pymatgen.io.lobster.outputs module

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

class Bandoverlaps(filename: str = 'bandOverlaps.lobster')

Bases: object

Class to read in bandOverlaps.lobster files. These files are not created during every Lobster run. .. attribute: bandoverlapsdict is a dict of the following 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 } }}

Parameters

filename – filename of the “bandOverlaps.lobster” file

has_good_quality_check_occupied_bands(number_occ_bands_spin_up: int, number_occ_bands_spin_down: Optional[int] = None, spin_polarized: bool = False, limit_deviation: float = 0.1) → bool

will check if the deviation from the ideal bandoverlap of all occupied bands is smaller or equal to limit_deviation

Args: 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): If True, then it was a spin polarized calculation limit_deviation (float): limit of the maxDeviation :returns: Boolean that will give you information about the quality of the projection

has_good_quality_maxDeviation(limit_maxDeviation: float = 0.1) → bool

will check if the maxDeviation from the ideal bandoverlap is smaller or equal to limit_maxDeviation :param limit_maxDeviation: limit of the maxDeviation

Returns

Boolean that will give you information about the quality of the projection

class Charge(filename: str = 'CHARGE.lobster')

Bases: object

Class to read CHARGE files generated by LOBSTER

Parameters

filename – filename for the CHARGE file, typically “CHARGE.lobster”

get_structure_with_charges(structure_filename)

get a Structure with Mulliken and Loewdin charges as site properties :param structure_filename: filename of POSCAR

Returns

Structure Object with Mulliken and Loewdin charges as site properties

class Cohpcar(are_coops: bool = False, are_cobis: bool = False, filename: str = None)

Bases: object

Class to read COHPCAR/COOPCAR files generated by LOBSTER.

Parameters

• are_coops – Determines if the file is a list of COHPs or COOPs. Default is False for COHPs.

• are_cobis – Determines if the file is a list of COHPs or COOPs. Default is False for COHPs.

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

class Doscar(doscar: str = 'DOSCAR.lobster', structure_file: str = 'POSCAR', dftprogram: str = 'Vasp')

Bases: object

Class to deal with Lobster’s projected DOS and local projected DOS. The beforehand quantum-chemical calculation was performed with VASP

completedos

LobsterCompleteDos Object

pdos

List of Dict including numpy arrays with pdos. Access as pdos[atomindex]['orbitalstring']['Spin.up/Spin.down']

tdos

Dos Object of the total density of states

energies

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

tdensities

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

itdensities:

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

is_spin_polarized

Boolean. Tells if the system is spin polarized

Parameters

• doscar – DOSCAR filename, typically “DOSCAR.lobster”

• structure_file – for vasp, this is typically “POSCAR”

• dftprogram – so far only “vasp” is implemented

property completedos

CompleteDos

Type

return

property energies

Energies

Type

return

property is_spin_polarized

Whether run is spin polarized.

Type

return

property itdensities

integrated total densities as a np.ndarray

Type

return

property pdos

Projected DOS

Type

return

property tdensities

total densities as a np.ndarray

Type

return

property tdos

Total DOS

Type

return

class Fatband(filenames='.', vasprun='vasprun.xml', Kpointsfile='KPOINTS')

Bases: object

Reads in FATBAND_x_y.lobster files

Parameters

• filenames (list or string) – can be a list of file names or a path to a folder folder from which all “FATBAND_*” files will be read

• vasprun – corresponding vasprun file

• Kpointsfile – KPOINTS file for bandstructure calculation, typically “KPOINTS”

get_bandstructure()

returns a LobsterBandStructureSymmLine object which can be plotted with a normal BSPlotter

class Grosspop(filename: str = 'GROSSPOP.lobster')

Bases: object

Class to read in GROSSPOP.lobster files.

Parameters

filename – filename of the “GROSSPOP.lobster” file

get_structure_with_total_grosspop(structure_filename: str) → pymatgen.core.structure.Structure

get a Structure with Mulliken and Loewdin total grosspopulations as site properties :param structure_filename: filename of POSCAR :type structure_filename: str

Returns

Structure Object with Mulliken and Loewdin total grosspopulations as site properties

class Icohplist(are_coops: bool = False, are_cobis: bool = False, filename: str = None)

Bases: object

Class to read ICOHPLIST/ICOOPLIST files generated by LOBSTER.

Parameters

• are_coops – Determines if the file is a list of ICOOPs. Defaults to False for ICOHPs.

• are_cobis – Determines if the file is a list of ICOBIs. Defaults to False for ICOHPs.

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

property icohpcollection

IcohpCollection object

Type

Returns

property icohplist

icohplist compatible with older version of this class

Type

Returns

class Lobsterout(filename='lobsterout')

Bases: object

Class to read in the lobsterout and evaluate the spilling, save the basis, save warnings, save infos

Parameters

filename – filename of lobsterout

get_doc()

Returns: LobsterDict with all the information stored in lobsterout

class MadelungEnergies(filename: str = 'MadelungEnergies.lobster')

Bases: object

Class to read MadelungEnergies.lobster files generated by LOBSTER

Parameters

filename – filename of the “MadelungEnergies.lobster” file

class SitePotential(filename: str = 'SitePotentials.lobster')

Bases: object

Class to read SitePotentials.lobster files generated by LOBSTER

Parameters

filename – filename for the SitePotentials file, typically “SitePotentials.lobster”

get_structure_with_site_potentials(structure_filename)

get a Structure with Mulliken and Loewdin charges as site properties :param structure_filename: filename of POSCAR

Returns

Structure Object with Mulliken and Loewdin charges as site properties

class Wavefunction(filename, structure)

Bases: object

Class to read in wave function files from Lobster and transfer them into an object of the type VolumetricData

Parameters

• filename – filename of wavecar file from Lobster

• structure – Structure object (e.g., created by Structure.from_file(“”))

get_volumetricdata_density()

will return a VolumetricData object including the imaginary part of the wave function

Returns: VolumetricData object

get_volumetricdata_imaginary()

will return a VolumetricData object including the imaginary part of the wave function

Returns: VolumetricData object

get_volumetricdata_real()

will return a VolumetricData object including the real part of the wave function

Returns: VolumetricData object

set_volumetric_data(grid, structure)

Will create the VolumetricData Objects

Parameters

• grid – grid on which wavefunction was calculated, e.g. [1,2,2]

• structure – Structure object

Returns:

write_file(filename='WAVECAR.vasp', part='real')

will save the wavefunction in a file format that can be read by VESTA This will only work if the wavefunction from lobster was 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 – Filename for the output, e.g., WAVECAR.vasp

• part – which part of the wavefunction will be saved (“real” or “imaginary”)

Returns: