sisl.physics.RealSpaceSE
- class sisl.physics.RealSpaceSE(parent, semi_axis, k_axes, unfold=(1, 1, 1), **options)
Bases:
SelfEnergy
Bulk real-space self-energy (or Green function) for a given physical object with periodicity
The real-space self-energy is calculated via the k-averaged Green function:
\[\boldsymbol\Sigma^\mathcal{R}(E) = \mathbf S^\mathcal{R} (E+i\eta) - \mathbf H^\mathcal{R} - \Big[\sum_{\mathbf k} \mathbf G_{\mathbf k}(E)\Big]^{-1}\]The method actually used is relying on
RecursiveSI
andBloch
objects.- Parameters
parent (SparseOrbitalBZ) – a physical object from which to calculate the real-space self-energy. The parent object must have only 3 supercells along the direction where self-energies are used.
semi_axis (int) – semi-infinite direction (where self-energies are used and thus exact precision)
k_axes (array_like of int) – the axes where k-points are desired. 1 or 2 values are required and the semi_axis cannot be one of them
unfold ((3,) of int) – number of times the parent structure is tiled along each direction The resulting Green function/self-energy ordering is always tiled along the semi-infinite direction first, and then the other directions in order.
eta (float, optional) – imaginary part in the self-energy calculations (default 1e-4 eV)
dk (float, optional) – fineness of the default integration grid, specified in units of Ang, default to 1000 which translates to 1000 k-points along reciprocal cells of length 1. Ang^-1.
bz (BrillouinZone, optional) – integration k-points, if not passed the number of k-points will be determined using dk and time-reversal symmetry will be determined by trs, the number of points refers to the unfolded system.
trs (bool, optional) – whether time-reversal symmetry is used in the BrillouinZone integration, default to true.
Examples
>>> graphene = geom.graphene() >>> H = Hamiltonian(graphene) >>> H.construct([(0.1, 1.44), (0, -2.7)]) >>> rse = RealSpaceSE(H, 0, 1, (3, 4, 1)) >>> rse.green(0.1)
The Brillouin zone integration is determined naturally.
>>> graphene = geom.graphene() >>> H = Hamiltonian(graphene) >>> H.construct([(0.1, 1.44), (0, -2.7)]) >>> rse = RealSpaceSE(H, 0, 1, (3, 4, 1)) >>> rse.set_options(eta=1e-3, bz=MonkhorstPack(H, [1, 1000, 1])) >>> rse.initialize() >>> rse.green(0.1) # eta = 1e-3 >>> rse.green(0.1 + 1j * 1e-4) # eta = 1e-4
Manually specify Brillouin zone integration and default \(\eta\) value.
Methods
clear
()Clears the internal arrays created in
initialize
green
(E[, k, dtype])Calculate the real-space Green function
Initialize the internal data-arrays used for efficient calculation of the real-space quantities
real_space_coupling
([ret_indices])Real-space coupling parent where sites fold into the parent real-space unit cell
Return the parent object in the real-space unfolded region
scattering_matrix
(*args, **kwargs)Calculate the scattering matrix by first calculating the self-energy
se2scat
(SE)Calculate the scattering matrix from the self-energy
self_energy
(E[, k, bulk, coupling, dtype])Calculate the real-space self-energy
set_options
(**options)Update options in the real-space self-energy
- __init__(parent, semi_axis, k_axes, unfold=(1, 1, 1), **options)[source]
Initialize real-space self-energy calculator
- clear()[source]
Clears the internal arrays created in
initialize
- green(E, k=(0, 0, 0), dtype=None, **kwargs)[source]
Calculate the real-space Green function
The real space Green function is calculated via:
\[\mathbf G^\mathcal{R}(E) = \sum_{\mathbf k} \mathbf G_{\mathbf k}(E)\]- Parameters
E (float/complex) – energy to evaluate the real-space Green function at
k (array_like, optional) – only viable for 3D bulk systems with real-space Green functions along 2 directions. I.e. this would correspond to a circular real-space Green function
dtype (numpy.dtype, optional) – the resulting data type, default to
np.complex128
**kwargs (dict, optional) – arguments passed directly to the
self.parent.Pk
method (notself.parent.Sk
), for instancespin
- initialize()[source]
Initialize the internal data-arrays used for efficient calculation of the real-space quantities
This method should first be called after all options has been specified.
If the user hasn’t specified the
bz
value as an option this method will update the internal integration Brillouin zone based ondk
andtrs
options. The \(\mathbf k\) point sampling corresponds to the number of points in the non-folded system and thus the final sampling is equivalent to the sampling times the unfolding (per \(\mathbf k\) direction).
- real_space_coupling(ret_indices=False)[source]
Real-space coupling parent where sites fold into the parent real-space unit cell
The resulting parent object only contains the inner-cell couplings for the elements that couple out of the real-space matrix.
- Parameters
ret_indices (bool, optional) – if true, also return the atomic indices (corresponding to
real_space_parent
) that encompass the coupling matrix- Returns
parent (object) – parent object only retaining the elements of the atoms that couple out of the primary unit cell
atoms (numpy.ndarray) – indices for the atoms that couple out of the geometry, only if ret_indices is true
- scattering_matrix(*args, **kwargs)
Calculate the scattering matrix by first calculating the self-energy
Any arguments that is passed to this method is directly passed to
self_energy
.See
self_energy
for details.This corresponds to:
\[\boldsymbol\Gamma = i(\boldsymbol\Sigma - \boldsymbol \Sigma ^\dagger)\]Examples
Calculating both the self-energy and the scattering matrix.
>>> SE = SelfEnergy(...) >>> self_energy = SE.self_energy(0.1) >>> gamma = SE.scattering_matrix(0.1)
For a huge performance boost, please do:
>>> SE = SelfEnergy(...) >>> self_energy = SE.self_energy(0.1) >>> gamma = SE.se2scat(self_energy)
Notes
When using both the self-energy and the scattering matrix please use
se2scat
after having calculated the self-energy, this will be much, MUCH faster!See also
se2scat
converting the self-energy to the scattering matrix
self_energy
the used routine to calculate the self-energy before calculating the scattering matrix
- static se2scat(SE)
Calculate the scattering matrix from the self-energy
\[\boldsymbol\Gamma = i(\boldsymbol\Sigma - \boldsymbol \Sigma ^\dagger)\]- Parameters
SE (matrix) – self-energy matrix
- self_energy(E, k=(0, 0, 0), bulk=False, coupling=False, dtype=None, **kwargs)[source]
Calculate the real-space self-energy
The real space self-energy is calculated via:
\[\boldsymbol\Sigma^{\mathcal{R}}(E) = \mathbf S^{\mathcal{R}} E - \mathbf H^{\mathcal{R}} - \Big[\sum_{\mathbf k} \mathbf G_{\mathbf k}(E)\Big]^{-1}\]- Parameters
E (float/complex) – energy to evaluate the real-space self-energy at
k (array_like, optional) – only viable for 3D bulk systems with real-space self-energies along 2 directions. I.e. this would correspond to circular self-energies.
bulk (bool, optional) – if true, \(\mathbf S^{\mathcal{R}} E - \mathbf H^{\mathcal{R}} - \boldsymbol\Sigma^\mathcal{R}\) is returned, otherwise \(\boldsymbol\Sigma^\mathcal{R}\) is returned
coupling (bool, optional) – if True, only the self-energy terms located on the coupling geometry (coupling_geometry) are returned
dtype (numpy.dtype, optional) – the resulting data type, default to
np.complex128
**kwargs (dict, optional) – arguments passed directly to the
self.parent.Pk
method (notself.parent.Sk
), for instancespin
- set_options(**options)[source]
Update options in the real-space self-energy
After updating options one should re-call
initialize
for consistency.- Parameters
eta (float, optional) – imaginary part in the self-energy calculations (default 1e-4 eV)
dk (float, optional) – fineness of the default integration grid, specified in units of Ang, default to 1000 which translates to 1000 k-points along reciprocal cells of length 1. Ang^-1.
bz (BrillouinZone, optional) – integration k-points, if not passed the number of k-points will be determined using dk and time-reversal symmetry will be determined by trs, the number of points refers to the unfolded system.
trs (bool, optional) – whether time-reversal symmetry is used in the BrillouinZone integration, default to true.