pymatgen.io.lobster.outputs module¶
Module for reading Lobster output files. For more information on LOBSTER see www.cohp.de.
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class
Bandoverlaps
(filename: str = 'bandOverlaps.lobster')[source]¶ 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
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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[source]¶ 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
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has_good_quality_maxDeviation
(limit_maxDeviation: float = 0.1) → bool[source]¶ 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
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class
Charge
(filename: str = 'CHARGE.lobster')[source]¶ Bases:
object
Class to read CHARGE files generated by LOBSTER
- Parameters
filename – filename for the CHARGE file, typically “CHARGE.lobster”
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class
Cohpcar
(are_coops: bool = False, filename: str = None)[source]¶ 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.
filename – Name of the COHPCAR file. If it is None, the default file name will be chosen, depending on the value of are_coops.
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class
Doscar
(doscar: str = 'DOSCAR.lobster', structure_file: str = 'POSCAR', dftprogram: str = 'Vasp')[source]¶ Bases:
object
Class to deal with Lobster’s projected DOS and local projected DOS. The beforehand quantum-chemical calculation was performed with VASP
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pdos
[source]¶ -
List of Dict including numpy arrays with pdos. Access as pdos[atomindex]['orbitalstring']['Spin.up/Spin.down']
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energies
[source]¶ -
numpy array of the energies at which the DOS was calculated (in eV, relative to Efermi)
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tdensities
[source]¶ -
tdensities[Spin.up]: numpy array of the total density of states for the Spin.up contribution at each of the
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energies
¶ -
tdensities[Spin.down]: numpy array of the total density of states for the Spin.down contribution at each of the
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energies
if is_spin_polarized=False: tdensities[Spin.up]: numpy array of the total density of states
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itdensities:
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itdensities[Spin.up]: numpy array of the total density of states for the Spin.up contribution at each of the
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energies
[source]¶ -
itdensities[Spin.down]: numpy array of the total density of states for the Spin.down contribution at each of the
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energies
if is_spin_polarized=False: itdensities[Spin.up]: numpy array of the total density of states
- Parameters
doscar – DOSCAR filename, typically “DOSCAR.lobster”
structure_file – for vasp, this is typically “POSCAR”
dftprogram – so far only “vasp” is implemented
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class
Fatband
(filenames='.', vasprun='vasprun.xml', Kpointsfile='KPOINTS')[source]¶ 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”
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class
Grosspop
(filename: str = 'GROSSPOP.lobster')[source]¶ Bases:
object
Class to read in GROSSPOP.lobster files.
- Parameters
filename – filename of the “GROSSPOP.lobster” file
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get_structure_with_total_grosspop
(structure_filename: str) → pymatgen.core.structure.Structure[source]¶ 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
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class
Icohplist
(are_coops: bool = False, filename: str = None)[source]¶ Bases:
object
Class to read ICOHPLIST/ICOOPLIST files generated by LOBSTER.
- Parameters
are_coops – Determines if the file is a list of ICOHPs or ICOOPs. 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.
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class
Lobsterout
(filename='lobsterout')[source]¶ Bases:
object
Class to read in the lobsterout and evaluate the spilling, save the basis, save warnings, save infos
- Parameters
filename – filename of lobsterout
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class
Wavefunction
(filename, structure)[source]¶ 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(“”))
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get_volumetricdata_density
()[source]¶ will return a VolumetricData object including the imaginary part of the wave function
Returns: VolumetricData object
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get_volumetricdata_imaginary
()[source]¶ will return a VolumetricData object including the imaginary part of the wave function
Returns: VolumetricData object
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get_volumetricdata_real
()[source]¶ will return a VolumetricData object including the real part of the wave function
Returns: VolumetricData object
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set_volumetric_data
(grid, structure)[source]¶ Will create the VolumetricData Objects
- Parameters
grid – grid on which wavefunction was calculated, e.g. [1,2,2]
structure – Structure object
Returns:
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write_file
(filename='WAVECAR.vasp', part='real')[source]¶ 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: