sisl.io.tbtrans.phtsencSilePHtrans
- class sisl.io.tbtrans.phtsencSilePHtrans(filename, mode='r', lvl=0, access=1, *args, **kwargs)
Bases:
tbtsencSileTBtrans
PHtrans file object
Methods
Eindex
(E)Return the closest energy index corresponding to the energy
E
a2p
(atoms)Return the pivoting orbital indices (0-based) for the atoms, possibly on an electrode
a_down
(elec[, bulk])Down-folding atomic indices for a given electrode
a_elec
(elec)Electrode atomic indices for the full geometry (sorted)
bloch
(elec)Bloch-expansion coefficients for an electrode
btd
([elec])Block-sizes for the BTD method in the device/electrode region
chemical_potential
(elec)Return the chemical potential associated with the electrode elec
close
()dir_file
([filename, filename_base])File of the current Sile
electron_temperature
(elec)Electron bath temperature [Kelvin]
eta
([elec])The imaginary part used when calculating the self-energies in eV (or for the device
info
([elec])Information about the self-energy file available for extracting in this file
iter
([group, dimension, variable, levels, root])Iterator on all groups, variables and dimensions.
kT
(elec)Electron bath temperature [eV]
kindex
(k)Return the index of the k-point that is closests to the queried k-point (in reduced coordinates)
mu
(elec)Return the chemical potential associated with the electrode elec
n_btd
([elec])Number of blocks in the BTD partioning
na_down
(elec)Number of atoms in the downfolding region (without device downfolded region)
no_down
(elec)Number of orbitals in the downfolding region (plus device downfolded region)
no_e
(elec)Number of orbitals in the downfolded region of the electrode in the device
o2p
(orbitals[, elec])Return the pivoting indices (0-based) for the orbitals, possibly on an electrode
pivot
([elec, in_device, sort])Return the pivoting indices for a specific electrode (in the device region) or the device
pivot_down
(elec)Pivoting orbitals for the downfolding region of a given electrode
read
(*args, **kwargs)Generic read method which should be overloaded in child-classes
read_geometry
(*args, **kwargs)Returns Geometry object from this file
Returns SuperCell object from this file
scattering_matrix
(elec, E[, k, sort])Return the scattering matrix from the electrode elec
self_energy
(elec, E[, k, sort])Return the self-energy from the electrode elec
self_energy_average
(elec, E[, sort])Return the k-averaged average self-energy from the electrode elec
write
(*args, **kwargs)Generic write method which should be overloaded in child-classes
Sampled energy-points in file
Atomic indices (0-based) of device atoms
Atomic indices (0-based) of device atoms (sorted)
File of the current Sile
Unit cell in file
List of electrodes
File of the current Sile
The associated geometry from this file
The associated geometry from this file
Sampled k-points in file
Sampled k-points in file
Last orbital of corresponding atom
Number of energy-points in file
Returns number of atoms in the cell
Number of atoms in the buffer region
Number of atoms in the buffer region
Number of atoms in the device region
Number of atoms in the device region
Returns number of atoms in the cell
Number of energy-points in file
Number of k-points in file
Number of k-points in file
Returns number of orbitals in the cell
Number of orbitals in the device region
Returns number of orbitals in the cell
Orbital indices (0-based) of device orbitals (sorted)
Weights of k-points in file
Weights of k-points in file
Atomic coordinates in file
Atomic coordinates in file
- property E
Sampled energy-points in file
- Eindex(E)
Return the closest energy index corresponding to the energy
E
- __init__(filename, mode='r', lvl=0, access=1, *args, **kwargs)
- a2p(atoms)
Return the pivoting orbital indices (0-based) for the atoms, possibly on an electrode
This is equivalent to:
>>> p = self.o2p(self.geometry.a2o(atom, True))
Will warn if an atom requested is not in the device list of atoms.
- Parameters
atoms (array_like or int) – atomic indices (0-based)
- property a_buf
Atomic indices (0-based) of device atoms
- property a_dev
Atomic indices (0-based) of device atoms (sorted)
- a_down(elec, bulk=False)
Down-folding atomic indices for a given electrode
- a_elec(elec)
Electrode atomic indices for the full geometry (sorted)
- property base_file
File of the current Sile
- bloch(elec)
Bloch-expansion coefficients for an electrode
- btd(elec=None)
Block-sizes for the BTD method in the device/electrode region
- property cell
Unit cell in file
- chemical_potential(elec)
Return the chemical potential associated with the electrode elec
- close()
- dir_file(filename=None, filename_base='')
File of the current Sile
- property elecs
List of electrodes
- eta(elec=None)
The imaginary part used when calculating the self-energies in eV (or for the device
- property file
File of the current Sile
- property geom
The associated geometry from this file
- property geometry
The associated geometry from this file
- info(elec=None)
Information about the self-energy file available for extracting in this file
- iter(group=True, dimension=True, variable=True, levels=- 1, root=None)
Iterator on all groups, variables and dimensions.
This iterator iterates through all groups, variables and dimensions in the
Dataset
The generator sequence will _always_ be:
Group
Dimensions in group
Variables in group
As the dimensions are generated before the variables it is possible to copy groups, dimensions, and then variables such that one always ensures correct dependencies in the generation of a new
SileCDF
.- Parameters
group (
bool
(True)) – whether the iterator yields Group instancesdimension (
bool
(True)) – whether the iterator yields Dimension instancesvariable (
bool
(True)) – whether the iterator yields Variable instanceslevels (
int
(-1)) – number of levels to traverse, with respect toroot
variable, i.e. number of sub-groups this iterator will return.root (
str
(None)) – the base root to start iterating from.
Examples
Script for looping and checking each instance.
>>> for gv in self.iter(): ... if self.isGroup(gv): ... # is group ... elif self.isDimension(gv): ... # is dimension ... elif self.isVariable(gv): ... # is variable
- property k
Sampled k-points in file
- kT(elec)
Electron bath temperature [eV]
See also
electron_temperature
bath temperature in [K]
- kindex(k)
Return the index of the k-point that is closests to the queried k-point (in reduced coordinates)
- Parameters
k (array_like of float or int) – the queried k-point in reduced coordinates \(]-0.5;0.5]\). If
int
return it-self.
- property kpt
Sampled k-points in file
- property lasto
Last orbital of corresponding atom
- mu(elec)
Return the chemical potential associated with the electrode elec
- property nE
Number of energy-points in file
- n_btd(elec=None)
Number of blocks in the BTD partioning
- property na
Returns number of atoms in the cell
- property na_b
Number of atoms in the buffer region
- property na_buffer
Number of atoms in the buffer region
- property na_d
Number of atoms in the device region
- property na_dev
Number of atoms in the device region
- na_down(elec)
Number of atoms in the downfolding region (without device downfolded region)
- property na_u
Returns number of atoms in the cell
- property ne
Number of energy-points in file
- property nk
Number of k-points in file
- property nkpt
Number of k-points in file
- property no
Returns number of orbitals in the cell
- property no_d
Number of orbitals in the device region
- no_down(elec)
Number of orbitals in the downfolding region (plus device downfolded region)
- no_e(elec)
Number of orbitals in the downfolded region of the electrode in the device
- property no_u
Returns number of orbitals in the cell
- o2p(orbitals, elec=None)
Return the pivoting indices (0-based) for the orbitals, possibly on an electrode
Will warn if an orbital requested is not in the device list of orbitals.
- property o_dev
Orbital indices (0-based) of device orbitals (sorted)
See also
pivot
retrieve the device orbitals, non-sorted
- pivot(elec=None, in_device=False, sort=False)
Return the pivoting indices for a specific electrode (in the device region) or the device
- Parameters
elec (str or int) – the corresponding electrode to return the pivoting indices from
in_device (bool, optional) – If
True
the pivoting table will be translated to the device region orbitals. If sort is also true, this would correspond to the orbitals directly translated to the geometryself.geometry.sub(self.a_dev)
.sort (bool, optional) – Whether the returned indices are sorted. Mostly useful if you want to handle the device in a non-pivoted order.
Examples
>>> se = tbtncSileTBtrans(...) >>> se.pivot() [3, 4, 6, 5, 2] >>> se.pivot(sort=True) [2, 3, 4, 5, 6] >>> se.pivot(0) [2, 3] >>> se.pivot(0, in_device=True) [4, 0] >>> se.pivot(0, in_device=True, sort=True) [0, 1] >>> se.pivot(0, sort=True) [2, 3]
See also
pivot_down
for the pivot table for electrodes down-folding regions
- pivot_down(elec)
Pivoting orbitals for the downfolding region of a given electrode
- plot
Handles all plotting possibilities for a class
- read(*args, **kwargs)
Generic read method which should be overloaded in child-classes
- Parameters
kwargs – keyword arguments will try and search for the attribute
read_<>
and call it with the remaining**kwargs
as arguments.
- read_geometry(*args, **kwargs)
Returns Geometry object from this file
- read_supercell()
Returns SuperCell object from this file
- scattering_matrix(elec, E, k=0, sort=False)
Return the scattering matrix from the electrode elec
The scattering matrix is calculated as:
\[\Gamma(E) = i [\Sigma(E) - \Sigma^\dagger(E)]\]- Parameters
elec (str or int) – the corresponding electrode to return the scattering matrix from
E (float or int) – energy to retrieve the scattering matrix at, if a floating point the closest energy value will be found and returned, if an integer it will correspond to the exact index
k (array_like or int) – k-point to retrieve, if an integer it is the k-index in the file
sort (bool, optional) – if
True
the returned scattering matrix will be sorted according to the order of the orbitals in the non-pivoted geometry, otherwise the scattering matrix will be returned according to the pivoted orbitals in the device region.
- self_energy(elec, E, k=0, sort=False)
Return the self-energy from the electrode elec
- Parameters
elec (str or int) – the corresponding electrode to return the self-energy from
E (float or int) – energy to retrieve the self-energy at, if a floating point the closest energy value will be found and returned, if an integer it will correspond to the exact index
k (array_like or int) – k-point to retrieve, if an integer it is the k-index in the file
sort (bool, optional) – if
True
the returned self-energy will be sorted according to the order of the orbitals in the non-pivoted geometry, otherwise the self-energy will be returned according to the pivoted orbitals in the device region.
- self_energy_average(elec, E, sort=False)
Return the k-averaged average self-energy from the electrode elec
- Parameters
elec (str or int) – the corresponding electrode to return the self-energy from
E (float or int) – energy to retrieve the self-energy at, if a floating point the closest energy value will be found and returned, if an integer it will correspond to the exact index
sort (bool, optional) – if
True
the returned self-energy will be sorted according to the order of the orbitals in the non-pivoted geometry, otherwise the self-energy will be returned according to the pivoted orbitals in the device region.
- to_json()
- property wk
Weights of k-points in file
- property wkpt
Weights of k-points in file
- write(*args, **kwargs)
Generic write method which should be overloaded in child-classes
- Parameters
**kwargs – keyword arguments will try and search for the attribute write_ and call it with the remaining
**kwargs
as arguments.
- property xa
Atomic coordinates in file
- property xyz
Atomic coordinates in file