pymatgen.io.lobster.inputs module

Module for reading Lobster output files. For more information on LOBSTER see www.cohp.de.

class Lobsterin(settingsdict: dict)

Bases: dict, monty.json.MSONable

This class can handle and generate lobsterin files Furthermore, it can also modify INCAR files for lobster, generate KPOINT 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.

Parameters

settingsdict – dict to initialize Lobsterin

AVAILABLEKEYWORDS = ['COHPstartEnergy', 'COHPendEnergy', 'basisSet', 'cohpGenerator', 'gaussianSmearingWidth', 'saveProjectionToFile', 'basisfunctions', 'skipdos', 'skipcohp', 'skipcoop', 'skipPopulationAnalysis', 'skipGrossPopulation', 'userecommendedbasisfunctions', 'loadProjectionFromFile', 'forceEnergyRange', 'DensityOfEnergy', 'BWDF', 'BWDFCOHP', 'skipProjection', 'createFatband', 'writeBasisFunctions', 'writeMatricesToFile', 'realspaceHamiltonian', 'realspaceOverlap', 'printPAWRealSpaceWavefunction', 'printLCAORealSpaceWavefunction', 'noFFTforVisualization', 'RMSp', 'onlyReadVasprun.xml', 'noMemoryMappedFiles', 'skipPAWOrthonormalityTest', 'doNotIgnoreExcessiveBands', 'doNotUseAbsoluteSpilling', 'skipReOrthonormalization', 'forceV1HMatrix', 'useOriginalTetrahedronMethod', 'useDecimalPlaces', 'kSpaceCOHP']

BOOLEANKEYWORDS = ['saveProjectionToFile', 'skipdos', 'skipcohp', 'skipcoop', 'loadProjectionFromFile', 'forceEnergyRange', 'DensityOfEnergy', 'BWDF', 'BWDFCOHP', 'skipPopulationAnalysis', 'skipGrossPopulation', 'userecommendedbasisfunctions', 'skipProjection', 'writeBasisFunctions', 'writeMatricesToFile', 'noFFTforVisualization', 'RMSp', 'onlyReadVasprun.xml', 'noMemoryMappedFiles', 'skipPAWOrthonormalityTest', 'doNotIgnoreExcessiveBands', 'doNotUseAbsoluteSpilling', 'skipReOrthonormalization', 'forceV1HMatrix', 'useOriginalTetrahedronMethod', 'forceEnergyRange', 'bandwiseSpilling', 'kpointwiseSpilling']

FLOATKEYWORDS = ['COHPstartEnergy', 'COHPendEnergy', 'gaussianSmearingWidth', 'useDecimalPlaces', 'COHPSteps']

LISTKEYWORDS = ['basisfunctions', 'cohpbetween', 'createFatband']

STRINGKEYWORDS = ['basisSet', 'cohpGenerator', 'realspaceHamiltonian', 'realspaceOverlap', 'printPAWRealSpaceWavefunction', 'printLCAORealSpaceWavefunction', 'kSpaceCOHP']

as_dict()

Returns

MSONable dict

diff(other)

Diff function for lobsterin. Compares two lobsterin and indicates which parameters are the same. Similar to the diff in INCAR. :param other: Lobsterin object to compare to :type other: Lobsterin

Returns

dict with differences and similarities

classmethod from_dict(d)

Parameters

d – Dict representation

Returns

Lobsterin

classmethod from_file(lobsterin: str)

Parameters

lobsterin (str) – path to lobsterin

Returns

Lobsterin object

static get_all_possible_basis_functions(structure: pymatgen.core.structure.Structure, potcar_symbols: list, address_basis_file_min: str = '/Users/shyue/repos/pymatgen/pymatgen/io/lobster/lobster_basis/BASIS_PBE_54_min.yaml', address_basis_file_max: str = '/Users/shyue/repos/pymatgen/pymatgen/io/lobster/lobster_basis/BASIS_PBE_54_max.yaml')

Parameters

• structure – Structure object

• potcar_symbols – list of the potcar symbols

• address_basis_file_min – path to file with the minium required basis by the POTCAR

• address_basis_file_max – path to file with the largest possible basis of the POTCAR

Returns: List of dictionaries that can be used to create new Lobsterin objects in standard_calculations_from_vasp_files as dict_for_basis

static get_basis(structure: pymatgen.core.structure.Structure, potcar_symbols: list, address_basis_file: str = '/Users/shyue/repos/pymatgen/pymatgen/io/lobster/lobster_basis/BASIS_PBE_54_standard.yaml')

will get the basis from given potcar_symbols (e.g., [“Fe_pv”,”Si”] #include this in lobsterin class :param structure: Structure object :type structure: Structure :param potcar_symbols: list of potcar symbols

Returns

returns basis

classmethod standard_calculations_from_vasp_files(POSCAR_input: str = 'POSCAR', INCAR_input: str = 'INCAR', POTCAR_input: Optional[str] = None, dict_for_basis: Optional[dict] = None, option: str = 'standard')

will generate Lobsterin with standard settings

Parameters

• POSCAR_input (str) – path to POSCAR

• INCAR_input (str) – path to INCAR

• POTCAR_input (str) – path to POTCAR

• 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_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 Object with standard settings

write_INCAR(incar_input: str = 'INCAR', incar_output: str = 'INCAR.lobster', poscar_input: str = 'POSCAR', isym: int = - 1, further_settings: Optional[dict] = None)

Will only make the run static, insert nbands, make ISYM=-1, set LWAVE=True and write a new INCAR. You have to check for the rest. :param incar_input: path to input INCAR :type incar_input: str :param incar_output: path to output INCAR :type incar_output: str :param poscar_input: path to input POSCAR :type poscar_input: str :param isym: isym equal to -1 or 0 are possible. Current Lobster version only allow -1. :type isym: int :param further_settings: A dict can be used to include further settings, e.g. {“ISMEAR”:-5} :type further_settings: dict

static write_KPOINTS(POSCAR_input: str = 'POSCAR', KPOINTS_output='KPOINTS.lobster', reciprocal_density: int = 100, isym: int = - 1, from_grid: bool = False, input_grid: list = [5, 5, 5], line_mode: bool = True, kpoints_line_density: int = 20, symprec: float = 0.01)

writes a KPOINT file for lobster (only ISYM=-1 and ISYM=0 are possible), grids are gamma centered :param POSCAR_input: path to POSCAR :type POSCAR_input: str :param KPOINTS_output: path to output KPOINTS :type KPOINTS_output: str :param reciprocal_density: Grid density :type reciprocal_density: int :param isym: either -1 or 0. Current Lobster versions only allow -1. :type isym: int :param from_grid: 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

Parameters

• input_grid (list) – 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='POSCAR', POSCAR_output='POSCAR.lobster', symprec=0.01)

writes a POSCAR with the standard primitive cell. This is needed to arrive at the correct kpath :param POSCAR_input: filename of input POSCAR :type POSCAR_input: str :param POSCAR_output: filename of output POSCAR :type POSCAR_output: str :param symprec: precision to find symmetry :type symprec: float

write_lobsterin(path='lobsterin', overwritedict=None)

writes a lobsterin file :param path: filename of the lobsterin file that will be written :type path: str :param overwritedict: dict that can be used to overwrite lobsterin, e.g. {“skipdos”: True} :type overwritedict: dict

get_all_possible_basis_combinations(min_basis: list, max_basis: list) → list

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’]]