pymatgen.io.lobster package

Submodules

pymatgen.io.lobster.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, MSONable

Handle and generate lobsterin files. Furthermore, it can also modify INCAR files for LOBSTER, generate KPOINTS files for fatband calculations in LOBSTER, and generate the standard primitive cells in a POSCAR file that are needed for the fatband calculations. There are also several standard lobsterin files that can be easily generated.

Reminder: lobsterin keywords are not case sensitive.

Parameters:

settingsdict – dict to initialize Lobsterin.

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]

MSONable dict.

diff(other: Self) → dict[str, dict[str, Any]][source]

Compare two Lobsterin and find which parameters are the same. Similar to the diff method of Incar.

Parameters:

other (Lobsterin) – Lobsterin object to compare to.

Returns:

{“Same”: same_params, “Different”: diff_params}

Return type:

dict

classmethod from_dict(dct: dict) → Self[source]

Parameters:

dct (dict) – Dict representation.

Returns:

Lobsterin

classmethod from_file(lobsterin: PathLike) → Self[source]

Create Lobsterin from lobsterin file.

Parameters:

lobsterin (PathLike) – path to lobsterin.

Returns:

Lobsterin object

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]

Get the basis functions from given potcar_symbols, e.g., [“Fe_pv”, “Si”].

Parameters:

• structure (Structure) – Structure object

• potcar_symbols – list of potcar symbols

• address_basis_file (PathLike) – path to the basis file

Returns:

basis

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]

Write INCAR file. Will only make the run static, insert NBANDS, set ISYM=0, LWAVE=True and you have to check for the rest.

Parameters:

• incar_input (PathLike) – path to input INCAR

• incar_output (PathLike) – path to output INCAR

• poscar_input (PathLike) – path to input POSCAR

• isym (-1 | 0) – ISYM value.

• further_settings (dict) – A dict can be used to include further settings, e.g. {“ISMEAR”:-5}

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]

Write a POSCAR with the standard primitive cell. This is needed to arrive at the correct kpath.

Parameters:

• POSCAR_input (PathLike) – Input POSCAR file

• POSCAR_output (PathLike) – Output POSCAR file

• symprec (float) – precision to find symmetry

write_lobsterin(path: PathLike = 'lobsterin', overwritedict: dict | None = None) → None[source]

Write a lobsterin file, and recover keys to Camel case.

Parameters:

• path (str) – filename of the output lobsterin file

• overwritedict (dict) – dict that can be used to update lobsterin, e.g. {“skipdos”: True}

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.lobsterenv module

This module provides classes to perform analyses of the local environments (e.g., finding near neighbors) of single sites in molecules and structures based on bonding analysis with LOBSTER.

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 ICOHPNeighborsInfo(total_icohp: float, list_icohps: list[float], n_bonds: int, labels: list[str], atoms: list[list[str]], central_isites: list[int] | None)[source]

Bases: NamedTuple

Tuple to record information on relevant bonds.

Parameters:

• total_icohp (float) – Sum of ICOHP values of neighbors to the selected sites (given by the index in structure).

• list_icohps (list) – Summed ICOHP values for all identified interactions with neighbors.

• n_bonds (int) – Number of identified bonds to the selected sites.

• labels (list[str]) – Labels (from ICOHPLIST) for all identified bonds.

• atoms (list[list[str]]) – Lists describing the species present (from ICOHPLIST) in the identified interactions , e.g. [“Ag3”, “O5”].

• central_isites (list[int]) – The central site indexes for each identified interaction.

Create new instance of ICOHPNeighborsInfo(total_icohp, list_icohps, n_bonds, labels, atoms, central_isites)

atoms: list[list[str]][source]

Alias for field number 4

central_isites: list[int] | None[source]

Alias for field number 5

labels: list[str][source]

Alias for field number 3

list_icohps: list[float][source]

Alias for field number 1

n_bonds: int[source]

Alias for field number 2

total_icohp: float[source]

Alias for field number 0

class LobsterLightStructureEnvironments(strategy, coordination_environments=None, all_nbs_sites=None, neighbors_sets=None, structure=None, valences=None, valences_origin=None)[source]

Bases: LightStructureEnvironments

Store LightStructureEnvironments based on LOBSTER outputs.

Constructor for the LightStructureEnvironments object.

Parameters:

• strategy – ChemEnv strategy used to get the environments.

• coordination_environments – The coordination environments identified.

• all_nbs_sites – All the possible neighbors for each site in the structure.

• neighbors_sets – The neighbors sets of each site in the structure.

• structure – The structure.

• valences – The valences used to get the environments (if needed).

• valences_origin – How the valences were obtained (e.g. from the Bond-valence analysis or from the original structure).

as_dict() → dict[str, Any][source]

Bson-serializable dict representation of the object.

Returns:

Bson-serializable dict representation.

classmethod from_Lobster(list_ce_symbol: list[str], list_csm: list[float], list_permutation: list, list_neighsite: list[PeriodicSite], list_neighisite: list[list[int]], structure: Structure | IStructure, valences: list[float] | None = None) → Self[source]

Set up a LightStructureEnvironments from LOBSTER.

Parameters:

• list_ce_symbol (list[str]) – Coordination environments symbols.

• list_csm (list[float]) – Continuous symmetry measures.

• list_permutation (list) – Permutations.

• list_neighsite (list[PeriodicSite]) – Neighboring sites.

• list_neighisite (list[list[int]]) – Neighboring sites indexes.

• structure (Structure) – Structure object.

• valences (list[float]) – Valences.

Returns:

LobsterLightStructureEnvironments

property uniquely_determines_coordination_environments: Literal[True][source]

Whether the coordination environments are uniquely determined.

class LobsterNeighbors(structure: Structure | IStructure, filename_icohp: PathLike | None = 'ICOHPLIST.lobster', obj_icohp: Icohplist | None = None, are_coops: bool = False, are_cobis: bool = False, valences: list[float] | None = None, limits: tuple[float, float] | None = None, additional_condition: Literal[0, 1, 2, 3, 4, 5, 6] = 0, only_bonds_to: list[str] | None = None, perc_strength_icohp: float = 0.15, noise_cutoff: float = 0.1, valences_from_charges: bool = False, filename_charge: PathLike | None = None, obj_charge: Charge | None = None, which_charge: Literal['Mulliken', 'Loewdin'] = 'Mulliken', adapt_extremum_to_add_cond: bool = False, add_additional_data_sg: bool = False, filename_blist_sg1: PathLike | None = None, filename_blist_sg2: PathLike | None = None, id_blist_sg1: Literal['icoop', 'icobi'] = 'icoop', id_blist_sg2: Literal['icoop', 'icobi'] = 'icobi')[source]

Bases: NearNeighbors

This class combines capabilities from LocalEnv and ChemEnv to determine coordination environments based on bonding analysis.

Parameters:

• filename_icohp (PathLike) – Path to ICOHPLIST.lobster or ICOOPLIST.lobster or ICOBILIST.lobster.

• obj_icohp (Icohplist) – Icohplist object.

• structure (Structure) – Typically constructed by Structure.from_file(“POSCAR”).

• are_coops (bool) – Whether the file is a ICOOPLIST.lobster (True) or a ICOHPLIST.lobster (False). Only tested for ICOHPLIST.lobster so far.

• are_cobis (bool) – Whether the file is a ICOBILIST.lobster (True) or a ICOHPLIST.lobster (False).

• valences (list[float]) – Valence/charge for each element.

• limits (tuple[float, float]) – Range to decide which ICOHPs (ICOOP or ICOBI) should be considered.

• additional_condition (int) –

  Additional condition that decides which kind of bonds will be considered:

  0 - NO_ADDITIONAL_CONDITION 1 - ONLY_ANION_CATION_BONDS 2 - NO_ELEMENT_TO_SAME_ELEMENT_BONDS 3 - ONLY_ANION_CATION_BONDS_AND_NO_ELEMENT_TO_SAME_ELEMENT_BONDS 4 - ONLY_ELEMENT_TO_OXYGEN_BONDS 5 - DO_NOT_CONSIDER_ANION_CATION_BONDS 6 - ONLY_CATION_CATION_BONDS

• only_bonds_to (list[str]) – Only consider bonds to certain elements (e.g. [“O”] for oxygen).

• perc_strength_icohp (float) – If no “limits” are given, this will decide which ICOHPs will be considered (relative to the strongest ICOHP/ICOOP/ICOBI).

• noise_cutoff (float) – The lower limit of ICOHPs considered.

• valences_from_charges (bool) – If True and path to CHARGE.lobster is provided, will use LOBSTER charges (Mulliken) instead of valences.

• filename_charge (PathLike) – Path to Charge.lobster.

• obj_charge (Charge) – Charge object.

• which_charge ("Mulliken" | "Loewdin") – Source of charge.

• adapt_extremum_to_add_cond (bool) – Whether to adapt the limits to only focus on the bonds determined by the additional condition.

• add_additional_data_sg (bool) – Add the information from filename_add_bondinglist_sg1.

• filename_blist_sg1 (PathLike) – Path to additional ICOOP, ICOBI data for structure graphs.

• filename_blist_sg2 (PathLike) – Path to additional ICOOP, ICOBI data for structure graphs.

• id_blist_sg1 ("icoop" | "icobi") – Identity of data in filename_blist_sg1.

• id_blist_sg2 ("icoop" | "icobi") – Identity of data in filename_blist_sg2.

property anion_types: set[Element][source]

The set of anion types in crystal structure.

Returns:

Anions in the crystal structure.

Return type:

set[Element]

get_anion_types() → set[Element][source]

get_info_cohps_to_neighbors(path_to_cohpcar: PathLike | None = 'COHPCAR.lobster', obj_cohpcar: CompleteCohp | None = None, isites: list[int] | None = None, only_bonds_to: list[str] | None = None, onlycation_isites: bool = True, per_bond: bool = True, summed_spin_channels: bool = False) → tuple[str | None, CompleteCohp | None][source]

Get the COHPs (COOPs or COBIs) as a summed Cohp object and a label from all sites mentioned in isites with neighbors.

Parameters:

• path_to_cohpcar (PathLike) – Path to COHPCAR/COOPCAR/COBICAR.

• obj_cohpcar (CompleteCohp) – CompleteCohp object.

• isites (list[int]) – The indexes of the sites.

• only_bonds_to (list[str]) – Only show COHPs to selected element, e.g. [“O”].

• onlycation_isites (bool) – If isites is None, only cation sites will be returned.

• per_bond (bool) – Whether to normalize per bond.

• summed_spin_channels (bool) – Whether to sum both spin channels.

Returns:

Label for COHP. CompleteCohp: Describe all COHPs/COOPs/COBIs of the sites

as given by isites and the other arguments.

Return type:

str

get_info_icohps_between_neighbors(isites: list[int] | None = None, onlycation_isites: bool = True) → ICOHPNeighborsInfo[source]

Get interactions between neighbors of certain sites.

Parameters:

• isites (list[int]) – Site IDs. If is None, all sites will be used.

• onlycation_isites (bool) – Only use cations, if isite is None.

Returns:

ICOHPNeighborsInfo

get_info_icohps_to_neighbors(isites: list[int] | None = None, onlycation_isites: bool = True) → ICOHPNeighborsInfo[source]

Get information on the ICOHPs of neighbors for certain sites as identified by their site id.

This is useful for plotting the COHPs (ICOOPLIST.lobster/ ICOHPLIST.lobster/ICOBILIST.lobster) of a site in the structure.

Parameters:

• isites (list[int]) – Site IDs. If is None, all isites will be used to add the ICOHPs of the neighbors.

• onlycation_isites (bool) – If True and if isite is None, will only analyse the cations sites.

Returns:

ICOHPNeighborsInfo

get_light_structure_environment(only_cation_environments: bool = False, only_indices: list[int] | None = None) → LobsterLightStructureEnvironments[source]

Get a LobsterLightStructureEnvironments object if the structure only contains coordination environments smaller 13.

Parameters:

• only_cation_environments (bool) – Only return data for cations.

• only_indices (list[int]) – Only evaluate indexes in this list.

Returns:

LobsterLightStructureEnvironments

get_nn_info(structure: Structure | IStructure, n: int, use_weights: bool = False) → dict[str, Any][source]

Get coordination number (CN) of site by index.

Parameters:

• structure (Structure) – Input structure.

• n (int) – Index of site for which to determine CN.

• use_weights (bool) – Whether to use weights for computing the CN (True), or each coordinated site has equal weight (False). The former is not implemented yet.

Raises:

ValueError – If use_weights is True, or if arg “structure” and structure used to initialize LobsterNeighbors have different lengths.

Returns:

coordination number and a list of nearest neighbors.

Return type:

dict[str, Any]

property molecules_allowed: Literal[False][source]

Whether this LobsterNeighbors class can be used with Molecule objects.

plot_cohps_of_neighbors(path_to_cohpcar: PathLike | None = 'COHPCAR.lobster', obj_cohpcar: CompleteCohp | None = None, isites: list[int] | None = None, onlycation_isites: bool = True, only_bonds_to: list[str] | None = None, per_bond: bool = False, summed_spin_channels: bool = False, xlim: tuple[float, float] | None = None, ylim: tuple[float, float] = (-10, 6), integrated: bool = False) → mpl.axes.Axes[source]

Plot summed COHPs or COBIs or COOPs.

Please be careful in the spin polarized case (plots might overlap).

Parameters:

• path_to_cohpcar (PathLike) – Path to COHPCAR or COOPCAR or COBICAR.

• obj_cohpcar (CompleteCohp) – CompleteCohp object

• isites (list[int]) – Site IDs. If empty, all sites will be used to add the ICOHPs of the neighbors.

• onlycation_isites (bool) – Only use cations, if isite is empty.

• only_bonds_to (list[str]) – Only anions in this list will be considered.

• per_bond (bool) – Whether to plot a normalization of the plotted COHP per number of bond (True), or the sum (False).

• xlim (tuple[float, float]) – Limits of x values.

• ylim (tuple[float, float]) – Limits of y values.

• integrated (bool) – Whether to show integrated COHP instead of COHP.

Returns:

plt of the COHPs or COBIs or COOPs.

property structures_allowed: Literal[True][source]

Whether this LobsterNeighbors class can be used with Structure objects.

pymatgen.io.lobster.outputs module

Module for reading Lobster output 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 Bandoverlaps(filename: PathLike = 'bandOverlaps.lobster', band_overlaps_dict: dict[Spin, dict] | None = None, max_deviation: list[float] | None = None)[source]

Bases: MSONable

Read bandOverlaps.lobster files, which are not created during every LOBSTER run.

band_overlaps_dict[source]

A dictionary containing the band overlap data of the form: {spin: {“kpoint as string”: {“maxDeviation”: float that describes the max deviation, “matrix”: 2D array of the size number of bands times number of bands including the overlap matrices with}}}.

Type:

dict[Spin, Dict[str, Dict[str, Union[float, NDArray]]]]

max_deviation[source]

The maximal deviation for each problematic kpoint.

Type:

list[float]

Parameters:

• filename (PathLike) – The “bandOverlaps.lobster” file.

• band_overlaps_dict –

  The band overlap data of the form: {

  spin: {

  “k_points” : list of k-point array, “max_deviations”: list of max deviations associated with each k-point, “matrices”: list of the overlap matrices associated with each k-point,

  }

  }.

• max_deviation (list[float]) – The maximal deviations for each problematic k-point.

property bandoverlapsdict: dict[source]

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 the deviation from the ideal bandoverlap of all occupied bands is smaller or equal to limit_deviation.

Parameters:

• number_occ_bands_spin_up (int) – Number of occupied bands of spin up.

• number_occ_bands_spin_down (int) – Number of occupied bands of spin down.

• spin_polarized (bool) – Whether this is a spin polarized calculation.

• limit_deviation (float) – Upper limit of the maxDeviation.

Returns:

True if the quality of the projection is good.

Return type:

bool

has_good_quality_maxDeviation(limit_maxDeviation: float = 0.1) → bool[source]

Check if the maxDeviation from the ideal bandoverlap is smaller or equal to a limit.

Parameters:

limit_maxDeviation (float) – Upper Limit of the maxDeviation.

Returns:

Whether the ideal bandoverlap is smaller or equal to the limit.

Return type:

bool

class Bwdf(filename: PathLike = 'BWDF.lobster', centers: NDArray | None = None, bwdf: dict[Spin, NDArray] | None = None, bin_width: float | None = None)[source]

Bases: MSONable

Read BWDF.lobster/BWDFCOHP.lobster file generated by LOBSTER.

centers[source]

Bond length centers for the distribution.

Type:

NDArray

bwdf[source]

Bond weighted distribution function.

Type:

dict[Spin, NDArray]

bin_width[source]

Bin width used for computing the distribution by LOBSTER.

Type:

float

Parameters:

• filename (PathLike) – The “BWDF.lobster” file. Can also read BWDFCOHP.lobster.

• centers (NDArray) – Bond length centers for the distribution.

• bwdf (dict[Spin, NDArray]) – Bond weighted distribution function.

• bin_width (float) – Bin width used for computing the distribution by LOBSTER.

class Charge(filename: PathLike = 'CHARGE.lobster', is_lcfo: bool = False, num_atoms: int | None = None, atomlist: list[str] | None = None, types: list[str] | None = None, mulliken: list[float] | None = None, loewdin: list[float] | None = None)[source]

Bases: MSONable

Read CHARGE.lobster/ CHARGE.LCFO.lobster files generated by LOBSTER.

atomlist[source]

List of atoms in CHARGE.lobster.

Type:

list[str]

is_lcfo[source]

Whether the CHARGE file is from LCFO analysis. Default is False.

Type:

bool

types[source]

List of types of atoms in CHARGE.lobster.

Type:

list[str]

mulliken[source]

List of Mulliken charges of atoms in CHARGE.lobster.

Type:

list[float]

loewdin[source]

List of Loewdin charges of atoms in CHARGE.Loewdin.

Type:

list[float]

num_atoms[source]

Number of atoms in CHARGE.lobster.

Type:

int

Parameters:

• filename (PathLike) – The CHARGE file, typically “CHARGE.lobster”.

• is_lcfo (bool) – Whether the CHARGE file is from LCFO analysis. Default is False.

• num_atoms (int) – Number of atoms in the structure.

• atomlist (list[str]) – Atoms in the structure.

• types (list[str]) – Unique species in the structure.

• mulliken (list[float]) – Mulliken charges.

• loewdin (list[float]) – Loewdin charges.

property Loewdin: list[float][source]

property Mulliken: list[float][source]

get_structure_with_charges(structure_filename: PathLike) → Structure[source]

Get a Structure with Mulliken and Loewdin charges as site properties

Parameters:

structure_filename (PathLike) – The POSCAR file.

Returns:

Structure Object with Mulliken and Loewdin charges as site properties.

class Cohpcar(are_coops: bool = False, are_cobis: bool = False, are_multi_center_cobis: bool = False, is_lcfo: bool = False, filename: PathLike | None = None)[source]

Bases: object

Read COXXCAR.lobster/COXXCAR.LCFO.lobster files generated by LOBSTER.

cohp_data[source]

The COHP data of the form: {bond: {“COHP”: {Spin.up: cohps, Spin.down:cohps},

“ICOHP”: {Spin.up: icohps, Spin.down: icohps}, “length”: bond length, “sites”: sites corresponding to the bond}

Also contains an entry for the average, which does not have a “length” key.

Type:

dict[str, Dict[str, Any]]

efermi[source]

The Fermi level in eV.

Type:

float

energies[source]

Sequence of energies in eV. Note that LOBSTER shifts the energies so that the Fermi level is at zero.

Type:

Sequence[float]

is_spin_polarized[source]

True if the calculation is spin polarized.

Type:

bool

orb_res_cohp[source]

The orbital-resolved COHPs of the form: orb_res_cohp[label] = {bond_data[“orb_label”]: {

“COHP”: {Spin.up: cohps, Spin.down:cohps}, “ICOHP”: {Spin.up: icohps, Spin.down: icohps}, “orbitals”: orbitals, “length”: bond lengths, “sites”: sites corresponding to the bond},

}

Type:

dict[str, Dict[str, Dict[str, Any]]]

Parameters:

• are_coops (bool) – Whether the file includes COOPs (True) or COHPs (False). Default is False.

• are_cobis (bool) – Whether the file is COBIs (True) or COHPs (False). Default is False.

• are_multi_center_cobis (bool) – Whether the file include multi-center COBIs (True) or two-center COBIs (False). Default is False.

• is_lcfo (bool) – Whether the COXXCAR file is from LCFO analysis.

• filename (PathLike) – The COHPCAR file. If it is None, the default file name will be chosen, depending on the value of are_coops.

class Doscar(doscar: PathLike = 'DOSCAR.lobster', is_lcfo: bool = False, structure_file: PathLike | None = 'POSCAR', structure: IStructure | Structure | None = None)[source]

Bases: object

Store LOBSTER’s projected DOS and local projected DOS. The beforehand quantum-chemical calculation was performed with VASP.

completedos[source]

LobsterCompleteDos Object.

Type:

LobsterCompleteDos

pdos[source]

List of Dict including NumPy arrays with pdos. Access as pdos[atomindex][‘orbitalstring’][‘Spin.up/Spin.down’].

Type:

list

tdos[source]

Dos Object of the total density of states.

Type:

Dos

energies[source]

Numpy array of the energies at which the DOS was calculated (in eV, relative to Efermi).

Type:

NDArray

tdensities[source]

tdensities[Spin.up]: NumPy array of the total density of states for the Spin.up contribution at each of the energies. tdensities[Spin.down]: NumPy array of the total density of states for the Spin.down contribution at each of the energies. If is_spin_polarized=False, tdensities[Spin.up]: NumPy array of the total density of states.

Type:

dict

itdensities[source]

itdensities[Spin.up]: NumPy array of the total density of states for the Spin.up contribution at each of the energies. itdensities[Spin.down]: NumPy array of the total density of states for the Spin.down contribution at each of the energies. If is_spin_polarized=False, itdensities[Spin.up]: NumPy array of the total density of states.

Type:

dict

is_spin_polarized[source]

Whether the system is spin polarized.

Type:

bool

Parameters:

• doscar (PathLike) – The DOSCAR file, typically “DOSCAR.lobster”.

• is_lcfo (bool) – Whether the DOSCAR file is from LCFO analysis.

• structure_file (PathLike) – For VASP, this is typically “POSCAR”.

• structure (Structure) – Instead of a structure file (preferred), the Structure can be given directly.

property completedos: LobsterCompleteDos[source]

LobsterCompleteDos.

property energies: NDArray[source]

Energies.

property is_spin_polarized: bool[source]

Whether run is spin polarized.

property itdensities: dict[Spin, NDArray][source]

Integrated total DOS as a np.array.

property pdos: list[dict][source]

Projected DOS (PDOS).

property tdensities: dict[Spin, NDArray][source]

Total DOS as a np.array.

property tdos: Dos[source]

Total DOS (TDOS).

class Fatband(filenames: PathLike | list[PathLike] = '.', kpoints_file: PathLike = 'KPOINTS', vasprun_file: PathLike | None = 'vasprun.xml', structure: Structure | IStructure | None = None, efermi: float | None = None)[source]

Bases: object

Read FATBAND_x_y.lobster files.

efermi[source]

Fermi level read from vasprun.xml.

Type:

float

eigenvals[source]

Eigenvalues as a dictionary of NumPy arrays of shape (nbands, nkpoints). The first index of the array refers to the band and the second to the index of the kpoint. The kpoints are ordered according to the order of the kpoints_array attribute. If the band structure is not spin polarized, we only store one data set under Spin.up.

Type:

dict[Spin, NDArray]

is_spin_polarized[source]

Whether this was a spin-polarized calculation.

Type:

bool

kpoints_array[source]

List of kpoints as NumPy arrays, in frac_coords of the given lattice by default.

Type:

list[NDArray]

label_dict[source]

Dictionary that links a kpoint (in frac coords or Cartesian coordinates depending on the coords attribute) to a label.

Type:

dict[str, Union[str, NDArray]]

lattice[source]

Lattice object of reciprocal lattice as read from vasprun.xml.

Type:

Lattice

nbands[source]

Number of bands used in the calculation.

Type:

int

p_eigenvals[source]

Dictionary of orbital projections as {spin: array of dict}. The indices of the array are [band_index, kpoint_index]. The dict is then built the following way: {“string of element”: “string of orbital as read in from FATBAND file”}. If the band structure is not spin polarized, we only store one data set under Spin.up.

Type:

dict[Spin, NDArray]

structure[source]

Structure object.

Type:

Structure

Parameters:

• filenames (PathLike | list[PathLike]) – File names or path to a folder from which all “FATBAND_*” files will be read.

• kpoints_file (PathLike) – KPOINTS file for bandstructure calculation, typically “KPOINTS”.

• vasprun_file (PathLike) – Corresponding vasprun.xml file. Instead, the Fermi level from the DFT run can be provided. Then, this should be set to None.

• structure (Structure) – Structure object.

• efermi (float) – Fermi level in eV.

get_bandstructure() → LobsterBandStructureSymmLine[source]

Get a LobsterBandStructureSymmLine object which can be plotted with a normal BSPlotter.

class Grosspop(filename: PathLike = 'GROSSPOP.lobster', is_lcfo: bool = False, list_dict_grosspop: list[dict] | None = None)[source]

Bases: MSONable

Read GROSSPOP.lobster/ GROSSPOP.LCFO.lobster files.

list_dict_grosspop[source]

List of dictionaries including all information about the grosspopulations. Each dictionary contains the following keys: - ‘element’: The element symbol of the atom. - ‘Mulliken GP’: A dictionary of Mulliken gross populations, where the keys are the orbital labels and the

values are the corresponding gross populations as strings.

• ‘Loewdin GP’: A dictionary of Loewdin gross populations, where the keys are the orbital labels and the

  values are the corresponding gross populations as strings.

The 0th entry of the list refers to the first atom in GROSSPOP.lobster and so on.

Type:

list[dict[str, str| dict[str, str]]]

Parameters:

• filename (PathLike) – The “GROSSPOP.lobster” file.

• is_lcfo (bool) – Whether the GROSSPOP file is in LCFO format.

• list_dict_grosspop (list[dict]) – All information about the gross populations.

get_structure_with_total_grosspop(structure_filename: PathLike) → Structure[source]

Get a Structure with Mulliken and Loewdin total grosspopulations as site properties.

Parameters:

structure_filename (PathLike) – The POSCAR file.

Returns:

Structure Object with Mulliken and Loewdin total grosspopulations as site properties.

class Icohplist(is_lcfo: bool = False, are_coops: bool = False, are_cobis: bool = False, filename: PathLike | None = None, is_spin_polarized: bool = False, orbitalwise: bool = False, icohpcollection: IcohpCollection | None = None)[source]

Bases: MSONable

Read ICOXXLIST/ICOXXLIST.LCFO.lobster files generated by LOBSTER.

are_coops[source]

Whether the file includes COOPs (True) or COHPs (False).

Type:

bool

is_lcfo[source]

Whether the ICOXXLIST file is from LCFO analysis.

Type:

bool

is_spin_polarized[source]

Whether the calculation is spin polarized.

Type:

bool

Icohplist[source]

The listfile data of the form: {

bond: {

“length”: Bond length, “number_of_bonds”: Number of bonds, “icohp”: {Spin.up: ICOHP(Ef)_up, Spin.down: …}, }

}

Type:

dict[str, Dict[str, Union[float, int, Dict[Spin, float]]]]

IcohpCollection[source]

IcohpCollection Object.

Type:

IcohpCollection

Parameters:

• is_lcfo (bool) – Whether the ICOHPLIST file is from LCFO analysis.

• are_coops (bool) – Whether the file includes COOPs (True) or COHPs (False). Default is False.

• are_cobis (bool) – Whether the file is COBIs (True) or COHPs (False). Default is False.

• filename (PathLike) – The ICOHPLIST file. If it is None, the default file name will be chosen, depending on the value of are_coops

• is_spin_polarized (bool) – Whether the calculation is spin polarized.

• orbitalwise (bool) – Whether the calculation is orbitalwise.

• icohpcollection (IcohpCollection) – IcohpCollection Object.

property icohpcollection: IcohpCollection | None[source]

The IcohpCollection object.

property icohplist: dict[Any, dict[str, Any]][source]

The ICOHP list compatible with older version of this class.

class LobsterMatrices(e_fermi: float | None = None, filename: PathLike = 'hamiltonMatrices.lobster')[source]

Bases: object

Read Matrices file generated by LOBSTER (e.g. hamiltonMatrices.lobster).

If filename == "hamiltonMatrices.lobster"

onsite_energies (list[NDArray]): Real parts of onsite energies from the

matrices each k-point.

average_onsite_energies (dict): Average onsite elements energies for

all k-points with keys as basis used in the LOBSTER computation (uses only real part of matrix).

hamilton_matrices (dict[Spin, NDArray]): The complex Hamilton matrix at each

k-point with k-point and spin as keys.

If filename == "coefficientMatrices.lobster"

onsite_coefficients (list[NDArray]): Real parts of onsite coefficients

from the matrices each k-point.

average_onsite_coefficient (dict): Average onsite elements coefficients

for all k-points with keys as basis used in the LOBSTER computation (uses only real part of matrix).

coefficient_matrices (dict[Spin, NDArray]): The coefficients matrix

at each k-point with k-point and spin as keys.

If filename == "transferMatrices.lobster"

onsite_transfer (list[NDArray]): Real parts of onsite transfer

coefficients from the matrices at each k-point.

average_onsite_transfer (dict): Average onsite elements transfer

coefficients for all k-points with keys as basis used in the LOBSTER computation (uses only real part of matrix).

transfer_matrices (dict[Spin, NDArray]): The coefficients matrix at

each k-point with k-point and spin as keys.

If filename == "overlapMatrices.lobster"

onsite_overlaps (list[NDArray]): Real parts of onsite overlaps

from the matrices each k-point.

average_onsite_overlaps (dict): Average onsite elements overlaps

for all k-points with keys as basis used in the LOBSTER computation (uses only real part of matrix).

overlap_matrices (dict[NDArray]): The overlap matrix at

each k-point with k-point as keys.

Parameters:

• e_fermi (float) – Fermi level in eV for the structure only. Relevant if input file contains Hamilton matrices data.

• filename (PathLike) – The hamiltonMatrices file, typically “hamiltonMatrices.lobster”.

class Lobsterout(filename: PathLike | None, **kwargs)[source]

Bases: MSONable

Read the lobsterout and evaluate the spilling, save the basis, save warnings, save info.

basis_functions[source]

Basis functions that were used in lobster run as strings.

Type:

list[str]

basis_type[source]

Basis types that were used in lobster run as strings.

Type:

list[str]

charge_spilling[source]

Charge spilling (first entry: result for spin 1, second entry: result for spin 2 or not present).

Type:

list[float]

dft_program[source]

The DFT program used for the calculation of the wave function.

Type:

str

elements[source]

Elements that were present in LOBSTER calculation.

Type:

list[str]

has_charge[source]

Whether CHARGE.lobster is present.

Type:

bool

has_cohpcar[source]

Whether COHPCAR.lobster and ICOHPLIST.lobster are present.

Type:

bool

has_madelung[source]

Whether SitePotentials.lobster and MadelungEnergies.lobster are present.

Type:

bool

has_coopcar[source]

Whether COOPCAR.lobster and ICOOPLIST.lobster are present.

Type:

bool

has_cobicar[source]

Whether COBICAR.lobster and ICOBILIST.lobster are present.

Type:

bool

has_doscar[source]

Whether DOSCAR.lobster is present.

Type:

bool

has_doscar_lso[source]

Whether DOSCAR.LSO.lobster is present.

Type:

bool

has_projection[source]

Whether projectionData.lobster is present.

Type:

bool

has_bandoverlaps[source]

Whether bandOverlaps.lobster is present.

Type:

bool

has_density_of_energies[source]

Whether DensityOfEnergy.lobster is present.

Type:

bool

has_fatbands[source]

Whether fatband calculation was performed.

Type:

bool

has_grosspopulation[source]

Whether GROSSPOP.lobster is present.

Type:

bool

has_polarization[source]

Whether POLARIZATION.lobster is present.

Type:

bool

info_lines[source]

Additional information on the run.

Type:

str

info_orthonormalization[source]

Information on orthonormalization.

Type:

str

is_restart_from_projection[source]

Whether that calculation was restarted from an existing projection file.

Type:

bool

lobster_version[source]

The LOBSTER version.

Type:

str

number_of_spins[source]

The number of spins.

Type:

int

number_of_threads[source]

How many threads were used.

Type:

int

timing[source]

Dict with infos on timing.

Type:

dict[str, float]

total_spilling[source]

The total spilling for spin channel 1 (and spin channel 2).

Type:

list[float]

warning_lines[source]

String with all warnings.

Type:

str

Parameters:

• filename (PathLike) – The lobsterout file.

• **kwargs – dict to initialize Lobsterout instance

as_dict() → dict[str, Any][source]

MSONable dict.

get_doc() → dict[str, Any][source]

Get a dict with all information stored in lobsterout.

class MadelungEnergies(filename: PathLike = 'MadelungEnergies.lobster', ewald_splitting: float | None = None, madelungenergies_mulliken: float | None = None, madelungenergies_loewdin: float | None = None)[source]

Bases: MSONable

Read MadelungEnergies.lobster files generated by LOBSTER.

madelungenergies_mulliken[source]

The Madelung energy based on the Mulliken approach.

Type:

float

madelungenergies_loewdin[source]

The Madelung energy based on the Loewdin approach.

Type:

float

ewald_splitting[source]

The Ewald splitting parameter to compute SitePotentials.

Type:

float

Parameters:

• filename (PathLike) – The “MadelungEnergies.lobster” file.

• ewald_splitting (float) – The Ewald splitting parameter to compute SitePotentials.

• madelungenergies_mulliken (float) – The Madelung energy based on the Mulliken approach.

• madelungenergies_loewdin (float) – The Madelung energy based on the Loewdin approach.

property madelungenergies_Loewdin: float | None[source]

property madelungenergies_Mulliken: float | None[source]

class NciCobiList(filename: PathLike | None = 'NcICOBILIST.lobster')[source]

Bases: object

Read NcICOBILIST (multi-center ICOBI) files generated by LOBSTER.

is_spin_polarized[source]

Whether the calculation is spin polarized.

Type:

bool

NciCobiList[source]

The listfile data of the form: {

bond: {

“number_of_atoms”: Number of atoms involved in the multi-center interaction, “ncicobi”: {Spin.up: Nc-ICOBI(Ef)_up, Spin.down: …}, “interaction_type”: Type of the multi-center interaction, }

}

Type:

dict

LOBSTER < 4.1.0: no COBI/ICOBI/NcICOBI

Parameters:

filename – Name of the NcICOBILIST file.

property ncicobi_list: dict[Any, dict[str, Any]][source]

Returns: dict: ncicobilist.

class Polarization(filename: PathLike = 'POLARIZATION.lobster', rel_mulliken_pol_vector: dict[str, float | str] | None = None, rel_loewdin_pol_vector: dict[str, float | str] | None = None)[source]

Bases: MSONable

Read POLARIZATION.lobster file generated by LOBSTER.

rel_mulliken_pol_vector[source]

Relative Mulliken polarization vector.

Type:

dict[str, float]

rel_loewdin_pol_vector[source]

Relative Mulliken polarization vector.

Type:

dict[str, float]

Parameters:

• filename (PathLike) – The “POLARIZATION.lobster” file.

• rel_mulliken_pol_vector (dict[str, Union[float, str]]) – Relative Mulliken polarization vector.

• rel_loewdin_pol_vector (dict[str, Union[float, str]]) – Relative Loewdin polarization vector.

class SitePotential(filename: PathLike = 'SitePotentials.lobster', ewald_splitting: float | None = None, num_atoms: int | None = None, atomlist: list[str] | None = None, types: list[str] | None = None, sitepotentials_loewdin: list[float] | None = None, sitepotentials_mulliken: list[float] | None = None, madelungenergies_mulliken: float | None = None, madelungenergies_loewdin: float | None = None)[source]

Bases: MSONable

Read SitePotentials.lobster files generated by LOBSTER.

atomlist[source]

Atoms in SitePotentials.lobster.

Type:

list[str]

types[source]

Types of atoms in SitePotentials.lobster.

Type:

list[str]

num_atoms[source]

Number of atoms in SitePotentials.lobster.

Type:

int

sitepotentials_mulliken[source]

Mulliken potentials of sites in SitePotentials.lobster.

Type:

list[float]

sitepotentials_loewdin[source]

Loewdin potentials of sites in SitePotentials.lobster.

Type:

list[float]

madelungenergies_mulliken[source]

The Madelung energy based on the Mulliken approach.

Type:

float

madelungenergies_loewdin[source]

The Madelung energy based on the Loewdin approach.

Type:

float

ewald_splitting[source]

The Ewald Splitting parameter to compute SitePotentials.

Type:

float

Parameters:

• filename (PathLike) – The SitePotentials file, typically “SitePotentials.lobster”.

• ewald_splitting (float) – Ewald splitting parameter used for computing Madelung energies.

• num_atoms (int) – Number of atoms in the structure.

• atomlist (list[str]) – Atoms in the structure.

• types (list[str]) – Unique atom types in the structure.

• sitepotentials_loewdin (list[float]) – Loewdin site potentials.

• sitepotentials_mulliken (list[float]) – Mulliken site potentials.

• madelungenergies_mulliken (float) – Madelung energy based on the Mulliken approach.

• madelungenergies_loewdin (float) – Madelung energy based on the Loewdin approach.

get_structure_with_site_potentials(structure_filename: PathLike) → Structure[source]

Get a Structure with Mulliken and Loewdin charges as site properties.

Parameters:

structure_filename (PathLike) – The POSCAR file.

Returns:

Structure Object with Mulliken and Loewdin charges as site properties.

property madelungenergies_Loewdin[source]

property madelungenergies_Mulliken[source]

property sitepotentials_Loewdin: list[float][source]

property sitepotentials_Mulliken: list[float][source]

class Wavefunction(filename: PathLike, structure: Structure)[source]

Bases: object

Read wave function files from LOBSTER and create an VolumetricData object.

grid[source]

Grid for the wave function [Nx+1, Ny+1, Nz+1].

Type:

tuple[int, int, int]

points[source]

Points.

Type:

list[Tuple[float, float, float]]

real[source]

Real parts of wave function.

Type:

list[float]

imaginary[source]

Imaginary parts of wave function.

Type:

list[float]

distance[source]

Distances to the first point in wave function file.

Type:

list[float]

Parameters:

• filename (PathLike) – The wavecar file from LOBSTER.

• structure (Structure) – The Structure object.

get_volumetricdata_density() → VolumetricData[source]

Get a VolumetricData object including the density part of the wave function.

Returns:

VolumetricData

get_volumetricdata_imaginary() → VolumetricData[source]

Get a VolumetricData object including the imaginary part of the wave function.

Returns:

VolumetricData

get_volumetricdata_real() → VolumetricData[source]

Get a VolumetricData object including the real part of the wave function.

Returns:

VolumetricData

set_volumetric_data(grid: tuple[int, int, int], structure: Structure) → None[source]

Create the VolumetricData instances.

Parameters:

• grid (tuple[int, int, int]) – Grid on which wavefunction was calculated, e.g. (1, 2, 2).

• structure (Structure) – The Structure object.

write_file(filename: PathLike = 'WAVECAR.vasp', part: Literal['real', 'imaginary', 'density'] = 'real') → None[source]

Save the wave function in a file that can be read by VESTA.

This will only work if the wavefunction from lobster is constructed with:

“printLCAORealSpaceWavefunction kpoint 1 coordinates 0.0 0.0 0.0 coordinates 1.0 1.0 1.0 box bandlist 1 2 3 4 5 6 ” or similar (the whole unit cell has to be covered!).

Parameters:

• filename (PathLike) – The output file, e.g. “WAVECAR.vasp”.

• part ("real" | "imaginary" | "density"]) – Part of the wavefunction to save.

get_orb_from_str(orbs: list[str]) → tuple[str, list[tuple[int, Orbital]]][source]

Get Orbitals from string representations.

Parameters:

orbs (list[str]) – Orbitals, e.g. [“2p_x”, “3s”].

Returns:

Orbital label, orbitals.

Return type:

tuple[str, list[tuple[int, Orbital]]]