filters.
- Return type:
list[dict]
- static get_label_from_interaction(interaction: LobsterInteraction, include_centers: bool = True, include_orbitals: bool = True, include_cells: bool = False, include_length: bool = False) str[source]
Generates a label string for a given interaction.
- Parameters:
interaction (LobsterInteraction) – Interaction metadata dictionary.
- Returns:
Formatted label string representing the interaction.
- Return type:
str
- interactions: list[LobsterInteractionData][source]
- abstractmethod process_data_into_interactions() None[source]
Abstract method to process raw data into structured interaction metadata. Must be implemented by subclasses. This method should populate the interactions attribute based on the raw data and any other relevant attributes. The exact processing logic will depend on the specific format and content of the data in the subclass.
pymatgen.io.lobster.future.inputs module
Module for reading LOBSTER input files. For more information on LOBSTER see www.cohp.de.
If you use this module, please cite: J. George, G. Petretto, A. Naik, M. Esters, A. J. Jackson, R. Nelson, R. Dronskowski, G.-M. Rignanese, G. Hautier, “Automated Bonding Analysis with Crystal Orbital Hamilton Populations”, ChemPlusChem 2022, e202200123, DOI: 10.1002/cplu.202200123.
- class LobsterIn(settingsdict: dict)[source]
Bases:
UserDict,MSONableHandles and generates lobsterin files for LOBSTER calculations.
This class provides methods to create, modify, and write lobsterin files, which are input files for the LOBSTER program. It also includes utilities for generating related files such as INCAR, KPOINTS, and POSCAR, and for comparing different lobsterin configurations.
Reminder: LOBSTER input keywords are not case-sensitive.
- AVAILABLE_KEYWORDS[source]
All known keywords mapped to their canonical forms.
- Type:
ClassVar[dict[str, str]]
Initializes a LobsterIn object with the given settings.
- Parameters:
settingsdict (dict) – Dictionary of settings to initialize the LobsterIn object.
- Raises:
KeyError – If there are duplicate keywords (case-insensitive).
- AVAILABLE_KEYWORDS: ClassVar[dict[str, str]] = {'autorotate': 'autoRotate', 'bandwisespilling': 'bandwiseSpilling', 'basisfunctions': 'basisfunctions', 'basisrotation': 'basisRotation', 'basisset': 'basisSet', 'bwdf': 'BWDF', 'bwdfcohp': 'BWDFCOHP', 'cobibetween': 'cobiBetween', 'cohpbetween': 'cohpbetween', 'cohpendenergy': 'COHPendEnergy', 'cohpgenerator': 'cohpGenerator', 'cohpstartenergy': 'COHPstartEnergy', 'cohpsteps': 'COHPSteps', 'createfatband': 'createFatband', 'customstoforatom': 'customSTOforAtom', 'densityofenergy': 'DensityOfEnergy', 'donotignoreexcessivebands': 'doNotIgnoreExcessiveBands', 'donotorthogonalizebasis': 'doNotOrthogonalizeBasis', 'donotuseabsolutespilling': 'doNotUseAbsoluteSpilling', 'ewaldsum': 'EwaldSum', 'forceenergyrange': 'forceEnergyRange', 'forcev1hmatrix': 'forceV1HMatrix', 'gaussiansmearingwidth': 'gaussianSmearingWidth', 'gridbufferforprinting': 'gridBufferForPrinting', 'griddensityforprinting': 'gridDensityForPrinting', 'kpointwisespilling': 'kpointwiseSpilling', 'kspacecohp': 'kSpaceCOHP', 'loadprojectionfromfile': 'loadProjectionFromFile', 'lsodos': 'LSODOS', 'nofftforvisualization': 'noFFTforVisualization', 'nomemorymappedfiles': 'noMemoryMappedFiles', 'onlyreadvasprun.xml': 'onlyReadVasprun.xml', 'printlcaorealspacewavefunction': 'printLCAORealSpaceWavefunction', 'printlmosonatoms': 'printLmosOnAtoms', 'printlmosonatomswriteatomicdensities': 'printLmosOnAtomswriteAtomicDensities', 'printmofeatomwise': 'printMofeAtomWise', 'printmofemoleculewise': 'printMofeMoleculeWise', 'printpawrealspacewavefunction': 'printPAWRealSpaceWavefunction', 'printtotalspilling': 'printTotalSpilling', 'realspacehamiltonian': 'realspaceHamiltonian', 'realspaceoverlap': 'realspaceOverlap', 'rmsp': 'RMSp', 'saveprojectiontofile': 'saveProjectionToFile', 'skipcar': 'skipCar', 'skipcobi': 'skipcobi', 'skipcohp': 'skipcohp', 'skipcoop': 'skipcoop', 'skipdos': 'skipdos', 'skipgrosspopulation': 'skipGrossPopulation', 'skipmadelungenergy': 'skipMadelungEnergy', 'skipmofe': 'skipMOFE', 'skipmolecularorbitals': 'skipMolecularOrbitals', 'skippaworthonormalitytest': 'skipPAWOrthonormalityTest', 'skippopulationanalysis': 'skipPopulationAnalysis', 'skipprojection': 'skipProjection', 'skipreorthonormalization': 'skipReOrthonormalization', 'usedecimalplaces': 'useDecimalPlaces', 'useoriginaltetrahedronmethod': 'useOriginalTetrahedronMethod', 'userecommendedbasisfunctions': 'userecommendedbasisfunctions', 'writeatomicorbitals': 'writeAtomicOrbitals', 'writebasisfunctions': 'writeBasisFunctions', 'writematricestofile': 'writeMatricesToFile'}[source]
- BOOLEAN_KEYWORDS: ClassVar[dict[str, str]] = {'autorotate': 'autoRotate', 'bandwisespilling': 'bandwiseSpilling', 'bwdf': 'BWDF', 'bwdfcohp': 'BWDFCOHP', 'densityofenergy': 'DensityOfEnergy', 'donotignoreexcessivebands': 'doNotIgnoreExcessiveBands', 'donotorthogonalizebasis': 'doNotOrthogonalizeBasis', 'donotuseabsolutespilling': 'doNotUseAbsoluteSpilling', 'forceenergyrange': 'forceEnergyRange', 'forcev1hmatrix': 'forceV1HMatrix', 'kpointwisespilling': 'kpointwiseSpilling', 'loadprojectionfromfile': 'loadProjectionFromFile', 'lsodos': 'LSODOS', 'nofftforvisualization': 'noFFTforVisualization', 'nomemorymappedfiles': 'noMemoryMappedFiles', 'onlyreadvasprun.xml': 'onlyReadVasprun.xml', 'printlmosonatoms': 'printLmosOnAtoms', 'printmofeatomwise': 'printMofeAtomWise', 'printmofemoleculewise': 'printMofeMoleculeWise', 'printtotalspilling': 'printTotalSpilling', 'rmsp': 'RMSp', 'saveprojectiontofile': 'saveProjectionToFile', 'skipcar': 'skipCar', 'skipcobi': 'skipcobi', 'skipcohp': 'skipcohp', 'skipcoop': 'skipcoop', 'skipdos': 'skipdos', 'skipgrosspopulation': 'skipGrossPopulation', 'skipmadelungenergy': 'skipMadelungEnergy', 'skipmofe': 'skipMOFE', 'skipmolecularorbitals': 'skipMolecularOrbitals', 'skippaworthonormalitytest': 'skipPAWOrthonormalityTest', 'skippopulationanalysis': 'skipPopulationAnalysis', 'skipprojection': 'skipProjection', 'skipreorthonormalization': 'skipReOrthonormalization', 'useoriginaltetrahedronmethod': 'useOriginalTetrahedronMethod', 'userecommendedbasisfunctions': 'userecommendedbasisfunctions', 'writeatomicorbitals': 'writeAtomicOrbitals', 'writebasisfunctions': 'writeBasisFunctions', 'writematricestofile': 'writeMatricesToFile'}[source]
- FLOAT_KEYWORDS: ClassVar[dict[str, str]] = {'basisrotation': 'basisRotation', 'cohpendenergy': 'COHPendEnergy', 'cohpstartenergy': 'COHPstartEnergy', 'cohpsteps': 'COHPSteps', 'gaussiansmearingwidth': 'gaussianSmearingWidth', 'gridbufferforprinting': 'gridBufferForPrinting', 'griddensityforprinting': 'gridDensityForPrinting', 'usedecimalplaces': 'useDecimalPlaces'}[source]
- LIST_KEYWORDS: ClassVar[dict[str, str]] = {'basisfunctions': 'basisfunctions', 'cobibetween': 'cobiBetween', 'cohpbetween': 'cohpbetween', 'createfatband': 'createFatband', 'customstoforatom': 'customSTOforAtom', 'printlmosonatomswriteatomicdensities': 'printLmosOnAtomswriteAtomicDensities'}[source]
- STRING_KEYWORDS: ClassVar[dict[str, str]] = {'basisset': 'basisSet', 'cohpgenerator': 'cohpGenerator', 'ewaldsum': 'EwaldSum', 'kspacecohp': 'kSpaceCOHP', 'printlcaorealspacewavefunction': 'printLCAORealSpaceWavefunction', 'printpawrealspacewavefunction': 'printPAWRealSpaceWavefunction', 'realspacehamiltonian': 'realspaceHamiltonian', 'realspaceoverlap': 'realspaceOverlap'}[source]
- as_dict() dict[source]
Converts the LobsterIn object to a dictionary.
- Returns:
A dictionary representation of the LobsterIn object.
- Return type:
dict
- diff(other: Self) dict[str, dict[str, Any]][source]
Compares two LobsterIn objects and identifies differences.
- Parameters:
other (LobsterIn) – The other LobsterIn object to compare.
- Returns:
- A dictionary with keys “Same” and “Different”,
containing the same and differing parameters, respectively.
- Return type:
dict[str, dict[str, Any]]
- classmethod from_dict(dct: dict) Self[source]
Creates a LobsterIn object from a dictionary.
- Parameters:
dct (dict) – A dictionary representation of a LobsterIn object.
- Returns:
The created LobsterIn object.
- Return type:
- classmethod from_file(lobsterin: PathLike) Self[source]
Creates a LobsterIn object from a lobsterin file.
- Parameters:
lobsterin (PathLike) – Path to the lobsterin file.
- Returns:
The created LobsterIn object.
- Return type:
- Raises:
RuntimeError – If the lobsterin file contains no data.
ValueError – If invalid keywords are found or if there are duplicate keywords.
- static get_all_possible_basis_functions(structure: Structure | IStructure, potcar_symbols: list[str], address_basis_file_min: PathLike | None = None, address_basis_file_max: PathLike | None = None) list[dict][source]
- Parameters:
structure – Structure object
potcar_symbols – list of the potcar symbols
address_basis_file_min – path to file with the minimum required basis by the POTCAR
address_basis_file_max – path to file with the largest possible basis of the POTCAR.
- Returns:
- Can be used to create new Lobsterin objects in
standard_calculations_from_vasp_files as dict_for_basis
- Return type:
list[dict]
- static get_basis(structure: Structure | IStructure, potcar_symbols: list[str], address_basis_file: PathLike | None = None) list[str][source]
Retrieves basis functions for the given structure and POTCAR symbols.
- Parameters:
structure (Structure | IStructure) – The structure object.
potcar_symbols (list[str]) – List of POTCAR symbols.
address_basis_file (PathLike | None) – Path to the basis file. Defaults to None.
- Returns:
List of basis functions.
- Return type:
list[str]
- Raises:
ValueError – If the POSCAR does not match the POTCAR or if basis information is missing.
- classmethod standard_calculations_from_vasp_files(POSCAR_input: PathLike = 'POSCAR', INCAR_input: PathLike = 'INCAR', POTCAR_input: PathLike | None = None, Vasprun_output: PathLike = 'vasprun.xml', dict_for_basis: dict | None = None, option: str = 'standard') Self[source]
Generate lobsterin with standard settings.
- Parameters:
POSCAR_input (PathLike) – path to POSCAR
INCAR_input (PathLike) – path to INCAR
POTCAR_input (PathLike) – path to POTCAR
Vasprun_output (PathLike) – path to vasprun.xml
dict_for_basis (dict) – can be provided: it should look the following: dict_for_basis={“Fe”:’3p 3d 4s 4f’, “C”: ‘2s 2p’} and will overwrite all settings from POTCAR_input
option (str) – ‘standard’ will start a normal LOBSTER run where COHPs, COOPs, DOS, CHARGE etc. will be calculated ‘standard_with_energy_range_from_vasprun’ will start a normal LOBSTER run for entire energy range of VASP static run. vasprun.xml file needs to be in current directory. ‘standard_from_projection’ will start a normal LOBSTER run from a projection ‘standard_with_fatband’ will do a fatband calculation, run over all orbitals ‘onlyprojection’ will only do a projection ‘onlydos’ will only calculate a projected dos ‘onlycohp’ will only calculate cohp ‘onlycoop’ will only calculate coop ‘onlycohpcoop’ will only calculate cohp and coop
- Returns:
Lobsterin with standard settings
- write_INCAR(incar_input: PathLike = 'INCAR', incar_output: PathLike = 'INCAR.lobster', poscar_input: PathLike = 'POSCAR', isym: Literal[-1, 0] = 0, further_settings: dict | None = None) None[source]
Writes a modified INCAR file for LOBSTER calculations.
- Parameters:
incar_input (PathLike) – Path to the input INCAR file.
incar_output (PathLike) – Path to the output INCAR file.
poscar_input (PathLike) – Path to the input POSCAR file.
isym (Literal[-1, 0]) – ISYM value to set. Defaults to 0.
further_settings (dict | None) – Additional settings to include in the INCAR file.
- Raises:
ValueError – If isym is not -1 or 0.
- static write_KPOINTS(POSCAR_input: PathLike = 'POSCAR', KPOINTS_output: PathLike = 'KPOINTS.lobster', reciprocal_density: int = 100, isym: Literal[-1, 0] = 0, from_grid: bool = False, input_grid: tuple[int, int, int] = (5, 5, 5), line_mode: bool = True, kpoints_line_density: int = 20, symprec: float = 0.01) None[source]
Write a gamma-centered KPOINTS file for LOBSTER.
- Parameters:
POSCAR_input (PathLike) – path to POSCAR
KPOINTS_output (PathLike) – path to output KPOINTS
reciprocal_density (int) – Grid density
isym (-1 | 0) – ISYM value.
from_grid (bool) – If True KPOINTS will be generated with the help of a grid given in input_grid. Otherwise, they will be generated from the reciprocal_density
input_grid (tuple) – grid to generate the KPOINTS file
line_mode (bool) – If True, band structure will be generated
kpoints_line_density (int) – density of the lines in the band structure
symprec (float) – precision to determine symmetry
- static write_POSCAR_with_standard_primitive(POSCAR_input: PathLike = 'POSCAR', POSCAR_output: PathLike = 'POSCAR.lobster', symprec: float = 0.01) None[source]
Writes a POSCAR file with the standard primitive cell.
- Parameters:
POSCAR_input (PathLike) – Path to the input POSCAR file.
POSCAR_output (PathLike) – Path to the output POSCAR file.
symprec (float) – Precision for symmetry determination. Defaults to 0.01.
- write_lobsterin(path: PathLike = 'lobsterin', overwritedict: dict | None = None) None[source]
Writes the LobsterIn object to a lobsterin file.
- Parameters:
path (PathLike) – The output file path. Defaults to “lobsterin”.
overwritedict (dict | None) – A dictionary of settings to overwrite before writing.
- get_all_possible_basis_combinations(min_basis: list, max_basis: list) list[list[str]][source]
Get all possible basis combinations.
- Parameters:
min_basis – list of basis entries: e.g., [“Si 3p 3s”]
max_basis – list of basis entries: e.g., [“Si 3p 3s”].
- Returns:
all possible combinations of basis functions, e.g. [[“Si 3p 3s”]]
- Return type:
list[list[str]]
pymatgen.io.lobster.future.lobsterenv module
Deprecated class for analyzing NearNeighbors using ICOHPs/ICOOPs/ICOBIs.
pymatgen.io.lobster.future.types module
- class LobsterBandOverlaps[source]
Bases:
TypedDictDictionary representing band overlaps in LOBSTER.
- class LobsterFatband[source]
Bases:
TypedDictDictionary representing fatband data in LOBSTER.
- class LobsterFatbands[source]
Bases:
TypedDictDictionary representing multiple fatbands in LOBSTER.
- bands[source]
List of fatband dictionaries.
- Type:
list[LobsterFatband]
- bands: list[LobsterFatband][source]
- class LobsterInteraction[source]
Bases:
TypedDictDictionary representing a chemical interaction in LOBSTER.
This dictionary stores information about a specific interaction between atoms in a structure.
- centers[source]
List of strings representing the centers of the interaction (e.g., “Fe1”, “O2”).
- Type:
list[str]
- cells[source]
List of lists of integers representing the cells of the interaction
- Type:
list[list[int]] | NDArray[integer]
- (e.g., [0, 0, 0]).
- orbitals[source]
List of strings representing the orbitals involved in the interaction
- Type:
list[str | None]
- (e.g., "2s", "2p_x").
pymatgen.io.lobster.future.utils module
- convert_spin_keys(obj: Any) Any[source]
Convert an object to a JSON-compatible format recursively.
This function ensures that the input object is converted into a format that can be serialized into JSON. It handles lists, tuples, dictionaries, and enums.
- Parameters:
obj (Any) – Input object to convert.
- Returns:
JSON-compatible representation of the input object.
- Return type:
Any
Example
>>> make_json_compatible({"key": Enum("Example", "value")}) {'key': 'value'}
- natural_sort(list_to_sort: str) list[Any][source]
Sort a list of strings in human order.
This function sorts strings in a way that humans would expect, taking into account numerical values within the strings.
- Parameters:
list_to_sort (str) – List of strings to sort.
- Returns:
Sorted list of strings in human order.
- Return type:
list[Any]
Example
>>> natural_sort(["file10", "file2", "file1"]) ['file1', 'file2', 'file10']
- parse_orbital_from_text(text: str) str | None[source]
Parse the orbital from a text string of an ICOXXLIST file.
This function extracts the orbital information from a given text string. It checks for valid orbital patterns and returns the matched orbital.
- Parameters:
text (str) – Text string to parse the orbital from.
- Returns:
Parsed orbital string if a valid orbital is found, otherwise None.
- Return type:
str | None
Example
>>> parse_orbital_from_text("1s_2p_x") '2p_x'
- restore_spin_keys(obj: Any) Any[source]
Restore Spin enum keys from JSON-serialized format.
This function recursively processes an object and converts string keys “1” and “-1” back to Spin.up and Spin.down enum values. It handles nested lists, tuples, and dictionaries.
- Parameters:
obj (Any) – Input object with potential Spin keys as strings.
- Returns:
Object with Spin enum keys restored.
- Return type:
Any
Example
>>> restore_spin_keys({"1": [1, 2], "-1": [3, 4]}) {<Spin.up: 1>: [1, 2], <Spin.down: -1>: [3, 4]}