pyiron_atomistics.dft.waves.electronic.ElectronicStructure

pyiron_atomistics.dft.waves.electronic.ElectronicStructure#

class pyiron_atomistics.dft.waves.electronic.ElectronicStructure[source]#

Bases: ElectronicStructure

__init__()[source]#

Methods

`__init__`()
`add_kpoint`(value, weight)	Appends a Kpoint() instance to the kpoints attribute
`from_hdf`(hdf[, group_name])	Retrieve the object from the hdf5 file :param hdf: Path to the hdf5 file/group in the file :param group_name: Name of the group under which the attributes are stored
`from_hdf_old`(hdf[, group_name])	Retrieve the object from the hdf5 file :param hdf: Path to the hdf5 file/group in the file :param group_name: Name of the group under which the attributes are stored
`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`()
`to_hdf`(hdf[, group_name])	Store the object to hdf5 file :param hdf: Path to the hdf5 file/group in the file :param group_name: Name of the group under which the attributes are o be stored

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)[source]#

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

from_hdf(hdf, group_name='electronic_structure')[source]#: Retrieve the object from the hdf5 file :param hdf: Path to the hdf5 file/group in the file :param group_name: Name of the group under which the attributes are stored

from_hdf_old(hdf, group_name='electronic_structure')[source]#: Retrieve the object from the hdf5 file :param hdf: Path to the hdf5 file/group in the file :param group_name: Name of the group under which the attributes are stored

generate_from_matrices()[source]#: Generate the Kpoints and Bands from the kpoint lists and sometimes grand_dos_matrix

get_band_gap(resolution=1e-06)[source]#

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)[source]#

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)[source]#

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)[source]#

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)[source]#

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)[source]#

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()[source]#: 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_hdf(hdf, group_name='electronic_structure')[source]#: Store the object to hdf5 file :param hdf: Path to the hdf5 file/group in the file :param group_name: Name of the group under which the attributes are o be stored

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

pyiron_atomistics.dft.waves.electronic.ElectronicStructure

Contents

pyiron_atomistics.dft.waves.electronic.ElectronicStructure#