phtsencSileTBtrans¶

class sisl.io.tbtrans.phtsencSileTBtrans(filename, mode='r', lvl=0, access=1, *args, **kwargs)[source]¶

PHtrans file object

Attributes

`E`	Sampled energy-points in file
`a_buf`	Atomic indices (0-based) of device atoms
`a_dev`	Atomic indices (0-based) of device atoms
`base_file`	File of the current Sile
`cell`	Unit cell in file
`elecs`	List of electrodes
`file`	File of the current Sile
`geom`	The associated geometry from this file
`geometry`	The associated geometry from this file
`k`	Sampled k-points in file
`kpt`	Sampled k-points in file
`lasto`	Last orbital of corresponding atom
`nE`	Number of energy-points in file
`na`	Returns number of atoms in the cell
`na_b`	Number of atoms in the buffer region
`na_buffer`	Number of atoms in the buffer region
`na_d`	Number of atoms in the device region
`na_dev`	Number of atoms in the device region
`na_u`	Returns number of atoms in the cell
`ne`	Number of energy-points in file
`nk`	Number of k-points in file
`nkpt`	Number of k-points in file
`no`	Returns number of orbitals in the cell
`no_d`	Number of orbitals in the device region
`no_u`	Returns number of orbitals in the cell
`o_dev`	Orbital indices (0-based) of device orbitals
`wk`	Weights of k-points in file
`wkpt`	Weights of k-points in file
`xa`	Atomic coordinates in file
`xyz`	Atomic coordinates in file

Methods

`Eindex`(E)	Return the closest energy index corresponding to the energy `E`
`__init__`(filename[, mode, lvl, access])	Initialize self.
`a2p`(atom[, elec])	Return the pivoting orbital indices (0-based) for the atoms, possibly on an electrode
`btd`()	Block-sizes for the BTD method in the device region
`chemical_potential`(elec)	Return the chemical potential associated with the electrode elec
`close`()
`dir_file`([filename])	File of the current Sile
`eta`(elec)	The imaginary part used when calculating the self-energies in eV
`exist`()	Query whether the file exists
`iter`([group, dimension, variable, levels, root])	Iterator on all groups, variables and dimensions.
`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`()	Number of blocks in the BTD partioning in the device region
`o2p`(orbital[, 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
`read`(args, *kwargs)	Generic read method which should be overloaded in child-classes
`read_geometry`(args, *kwargs)	Returns Geometry object from this file
`read_supercell`()	Returns SuperCell object from this file
`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
`write_geometry`(args, *kwargs)	This is not meant to be used

E¶: Sampled energy-points in file

Eindex(E)¶

Return the closest energy index corresponding to the energy E

Parameters:	E : float or int if `int`, return it-self, else return the energy index which is closests to the energy.

a2p(atom, elec=None)¶

Return the pivoting orbital indices (0-based) for the atoms, possibly on an electrode

This is equivalent to:

>>> p = self.o2p(self.geom.a2o(atom, True)) 

Parameters:	atom : array_like or int atomic indices (0-based) elec : str or int or None electrode to return pivoting indices of (if None it is the device pivoting indices).

a_buf¶: Atomic indices (0-based) of device atoms

a_dev¶: Atomic indices (0-based) of device atoms

base_file¶: File of the current Sile

btd()¶: Block-sizes for the BTD method in the device region

cell¶: Unit cell in file

chemical_potential(elec)¶: Return the chemical potential associated with the electrode elec

close()¶

dir_file(filename=None)¶: File of the current Sile

elecs¶: List of electrodes

eta(elec)¶: The imaginary part used when calculating the self-energies in eV

exist()¶: Query whether the file exists

file¶: File of the current Sile

geom¶: The associated geometry from this file

geometry¶: The associated geometry from 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 instances
dimension : bool (True): whether the iterator yields Dimension instances
variable : bool (True): whether the iterator yields Variable instances
levels : int (-1): number of levels to traverse, with respect to root 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 

k¶: Sampled k-points in file

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 the queried k-point in reduced coordinates \(]-0.5;0.5]\).

kpt¶: Sampled k-points in file

lasto¶: Last orbital of corresponding atom

mu(elec)¶: Return the chemical potential associated with the electrode elec

nE¶: Number of energy-points in file

n_btd()¶: Number of blocks in the BTD partioning in the device region

na¶: Returns number of atoms in the cell

na_b¶: Number of atoms in the buffer region

na_buffer¶: Number of atoms in the buffer region

na_d¶: Number of atoms in the device region

na_dev¶: Number of atoms in the device region

na_u¶: Returns number of atoms in the cell

ne¶: Number of energy-points in file

nk¶: Number of k-points in file

nkpt¶: Number of k-points in file

no¶: Returns number of orbitals in the cell

no_d¶: Number of orbitals in the device region

no_u¶: Returns number of orbitals in the cell

o2p(orbital, elec=None)¶

Return the pivoting indices (0-based) for the orbitals, possibly on an electrode

Parameters:	orbital : array_like or int orbital indices (0-based) elec : str or int or None electrode to return pivoting indices of (if None it is the device pivoting indices).

o_dev¶: Orbital indices (0-based) of device orbitals

pivot(elec=None, in_device=False, sort=False)¶

Return the pivoting indices for a specific electrode

Parameters:	elec : str or int the corresponding electrode to return the self-energy from in_device : bool, optional If `True` the pivoting table will be translated to the device region orbitals sort : bool, optional Whether the returned indices are sorted. Mostly useful if the self-energies are returned sorted as well.

Examples

>>> se = tbtsencSileTBtrans(...) 
>>> 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]

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

self_energy(elec, E, k, 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 (equivalent to pivoting the self-energy)

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 but not necessarily consecutive in the device region.

wk¶: Weights of k-points in file

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.

write_geometry(*args, **kwargs)¶: This is not meant to be used

xa¶: Atomic coordinates in file

xyz¶: Atomic coordinates in file