vasp_dos¶

The `get_data_path` function¶

get_data_path()[source]¶

Get default paths to package data.

Returns: data_path – path to package data
Return type: str

The `get_example_data` function¶

get_example_data()[source]¶

Get default path to vasp_dos data

Returns: data_path – path to example VASP data
Return type: str

The `get_all_VASP_files` function¶

get_all_VASP_files(directory)[source]¶

Get all DOSCAR and CONTCAR file paths

Parameters

directory (str) – root directory to look for DOSCAR files

Returns

DOSCAR_files (list) – list of all DOSCAR files
CONTCAR_files (list) – list of all CONTCAR files

The `get_band_center` function¶

get_band_center(energies, densities, max_energy=None, min_energy=None, axis=- 1)[source]¶

Get band center given energies and densities

Parameters

energies (numpy.ndarray) – discretized orbital energies
densities (numpy.ndarray) – projected state densities
max_energy (float) – cutoff energy (often the fermi energy)
min_energy (float) – cutoff energy (often the fermi energy)
axis (int) – axis of densities on which to integrate

Returns

band_center – center of the band(s) up to max_energy

Return type

numpy.float64 or numpy.ndarray

Notes

trapezoidal rule is better for narrow gaussian peaks and for “rough” functions https://doi.org/10.1016/j.chemolab.2018.06.001 http://emis.icm.edu.pl/journals/JIPAM/v3n4/031_02.html

The `get_bond_energy` function¶

get_bond_energy(energies, densities, e_fermi)[source]¶

Get bond energy from density

Parameters

energies (numpy.ndarray) – discretized orbital energies
densities (numpy.ndarray) – projected state densities
e_fermi (float) – highest occupied energy level

Returns

bond_energy – total energy in the bonds

Return type

numpy.float64 or numpy.ndarray

The `get_band_width` function¶

get_band_width(energies, densities, fraction=0)[source]¶

Get band width given energies and densities

Parameters

energies (numpy.ndarray) – discretized orbital energies
densities (numpy.ndarray) – projected state densities
fraction (float) – maximum projected density considered part of a band

Returns

band_width – width of the band(s)

Return type

numpy.float64 or numpy.ndarray

The `get_orbital_proximity` function¶

get_orbital_proximity(energies, densities, energy, moment=1)[source]¶

Get width between to band centers given a division

Parameters

energies (numpy.ndarray) – discretized orbital energies
densities (numpy.ndarray) – projected state densities
energy (int) – some energy with which the proximity of states is calculated
moment (int) – moment with which to calculate the orbital proximity

Returns

orbital_proximity – proximity of orbitals to some energy

Return type

numpy.float64 or numpy.ndarray

The `get_second_moment` function¶

get_second_moment(energies, densities)[source]¶

Get the second moment

Parameters

energies (numpy.ndarray) – discretized orbital energies
densities (numpy.ndarray) – projected state densities

Returns

second_moment – second moment of the densities

Return type

numpy.float64 or numpy.ndarray

Notes

Utilizeds get_orbital_proximity

The `get_filling` function¶

get_filling(energies, densities, max_energy=None, min_energy=None, axis=- 1)[source]¶

Get band center given energies and densities

Parameters

energies (numpy.ndarray) – discretized orbital energies
densities (numpy.ndarray) – projected state densities
max_energy (float) – cutoff energy (often the fermi energy)
min_energy (float) – cutoff energy (often the fermi energy)
axis (int) – axis of densities on which to integrate

Returns

Integrated_Filling – Total filling between min and max energy

Return type

float or numpy.ndarray

Notes

trapezoidal rule is better for narrow gaussian peaks and for “rough” functions https://doi.org/10.1016/j.chemolab.2018.06.001 http://emis.icm.edu.pl/journals/JIPAM/v3n4/031_02.html

The `VASP_DOS` class¶

class VASP_DOS(file_name='DOSCAR', no_negatives=True, add_p2s=False)[source]¶

Class for extracting projected density of states from VASP

Parameters

file_name (str) – full DOSCAR file location
no_negatives (bool) – Indicates wheather negative occupances will be converted to zero. Negative occupances can occur if Methfessel-Paxton is used.

Variables

no_negatives (bool) – Indicates wheather negative occupances will be converted to zero. Negative occupances can occur if Methfessel-Paxton is used.
natoms (int) – number of atoms in the system
emax (float) – maximum energy level
emin (float) – minimum energy level
ndos (int) – number of descritized energy levels
e_fermi (float) – highest occupied energy level
is_spin (bool) – indicates if projected density is spin resolved
m_projected (bool) – indicates if projected density is orbital resolved
orbital_dictionary (dict) – dictionary that maps resolved sublevels/orbitals to indices
add_p2s (bool) – if true adds the p density to the s density (useful for metals)

Methods

_read_doscar(file_name='DOSCAR', no_negatives=True)[source]¶

Read VASP DOSCAR and extract projected densities

Parameters

file_name (str) – file location of the DOSCAR file
no_negatives (bool) – Indicates wheather negative occupances will be converted to zero. Negative occupances can occur if Methfessel-Paxton is used.

Variables

_total_dos (numpy.ndarray) – numpy array that contains the energy of the orbitals and the total projected and integrated density
_site_dos (numpy.ndarray) – numpy array that contains the energy of the orbitals and the site and orbital projected density of states. Only available if a site projected calculation was performed.

Returns

emax (float) – maximum energy level
emin (float) – minimum energy level
ndos (int) – number of descritized energy levels
e_fermi (float) – highest occupied energy level
is_spin (bool) – indicates if projected density is spin resolved
m_projected (bool) – indicates if projected density is orbital resolved
orbital_dictionary (dict) – dictionary that maps resolved sublevels/orbitals to indices

_read_lobster(file_name='DOSCAR.lobster', no_negatives=True)[source]¶

Read VASP DOSCAR and extract projected densities

Parameters

file_name (str) – file location of the DOSCAR file
no_negatives (bool) – Indicates wheather negative occupances will be converted to zero. Negative occupances can occur if Methfessel-Paxton is used.

Variables

_total_dos (numpy.ndarray) – numpy array that contains the energy of the orbitals and the total projected and integrated density
_site_dos (numpy.ndarray) – numpy array that contains the energy of the orbitals and the site and orbital projected density of states. Only available if a site projected calculation was performed.

Returns

emax (float) – maximum energy level
emin (float) – minimum energy level
ndos (int) – number of descritized energy levels
e_fermi (float) – highest occupied energy level
is_spin (bool) – indicates if projected density is spin resolved
m_projected (bool) – indicates if projected density is orbital resolved
orbital_dictionary (dict) – dictionary that maps resolved sublevels/orbitals to indices

apply_gaussian_filter(sigma)[source]¶

Applies Gaussian filter to self._total_dos and self._site_dos

Parameters

sigma (float) – standard deviation of Gaussian Kernel

Variables

_total_dos_original (numpy.ndarray) – self._total_dos array without filter
_site_dos_original (numpy.ndarray) – self._site_dos array without filter

get_band_center(atom_indices, orbital_list, sum_density=False, sum_spin=True, max_energy=None, min_energy=None, axis=- 1)[source]¶

Get band center for a given atom and list of orbitals

Parameters

atom_indices (list[int]) – list of atom indices
orbital_list (list[str]) – Which orbitals to return
sum_density (bool) – if a sub-level is provided instead of an orbital, sum_density indicates if the individual sub-level densities should be summed
sum_spin (bool) – different spin densities are summed.
max_energy (float) – cutoff energy (often the fermi energy)
min_energy (float) – cutoff energy (often the fermi energy)
axis (int) – axis of densities on which to integrate

Returns

band_center – center of the band(s) up to max_energy

Return type

float or numpy.ndarray

get_band_width(atom_indices, orbital_list, sum_density=False, sum_spin=True, fraction=0)[source]¶

Get band width given energies and densities

Parameters

atom_indices (list[int]) – list of atom indices
orbital_list (list[str]) – Which orbitals to return
sum_density (bool) – if a sub-level is provided instead of an orbital, sum_density indicates if the individual sub-level densities should be summed
sum_spin (bool) – different spin densities are summed.
fraction (float) – maximum projected density considered part of a band

Returns

band_width – width of the band(s)

Return type

float or numpy.ndarray

get_bond_energy(atom_indices, orbital_list, sum_density=False, sum_spin=True)[source]¶

Get second moment of the density projected onto atomic orbitals

Parameters

atom_indices (list[int]) – list of atom indices
orbital_list (list[str]) – Which orbitals to return
sum_density (bool) – if a sub-level is provided instead of an orbital, sum_density indicates if the individual sub-level densities should be summed
sum_spin (bool) – different spin densities are summed.

Returns

bond_energy – bond enegy of the orbitals on atom_indices

Return type

float or numpy.ndarray

get_center_width(energy, atom_indices, orbital_list, sum_density=False, sum_spin=True)[source]¶

Get width between to band centers given a division

Parameters

energy (int) – energy that divides band centers
atom_indices (list[int]) – list of atom indices
orbital_list (list[str]) – Which orbitals to return
sum_density (bool) – if a sub-level is provided instead of an orbital, sum_density indicates if the individual sub-level densities should be summed
sum_spin (bool) – different spin densities are summed.

Returns

center_width – width of two band centers separated by some ennergy

Return type

float or numpy.ndarray

get_energies()[source]¶

method for obtaining energy levels

Returns: energies – 1-D array of energies
Return type: numpy.ndarray

get_filling(atom_indices, orbital_list, sum_density=False, sum_spin=True, max_energy=None, min_energy=None, axis=- 1)[source]¶

Get band center for a given atom and list of orbitals

Parameters

atom_indices (list[int]) – list of atom indices
orbital_list (list[str]) – Which orbitals to return
sum_density (bool) – if a sub-level is provided instead of an orbital, sum_density indicates if the individual sub-level densities should be summed
sum_spin (bool) – different spin densities are summed.
max_energy (float) – cutoff energy (often the fermi energy)
min_energy (float) – cutoff energy (often the fermi energy)
axis (int) – axis of densities on which to integrate

Returns

band_center – center of the band(s) up to max_energy

Return type

float or numpy.ndarray

get_integrated_dos(sum_spin=True)[source]¶

method for obtaining total integrated density of states

Returns: integrated_dos – 1-D or 2-D array of state integrated densities
Return type: numpy.ndarray

get_orbital_proximity(energy, atom_indices, orbital_list, moment=1, sum_density=False, sum_spin=True)[source]¶

Get width between to band centers given a division

Parameters

energy (int) – some energy with which the proximity of states is calculated
moment (int) – moment with which to calculate the orbital proximity
atom_indices (list[int]) – list of atom indices
orbital_list (list[str]) – Which orbitals to return
sum_density (bool) – if a sub-level is provided instead of an orbital, sum_density indicates if the individual sub-level densities should be summed
sum_spin (bool) – different spin densities are summed.

Returns

orbital_proximity – proximity of orbitals to some energy

Return type

float or numpy.ndarray

get_second_moment(atom_indices, orbital_list, sum_density=False, sum_spin=True)[source]¶

Get second moment of the density projected onto atomic orbitals

Parameters

atom_indices (list[int]) – list of atom indices
orbital_list (list[str]) – Which orbitals to return
sum_density (bool) – if a sub-level is provided instead of an orbital, sum_density indicates if the individual sub-level densities should be summed
sum_spin (bool) – different spin densities are summed.

Returns

second_moment – width of two band centers separated by some ennergy

Return type

float or numpy.ndarray

get_site_dos(atom_indices, orbital_list=[], sum_density=False, sum_spin=True)[source]¶

Return an NDOSxM array with dos for the chosen atom and orbital(s).

Parameters

atom_list (list[int]) – List of atom index/indices
orbital_list (list[str]) – Which orbitals to return
sum_density (bool) – if a sub-level is provided instead of an orbital, sum_density indicates if the individual orbital densities should be summed
sum_spin (bool) – different spin densities are summed.

Returns

new_orbital_list (list[str]) – If sum_density is True, new_orbital_list is the same as orbital_list. If sum_density is False, new_orbital_list is resolved by both orbital and spin (if available)
projected_density (np.array) – Array of shape (len(new_orbital_list), ndos)

get_total_dos(sum_spin=True)[source]¶

method for obtaining total density of states

Returns: total_dos – 1-D or 2-D array of state densities
Return type: numpy.ndarray

vasp_dos¶

The get_data_path function¶

The get_example_data function¶

The get_all_VASP_files function¶

The get_band_center function¶

The get_bond_energy function¶

The get_band_width function¶

The get_orbital_proximity function¶

The get_second_moment function¶

The get_filling function¶

The VASP_DOS class¶

The `get_data_path` function¶

The `get_example_data` function¶

The `get_all_VASP_files` function¶

The `get_band_center` function¶

The `get_bond_energy` function¶

The `get_band_width` function¶

The `get_orbital_proximity` function¶

The `get_second_moment` function¶

The `get_filling` function¶

The `VASP_DOS` class¶