tbtavncSileTBtrans¶

class sisl.io.tbtrans.tbtavncSileTBtrans(filename, mode='r', lvl=0, access=1, _open=True)[source]¶

TBtrans average file object

This Sile implements the writing of the TBtrans output *.TBT.AV.nc sile which contains the k-averaged quantities related to the NEGF code TBtrans.

See tbtncSileTBtrans for details as this object is essentially a copy of it.

Attributes

`E`	Sampled energy-points in file
`a_d`	Atomic indices (0-based) of device atoms
`a_dev`	Atomic indices (0-based) of device atoms
`cell`	Unit cell in file
`elecs`	List of electrodes
`file`	Filename of the current Sile
`geom`	The associated geometry from this file
`geometry`	The associated geometry from this 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_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
`nkpt`	Always return 1, this is to signal other routines
`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
`pivot`	Pivot table of device orbitals to obtain input sorting
`wkpt`	Always return [1.], this is to signal other routines
`xa`	Atomic coordinates in file
`xyz`	Atomic coordinates in file

Methods

`ADOS`([elec, E, kavg, atom, orbital, sum, norm])	Spectral density of states (DOS) (1/eV).
`BDOS`([elec, E, kavg, sum, norm])	Bulk density of states (DOS) (1/eV).
`DOS`([E, kavg, atom, orbital, sum, norm])	Green function density of states (DOS) (1/eV).
`Eindex`(E)	Return the closest energy index corresponding to the energy `E`
`__init__`(filename[, mode, lvl, access, _open])	Creates/Opens a SileCDF
`a2p`(atom)	Return the pivoting indices (0-based) for the atoms
`atom_current`(elec, E[, kavg, activity])	Atomic current of atoms
`atom_current_from_orbital`(Jij[, activity])	Atomic current of atoms by passing the orbital current
`bond_current`(elec, E[, kavg, isc, sum, uc])	Bond-current between atoms (sum of orbital currents)
`bond_current_from_orbital`(Jij[, sum, uc])	Bond-current between atoms (sum of orbital currents) from an external orbital current
`chemical_potential`(elec)	Return the chemical potential associated with the electrode elec
`close`()
`current`([elec_from, elec_to, kavg])	Current from from to to using the k-weights and energy spacings in the file.
`current_parameter`(elec_from, mu_from, ...[, ...])	Current from from to to using the k-weights and energy spacings in the file.
`electronic_temperature`(elec)	Return temperature of the electrode electronic distribution in Kelvin
`eta`(elec)	The imaginary part used when calculating the self-energies in eV
`exist`()	Query whether the file exists
`info`([elec])	Information about the calculated quantities available for extracting in this file
`isDataset`(obj)	Return true if `obj` is an instance of the NetCDF4 `Dataset` type
`isDimension`(obj)	Return true if `obj` is an instance of the NetCDF4 `Dimension` type
`isGroup`(obj)	Return true if `obj` is an instance of the NetCDF4 `Group` type
`isRoot`(obj)	Return true if `obj` is an instance of the NetCDF4 `Dataset` type
`isVariable`(obj)	Return true if `obj` is an instance of the NetCDF4 `Variable` type
`iter`([group, dimension, variable, levels, root])	Iterator on all groups, variables and dimensions.
`kT`(elec)	Return temperature of the electrode electronic distribution in 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
`norm`([atom, orbital, norm])	Normalization factor depending on the input
`o2p`(orbital)	Return the pivoting indices (0-based) for the orbitals
`orbital_current`(elec, E[, kavg, isc, take])	Orbital current originating from elec as a sparse matrix
`read`(args, *kwargs)	Generic read method which should be overloaded in child-classes
`read_data`(args, *kwargs)	Read specific type of data.
`read_geometry`(args, *kwargs)	Returns Geometry object from this file
`read_supercell`()	Returns SuperCell object from this file
`transmission`([elec_from, elec_to, kavg])	Transmission from from to to.
`transmission_bulk`([elec, kavg])	Bulk transmission for the elec electrode
`transmission_eig`([elec_from, elec_to, kavg])	Transmission eigenvalues from from to to.
`vector_current`(elec, E[, kavg, sum])	Vector for each atom describing the mean path for the current travelling through the atom
`vector_current_from_bond`(Jab)	Vector for each atom being the sum of bond-current times the normalized bond between the atoms
`write`(args, *kwargs)	Generic write method which should be overloaded in child-classes
`write_geometry`(args, *kwargs)	This is not meant to be used
`write_tbtav`(args, *kwargs)	Wrapper for writing the k-averaged TBT.AV.nc file.

ADOS(elec=0, E=None, kavg=True, atom=None, orbital=None, sum=True, norm='none')¶

Spectral density of states (DOS) (1/eV).

Extract the spectral DOS from electrode elec on a selected subset of atoms/orbitals in the device region

\[\mathrm{ADOS}_\mathfrak{el}(E) = \frac{1}{2\pi N} \sum_{\nu\in \mathrm{atom}/\mathrm{orbital}} [\mathbf{G}(E)\Gamma_\mathfrak{el}\mathbf{G}^\dagger]_{\nu\nu}(E)\]

The normalization constant (\(N\)) is defined in the routine norm and depends on the arguments.

Parameters:

elec: str, int, optional

electrode originating spectral function

E : float or int, optional

optionally only return the DOS of atoms at a given energy point

kavg: bool, int or array_like, optional

whether the returned DOS is k-averaged, an explicit k-point or a selection of k-points

atom : array_like of int or bool, optional

only return for a given set of atoms (default to all). NOT allowed with orbital keyword

orbital : array_like of int or bool, optional

only return for a given set of orbitals (default to all) NOT allowed with atom keyword

sum : bool, optional

whether the returned quantities are summed or returned as is, i.e. resolved per atom/orbital.

norm : {‘none’, ‘atom’, ‘orbital’, ‘all’}

how the normalization of the summed DOS is performed (see norm routine).

See also

DOS: the total density of states (including bound states)
BDOS: the bulk density of states in an electrode

BDOS(elec=0, E=None, kavg=True, sum=True, norm='none')¶

Bulk density of states (DOS) (1/eV).

Extract the bulk DOS from electrode elec on a selected subset of atoms/orbitals in the device region

\[\mathrm{BDOS}_\mathfrak{el}(E) = -\frac{1}{\pi} \Im\mathbf{G}(E)\]

Parameters:

elec: str, int, optional

electrode where the bulk DOS is returned

E : float or int, optional

optionally only return the DOS of atoms at a given energy point

kavg: bool, int or array_like, optional

whether the returned DOS is k-averaged, an explicit k-point or a selection of k-points

sum : bool, optional

whether the returned quantities are summed or returned as is, i.e. resolved per atom/orbital.

norm : {‘none’, ‘atom’, ‘orbital’, ‘all’}

whether the returned quantities are summed or normed by total number of orbitals. Currently one cannot extract DOS per atom/orbital.

See also

DOS: the total density of states (including bound states)
ADOS: the spectral density of states from an electrode

DOS(E=None, kavg=True, atom=None, orbital=None, sum=True, norm='none')¶

Green function density of states (DOS) (1/eV).

Extract the DOS on a selected subset of atoms/orbitals in the device region

\[\mathrm{DOS}(E) = -\frac{1}{\pi N} \sum_{\nu\in \mathrm{atom}/\mathrm{orbital}} \Im \mathbf{G}_{\nu\nu}(E)\]

The normalization constant (\(N\)) is defined in the routine norm and depends on the arguments.

Parameters:

E : float or int, optional

optionally only return the DOS of atoms at a given energy point

kavg: bool, int or array_like, optional

whether the returned DOS is k-averaged, an explicit k-point or a selection of k-points

atom : array_like of int or bool, optional

only return for a given set of atoms (default to all). NOT allowed with orbital keyword

orbital : array_like of int or bool, optional

only return for a given set of orbitals (default to all) NOT allowed with atom keyword

sum : bool, optional

whether the returned quantities are summed or returned as is, i.e. resolved per atom/orbital.

norm : {‘none’, ‘atom’, ‘orbital’, ‘all’}

how the normalization of the summed DOS is performed (see norm routine)

See also

ADOS: the spectral density of states from an electrode
BDOS: the bulk density of states in an electrode

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)¶

Return the pivoting indices (0-based) for the atoms

Parameters:

atom : array_like or int

atomic indices (0-based)

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

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

atom_current(elec, E, kavg=True, activity=True)¶

Atomic current of atoms

Short hand function for calling orbital_current and atom_current_from_orbital.

Parameters:

elec: str, int

the electrode of originating electrons

E: float or int

the energy or energy index of the atom current.

kavg: bool, int or array_like, optional

whether the returned atomic current is k-averaged, an explicit k-point or a selection of k-points

activity: bool, optional

whether the activity current is returned, see atom_current_from_orbital for details.

See also

orbital_current: the orbital current between individual orbitals
bond_current_from_orbital: transfer the orbital current to bond current
bond_current: the bond current (orbital current summed over orbitals)
vector_current: an atomic field current for each atom (Cartesian representation of bond-currents)

atom_current_from_orbital(Jij, activity=True)¶

Atomic current of atoms by passing the orbital current

The atomic current is a single number specifying a figure of the magnitude current flowing through each atom. It is thus not a quantity that can be related to the physical current flowing in/out of atoms but is merely a number that provides an idea of how much current this atom is redistributing.

The atomic current may have two meanings based on these two equations

\[\begin{split}J_\alpha^{|a|} &=\frac{1}{2} \sum_\beta \Big| \sum_{\nu\in \alpha}\sum_{\mu\in \beta} J_{\nu\mu} \Big| \\ J_\alpha^{|o|} &=\frac{1}{2} \sum_\beta \sum_{\nu\in \alpha}\sum_{\mu\in \beta} \big| J_{\nu\mu} \big|\end{split}\]

If the activity current is requested (activity=True) \(J_\alpha^{\mathcal A} = \sqrt{ J_\alpha^{|a|} J_\alpha^{|o|} }\) is returned.

If activity=False \(J_\alpha^{|a|}\) is returned.

For geometries with all atoms only having 1-orbital, they are equivalent.

Generally the activity current is a more rigorous figure of merit for the current flowing through an atom. More so than than the summed absolute atomic current due to the following reasoning. The activity current is a geometric mean of the absolute bond current and the absolute orbital current. This means that if there is an atom with a large orbital current it will have a larger activity current.

Parameters:

Jij: scipy.sparse.csr_matrix

the orbital currents as retrieved from orbital_current

activity: bool, optional

True to return the activity current, see explanation above

Examples

>>> Jij = tbt.orbital_current(0, -1.03) # orbital current @ E = -1 eV originating from electrode ``0`` 
>>> Ja = tbt.atom_current_from_orbital(Jij) 

bond_current(elec, E, kavg=True, isc=None, sum='+', uc=False)¶

Bond-current between atoms (sum of orbital currents)

Short hand function for calling orbital_current and bond_current_from_orbital.

Parameters:

elec : str, int

the electrode of originating electrons

E : float or int

A float for energy in eV, int for explicit energy index Unlike orbital_current this may not be None as the down-scaling of the orbital currents may not be equivalent for all energy points.

kavg : bool, int or array_like, optional

whether the returned bond current is k-averaged, an explicit k-point or a selection of k-points

isc : array_like, optional

the returned bond currents from the unit-cell ([None, None, None]) (default) to the given supercell. If [None, None, None] is passed all bond currents are returned.

sum : {‘+’, ‘all’, ‘-‘}

If “+” is supplied only the positive orbital currents are used, for “-”, only the negative orbital currents are used, else return the sum of both.

uc : bool, optional

whether the returned bond-currents are only in the unit-cell. If True this will return a sparse matrix of shape = (self.na, self.na), else, it will return a sparse matrix of shape = (self.na, self.na * self.n_s). One may figure out the connections via Geometry.sc_index.

See also

orbital_current: the orbital current between individual orbitals
bond_current_from_orbital: transfer the orbital current to bond current
atom_current: the atomic current for each atom (scalar representation of bond-currents)
vector_current: an atomic field current for each atom (Cartesian representation of bond-currents)

Examples

>>> Jij = tbt.orbital_current(0, -1.0) # orbital current @ E = -1 eV originating from electrode ``0`` 
>>> Jab1 = tbt.bond_current_from_orbital(Jij) 
>>> Jab2 = tbt.bond_current(0, -1.0) 
>>> Jab1 == Jab2 
True

bond_current_from_orbital(Jij, sum='+', uc=False)¶

Bond-current between atoms (sum of orbital currents) from an external orbital current

Conversion routine from orbital currents into bond currents.

The bond currents are a sum over all orbital currents:

\[J_{\alpha\beta} = \sum_{\nu\in\alpha}\sum_{\mu\in\beta} J_{\nu\mu}\]

where if

sum='+': only \(J_{\nu\mu} > 0\) are summed,
sum='-': only \(J_{\nu\mu} < 0\) are summed,
sum='all': all \(J_{\nu\mu}\) are summed.

Parameters:

Jij : scipy.sparse.csr_matrix

the orbital currents as retrieved from orbital_current

sum : {‘+’, ‘all’, ‘-‘}

If “+” is supplied only the positive orbital currents are used, for “-”, only the negative orbital currents are used, else return both.

uc : bool, optional

whether the returned bond-currents are only in the unit-cell. If True this will return a sparse matrix of shape = (self.na, self.na), else, it will return a sparse matrix of shape = (self.na, self.na * self.n_s). One may figure out the connections via Geometry.sc_index.

See also

orbital_current: the orbital current between individual orbitals
bond_current: the bond current (orbital current summed over orbitals)
atom_current: the atomic current for each atom (scalar representation of bond-currents)
vector_current: an atomic field current for each atom (Cartesian representation of bond-currents)

Examples

>>> Jij = tbt.orbital_current(0, -1.0) # orbital current @ E = -1 eV originating from electrode ``0`` 
>>> Jab = tbt.bond_current_from_orbital(Jij) 
>>> Jab[2,3] # bond current between atom 3 and 4 

cell¶: Unit cell in file

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

close()¶

current(elec_from=0, elec_to=1, kavg=True)¶

Current from from to to using the k-weights and energy spacings in the file.

Calculates the current as:

\[I(\mu_t - \mu_f) = \frac{e}{h}\int\!\mathrm{d}E\, T(E) [n_F(\mu_t, k_B T_t) - n_F(\mu_f, k_B T_f)]\]

The chemical potential and the temperature are taken from this object.

Parameters:

elec_from: str, int, optional

the originating electrode

elec_to: str, int, optional

the absorbing electrode (different from elec_from)

kavg: bool, int or array_like, optional

whether the returned current is k-averaged, an explicit k-point or a selection of k-points

See also

current_parameter: to explicitly set the electronic temperature and chemical potentials
chemical_potential: routine that defines the chemical potential of the queried electrodes
kT: routine that defines the electronic temperature of the queried electrodes

current_parameter(elec_from, mu_from, kt_from, elec_to, mu_to, kt_to, kavg=True)¶

Current from from to to using the k-weights and energy spacings in the file.

Calculates the current as:

\[I(\mu_t - \mu_f) = \frac{e}{h}\int\!\mathrm{d}E\, T(E) [n_F(\mu_t, k_B T_t) - n_F(\mu_f, k_B T_f)]\]

The chemical potential and the temperature are passed as arguments to this routine.

Parameters:

elec_from: str, int

the originating electrode

mu_from: float

the chemical potential of the electrode (in eV)

kt_from: float

the electronic temperature of the electrode (in eV)

elec_to: str, int

the absorbing electrode (different from elec_from)

mu_to: float

the chemical potential of the electrode (in eV)

kt_to: float

the electronic temperature of the electrode (in eV)

kavg: bool, int or array_like, optional

whether the returned current is k-averaged, an explicit k-point or a selection of k-points

See also

current: which calculates the current with the chemical potentials and temperatures set in the TBtrans calculation

elecs¶: List of electrodes

electronic_temperature(elec)¶: Return temperature of the electrode electronic distribution in Kelvin

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

exist()¶: Query whether the file exists

file¶: Filename of the current Sile

geom¶: The associated geometry from this file

geometry¶: The associated geometry from this file

info(elec=None)¶

Information about the calculated quantities available for extracting in this file

Parameters:

elec : str, int

the electrode to request information from

isDataset(obj)¶

Return true if obj is an instance of the NetCDF4 Dataset type

This is just a wrapper for isinstance(obj, netCDF4.Dataset).

isDimension(obj)¶

Return true if obj is an instance of the NetCDF4 Dimension type

This is just a wrapper for isinstance(obj, netCDF4.Dimension).

isGroup(obj)¶

Return true if obj is an instance of the NetCDF4 Group type

This is just a wrapper for isinstance(obj, netCDF4.Group).

isRoot(obj)¶

Return true if obj is an instance of the NetCDF4 Dataset type

This is just a wrapper for isinstance(obj, netCDF4.Dataset).

isVariable(obj)¶

Return true if obj is an instance of the NetCDF4 Variable type

This is just a wrapper for isinstance(obj, netCDF4.Variable).

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 

kT(elec)¶: Return temperature of the electrode electronic distribution in eV

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

na¶: Returns number of atoms in the cell

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

nkpt¶: Always return 1, this is to signal other routines

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

norm(atom=None, orbital=None, norm='none')¶

Normalization factor depending on the input

The normalization can be performed in one of the below methods. In the following \(N\) refers to the normalization constant that is to be used (i.e. the divisor):

'none': \(N=1\)
'all': \(N\) equals the number of orbitals in the total device region.
'atom': \(N\) equals the total number of orbitals in the selected atoms. If orbital is an argument a conversion of orbital to the equivalent unique atoms is performed, and subsequently the total number of orbitals on the atoms is used. This makes it possible to compare the fraction of orbital DOS easier.
'orbital': \(N\) is the sum of selected orbitals, if atom is specified, this is equivalent to the ‘atom’ option.

Parameters:

atom : array_like of int or bool, optional

only return for a given set of atoms (default to all). NOT allowed with orbital keyword

orbital : array_like of int or bool, optional

only return for a given set of orbitals (default to all) NOT allowed with atom keyword

norm : {‘none’, ‘atom’, ‘orbital’, ‘all’}

how the normalization of the summed DOS is performed (see norm routine)

o2p(orbital)¶

Return the pivoting indices (0-based) for the orbitals

Parameters:

orbital : array_like or int

orbital indices (0-based)

orbital_current(elec, E, kavg=True, isc=None, take='all')¶

Orbital current originating from elec as a sparse matrix

This will return a sparse matrix, see scipy.sparse.csr_matrix for details. Each matrix element of the sparse matrix corresponds to the orbital indices of the underlying geometry.

Parameters:

elec: str, int

the electrode of originating electrons

E: float or int

the energy or the energy index of the orbital current. If an integer is passed it is the index, otherwise the index corresponding to Eindex(E) is used.

kavg: bool, int or array_like, optional

whether the returned orbital current is k-averaged, an explicit k-point or a selection of k-points

isc: array_like, optional

the returned bond currents from the unit-cell ([None, None, None]) to the given supercell, the default is all orbital currents for the supercell. To only get unit cell orbital currents, pass [0, 0, 0].

take : {‘all’, ‘+’, ‘-‘}

which orbital currents to return, all, positive or negative values only. Default to 'all' because it can then be used in the subsequent default arguments for bond_current_from_orbital and atom_current_from_orbital.

See also

bond_current_from_orbital: transfer the orbital current to bond current
bond_current: the bond current (orbital current summed over orbitals)
atom_current_from_orbital: transfer the orbital current to atomic current
atom_current: the atomic current for each atom (scalar representation of bond-currents)
vector_current: an atomic field current for each atom (Cartesian representation of bond-currents)

Examples

>>> Jij = tbt.orbital_current(0, -1.0) # orbital current @ E = -1 eV originating from electrode ``0`` 
>>> Jij[10, 11] # orbital current from the 11th to the 12th orbital 

pivot¶: Pivot table of device orbitals to obtain input sorting

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_data(*args, **kwargs)¶

Read specific type of data.

This is a generic routine for reading different parts of the data-file.

Parameters:

geom: bool, optional

return the geometry

atom_current: bool, optional

return the atomic current flowing through an atom (the activity current)

vector_current: bool, optional

return the orbital currents as vectors

read_geometry(*args, **kwargs)¶: Returns Geometry object from this file

read_supercell()¶: Returns SuperCell object from this file

transmission(elec_from=0, elec_to=1, kavg=True)¶

Transmission from from to to.

The transmission between two electrodes may be retrieved from the Sile.

Parameters:

elec_from: str, int, optional

the originating electrode

elec_to: str, int, optional

the absorbing electrode (different from elec_from)

kavg: bool, int or array_like, optional

whether the returned transmission is k-averaged, an explicit k-point or a selection of k-points

See also

transmission_eig: the transmission decomposed in eigenchannels
transmission_bulk: the total transmission in a periodic lead

transmission_bulk(elec=0, kavg=True)¶

Bulk transmission for the elec electrode

The bulk transmission is equivalent to creating a 2 terminal device with electrode elec tiled 3 times.

Parameters:

elec: str, int, optional

the bulk electrode

kavg: bool, int or array_like, optional

whether the returned transmission is k-averaged, an explicit k-point or a selection of k-points

See also

transmission: the total transmission
transmission_eig: the transmission decomposed in eigenchannels

transmission_eig(elec_from=0, elec_to=1, kavg=True)¶

Transmission eigenvalues from from to to.

Parameters:

elec_from: str, int, optional

the originating electrode

elec_to: str, int, optional

the absorbing electrode (different from elec_from)

kavg: bool, int or array_like, optional

whether the returned transmission is k-averaged, an explicit k-point or a selection of k-points

See also

transmission: the total transmission
transmission_bulk: the total transmission in a periodic lead

vector_current(elec, E, kavg=True, sum='+')¶

Vector for each atom describing the mean path for the current travelling through the atom

See vector_current_from_bond for details.

Parameters:

elec: str, int

the electrode of originating electrons

E: float or int

the energy or energy index of the vector current. Unlike orbital_current this may not be None as the down-scaling of the orbital currents may not be equivalent for all energy points.

kavg: bool, int or array_like, optional

whether the returned vector current is k-averaged, an explicit k-point or a selection of k-points

sum : {‘+’, ‘-‘, ‘all’}

By default only sum outgoing vector currents ('+'). The incoming vector currents may be retrieved by '-', while the average incoming and outgoing direction can be obtained with 'all'. In the last case the vector currents are divided by 2 to ensure the length of the vector is compatibile with the other options given a pristine system.

Returns:

numpy.ndarray : an array of vectors per atom in the Geometry (only non-zero for device atoms)

See also

orbital_current: the orbital current between individual orbitals
bond_current_from_orbital: transfer the orbital current to bond current
bond_current: the bond current (orbital current summed over orbitals)
atom_current: the atomic current for each atom (scalar representation of bond-currents)

vector_current_from_bond(Jab)¶

Vector for each atom being the sum of bond-current times the normalized bond between the atoms

The vector current is defined as:

\[\mathbf J_\alpha = \sum_\beta \frac{r_\beta - r_\alpha}{|r_\beta - r_\alpha|} \cdot J_{\alpha\beta}\]

Where \(J_{\alpha\beta}\) is the bond current between atom \(\alpha\) and \(\beta\) and \(r_\alpha\) are the atomic coordinates.

Parameters:

Jab: scipy.sparse.csr_matrix

the bond currents as retrieved from bond_current

Returns:

numpy.ndarray : an array of vectors per atom in the Geometry (only non-zero for device atoms)

See also

orbital_current: the orbital current between individual orbitals
bond_current_from_orbital: transfer the orbital current to bond current
bond_current: the bond current (orbital current summed over orbitals)
atom_current: the atomic current for each atom (scalar representation of bond-currents)

wkpt¶: Always return [1.], this is to signal other routines

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

write_tbtav(*args, **kwargs)[source]¶

Wrapper for writing the k-averaged TBT.AV.nc file.

This write requires the TBT.nc Sile object passed as the first argument, or as the keyword from=tbt argument.

Parameters:

from : tbtncSileTBtrans

the TBT.nc file object that has the k-sampled quantities.

xa¶: Atomic coordinates in file

xyz¶: Atomic coordinates in file