pyiron.dft.waves.electronic module¶

class
pyiron.dft.waves.electronic.
Band
[source]¶ Bases:
object
All data related to a single band for every kpoint is stored in this module

property
eigenvalue
¶ The eigenvalue of a given band at a given kpoint
 Type
float

property
occupancy
¶ The occupancy of a given band at a given kpoint
 Type
float

property
resolved_dos_matrix
¶ 2D matrix with n rows and m columns; n being the unmber of atoms and m being the number of orbitals
 Type
numpy.ndarray instance

property

class
pyiron.dft.waves.electronic.
ElectronicStructure
[source]¶ 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 kpoints and every kpoint 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

add_kpoint
(value, weight)[source]¶ Appends a Kpoint() instance to the kpoints attribute
 Parameters
value (list/numpy.ndarray) – Value of the kpoint in cartesian reciprocal coordinates
weight (float) – The weight of the particular kpoint

property
cbm
¶ The KohnSham CBM (value only) (eV)
 Type
float

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 Fermilevel of the system (eV). Please note that in the case of DFT this level is the KohnSham Fermi level computed by the DFT code.
 Type
float

property
eg
¶ The band gap (eV)
 Type
float

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
¶ Eigenvalues of the bands
 Type
numpy.ndarray

from_hdf
(hdf, group_name='electronic_structure')[source]¶ Retrieve the object from the hdf5 file
 Parameters
hdf – Path to the hdf5 file/group in the file
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
 Parameters
hdf – Path to the hdf5 file/group in the file
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=1e06)[source]¶ Gets the band gap of the system
 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=1e06)[source]¶ Gets the conduction band minimum (CBM) of the system
 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.objects.waves.dos.Dos instance
 Parameters
n_bins (int) – Number of histogram bins for the dos
 Returns
Dos instance
 Return type
pyiron.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=1e06)[source]¶ Gets the valence band maximum (VBM) of the system
 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. The Fermi level crosses bands in the cas of metals but is present in the band gap in the case of semiconductors.
 Type
bool

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
¶ Occupancies of the bands
 Type
numpy.ndarray

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

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

to_hdf
(hdf, group_name='electronic_structure')[source]¶ Store the object to hdf5 file
 Parameters
hdf – Path to the hdf5 file/group in the file
group_name – Name of the group under which the attributes are o be stored

to_hdf_old
(hdf, group_name='electronic_structure')[source]¶ Store the object to hdf5 file
 Parameters
hdf – Path to the hdf5 file/group in the file
group_name – Name of the group under which the attributes are o be stored

property
vbm
¶ The KohnSham VBM (value only) (eV)
 Type
float


class
pyiron.dft.waves.electronic.
Kpoint
[source]¶ Bases:
object
All data related to a single kpoint is stored in this module

bands
¶ List of pyiron.objects.waves.settings.Band object
 Type
list

.. value
Value of the kpoint
 Type
float

.. weight
Weight of the kpoint used in integration of quantities
 Type
float

.. eig_occ_matrix
A Nx2 matrix with the first column with eigenvalues and the second with occupancies of every band. N being the number of bands assoiated with the kpoint
 Type
numpy.ndarray

add_band
(eigenvalue, occupancy)[source]¶ Add a pyiron.objects.waves.core.Band instance
 Parameters
eigenvalue (float) – The eigenvalue associated with the Band instance
occupancy (flaot) – The occupancy associated with the Band instance

property
eig_occ_matrix
¶

property
value
¶

property
weight
¶
