vaspparser.dft.waves.electronic.ElectronicStructure

class vaspparser.dft.waves.electronic.ElectronicStructure

Bases: object

This is a generic module to store electronic structure data in a clean way. Kpoint and Band classes are used to store information related to kpoints and bands respectively. Every spin configuration has a set of k-points and every k-point has a set of bands associated with it. This is loosely adapted from the pymatgen electronic_structure modules. Many of the functions have been substantially modified for pyiron

__init__()

Methods

__init__()
add_kpoint(value, weight)	Appends a Kpoint() instance to the kpoints attribute
generate_from_matrices()	Generate the Kpoints and Bands from the kpoint lists and sometimes grand_dos_matrix
get_band_gap([resolution])	Gets the band gap of the system for each spin value
get_cbm([resolution])	Gets the conduction band minimum (CBM) of the system for each spin value
get_dos([n_bins])	Gives a pyiron_atomistics.objects.waves.dos.Dos instance
get_resolved_dos([spin_indices, ...])	Get resolved dos based on the specified spin, atom and orbital indices
get_spin_resolved_dos([spin_indices])	Gets the spin resolved DOS
get_vbm([resolution])	Gets the valence band maximum (VBM) of the system for each spin value
plot_fermi_dirac()	Plots the obtained eigenvalue vs occupation plot
to_dict()	Serialize the electronic structure to a dictionary.

Attributes

cbm	The Kohn-Sham conduction band minimum for each spin channel
dos_densities	A (SxN) vector containing the density of states for every spin configuration with S spin configurations and N grid points
dos_energies	A (1xN) vector containing the energies with N grid points
dos_idensities	A (SxN) vector containing the density of states for every spin configuration with S spin configurations and N grid points
efermi	The Fermi-level of the system (eV).
eg	The band gap for each spin channel
eigenvalue_matrix	A getter function to return the eigenvalue_matrix.
eigenvalues	Returns the eigenvalues for each spin value
grand_dos_matrix	Getter for the 5 dimensional grand_dos_matrix which gives the contribution of every spin, kpoint, band, atom and orbital to the total DOS.
is_metal	Tells if the given system is metallic or not in each spin channel (up and down respectively).
kpoint_list	The list of kpoints in cartesian coordinates
kpoint_weights	The weights of the kpoints of the electronic structure in cartesian coordinates
occupancies	Returns the occupancies for each spin value
occupancy_matrix	A getter function to return the occupancy_matrix.
orbital_dict	A dictionary of the ordering of the orbitals
resolved_densities	A (SxAxOxN) vector containing the density of states for every spin configuration with S spin configurations, A atoms, O orbitals and N grid points.
structure	The structure associated with the electronic structure object
vbm	The Kohn-Sham valence band maximum for each spin channel

add_kpoint(value, weight)

Appends a Kpoint() instance to the kpoints attribute

Parameters:

• value (list/numpy.ndarray) – Value of the k-point in cartesian reciprocal coordinates

• weight (float) – The weight of the particular k-point

property cbm

The Kohn-Sham conduction band minimum for each spin channel

Returns:

list of conduction band minimum values for each spin channel

Return type:

list

property dos_densities

A (SxN) vector containing the density of states for every spin configuration with S spin configurations and N grid points

Type:

numpy.ndarray

property dos_energies

A (1xN) vector containing the energies with N grid points

Type:

numpy.ndarray

property dos_idensities

A (SxN) vector containing the density of states for every spin configuration with S spin configurations and N grid points

Type:

numpy.ndarray

property efermi

The Fermi-level of the system (eV). Please note that in the case of DFT this level is the Kohn-Sham Fermi level computed by the DFT code.

Type:

float

property eg

The band gap for each spin channel

Returns:

list of band gap values for each spin channel

Return type:

list

property eigenvalue_matrix

A getter function to return the eigenvalue_matrix. The eigenvalue for a given kpoint index i and band index j is given by eigenvalue_matrix[i][j]

Type:

numpy.ndarray

property eigenvalues

Returns the eigenvalues for each spin value

numpy.ndarray: Eigenvalues of the bands

generate_from_matrices()

Generate the Kpoints and Bands from the kpoint lists and sometimes grand_dos_matrix

get_band_gap(resolution=1e-06)

Gets the band gap of the system for each spin value

Parameters:

resolution (float) – An occupancy above this value is considered occupied

Returns:

“band gap” (float): The band gap (eV)

”vbm”: The dictionary associated with the VBM “cbm”: The dictionary associated with the CBM

Return type:

dict

get_cbm(resolution=1e-06)

Gets the conduction band minimum (CBM) of the system for each spin value

Parameters:

resolution (float) – An occupancy above this value is considered occupied

Returns:

“value” (float): Absolute energy value of the CBM (eV)

”kpoint”: The Kpoint instance associated with the CBM “band”: The Band instance associated with the CBM

Return type:

dict

get_dos(n_bins=100)

Gives a pyiron_atomistics.objects.waves.dos.Dos instance

Parameters:

n_bins (int) – Number of histogram bins for the dos

Returns:

Dos instance

Return type:

pyiron_atomistics.objects.waves.dos.Dos

get_resolved_dos(spin_indices=0, atom_indices=None, orbital_indices=None)

Get resolved dos based on the specified spin, atom and orbital indices

Parameters:

• spin_indices (int/list/numpy.ndarray) – spin indices

• atom_indices (int/list/numpy.ndarray) – stom indices

• orbital_indices (int/list/numpy.ndarray) – orbital indices (based on orbital_dict)

Returns:

Required resolved dos

Return type:

rdos (numpy.ndarray)

get_spin_resolved_dos(spin_indices=0)

Gets the spin resolved DOS

Parameters:

spin_indices (int) – The index of the spin for which the DOS is required

Returns:

Spin resolved dos (numpy.ndarray instance)

get_vbm(resolution=1e-06)

Gets the valence band maximum (VBM) of the system for each spin value

Parameters:

resolution (float) – An occupancy below this value is considered unoccupied

Returns:

“value” (float): Absolute energy value of the VBM (eV) “kpoint”: The Kpoint instance associated with the VBM “band”: The Band instance associated with the VBM

Return type:

dict

property grand_dos_matrix

Getter for the 5 dimensional grand_dos_matrix which gives the contribution of every spin, kpoint, band, atom and orbital to the total DOS. For example the dos contribution with spin index s, kpoint k, band b, atom a and orbital o is:

grand_dos_matrix[s, k, b, a, o]

The grand sum of this matrix would equal 1.0. The spatial, spin, and orbital resolved DOS can be computed using this matrix

Returns:

numpy.ndarray (5 dimensional)

property is_metal

Tells if the given system is metallic or not in each spin channel (up and down respectively). The Fermi level crosses bands in the cas of metals but is present in the band gap in the case of semi-conductors.

Returns:

List of boolean values for each spin channel

Return type:

list

property kpoint_list

The list of kpoints in cartesian coordinates

Type:

list

property kpoint_weights

The weights of the kpoints of the electronic structure in cartesian coordinates

Type:

list

property occupancies

Returns the occupancies for each spin value

numpy.ndarray: Occupancies of the bands

property occupancy_matrix

A getter function to return the occupancy_matrix. The occupancy for a given kpoint index i and band index j is given by occupancy_matrix[i][j]

Type:

numpy.ndarray

property orbital_dict

A dictionary of the ordering of the orbitals

Examples

>>> self.orbital_dict[0]
's'

Type:

dict

plot_fermi_dirac()

Plots the obtained eigenvalue vs occupation plot

property resolved_densities

A (SxAxOxN) vector containing the density of states for every spin configuration with S spin configurations, A atoms, O orbitals and N grid points. The labels of the orbitals are found on the orbital_dict

Type:

numpy.ndarray

property structure

The structure associated with the electronic structure object

Type:

atomistics.structure.atoms.Atoms

to_dict() → dict

Serialize the electronic structure to a dictionary.

Returns:

Dictionary with keys "TYPE", "k_points", "k_weights",

"eig_matrix", "occ_matrix", optionally "efermi", "structure", and a "dos" sub-dictionary containing total and resolved DOS data.

Return type:

dict

property vbm

The Kohn-Sham valence band maximum for each spin channel

Returns:

list of valence band maximum values for each spin channel

Return type:

list