sisl.io.tbtrans.tbtprojncSileTBtrans

class sisl.io.tbtrans.tbtprojncSileTBtrans(filename, mode='r', lvl=0, access=1, *args, **kwargs)

Bases: sisl.io.tbtrans.tbtncSileTBtrans

TBtrans projection file object

Methods

`ADOS`(elec_mol_proj[, E, kavg, atoms, ...])	Projected spectral density of states (DOS) (1/eV)
`Adensity_matrix`(elec_mol_proj, E[, kavg, ...])	Projected spectral function density matrix at energy `E` (1/eV)
`BDOS`([elec, E, kavg, sum, norm])	Bulk density of states (DOS) (1/eV).
`DOS`([E, kavg, atoms, orbitals, sum, norm])	Green function density of states (DOS) (1/eV).
`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)
`atom_ACOHP`(elec, E[, kavg, isc, orbitals, uc])	Atomic COHP curve of the spectral function
`atom_ACOOP`(elec, E[, kavg, isc, orbitals, uc])	Atomic COOP curve of the spectral function
`atom_COHP_from_orbital`(COHP[, uc])	Calculate the atomic COHP curve from the orbital COHP
`atom_COOP_from_orbital`(COOP[, uc])	Calculate the atomic COOP curve from the orbital COOP
`atom_current`(elec, E[, kavg, activity, orbitals])	Atomic current of atoms
`atom_current_from_orbital`(Jij[, activity])	Atomic current of atoms by passing the orbital current
`bloch`(elec)	Bloch-expansion coefficients for an electrode
`bond_current`(elec, E[, kavg, isc, only, ...])	Bond-current between atoms (sum of orbital currents)
`bond_current_from_orbital`(Jij[, only, uc])	Bond-current between atoms (sum of orbital currents) from an external orbital current
`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
`eigenstate`(molecule[, k, all])	Return the eigenstate on the projected molecule
`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`([molecule])	Information about the calculated quantities 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
`norm`([atoms, orbitals, norm])	Normalization factor depending on the input
`o2p`(orbitals[, elec])	Return the pivoting indices (0-based) for the orbitals, possibly on an electrode
`orbital_ACOHP`(elec_mol_proj, E[, kavg, isc, ...])	Orbital COHP analysis of the projected spectral function
`orbital_ACOOP`(elec_mol_proj, E[, kavg, isc, ...])	Orbital COOP analysis of the projected spectral function
`orbital_current`(elec, E[, kavg, isc, only, ...])	Orbital current originating from elec as a sparse matrix
`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
`projections`(molecule)	List of projections on molecule
`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
`reflection`([elec, kavg, from_single])	Reflection into electrode elec
`transmission`(elec_mol_proj_from, ...[, kavg])	Transmission from mol_proj_elec_from to mol_proj_elec_to
`transmission_bulk`([elec, kavg])	Bulk transmission for the elec electrode
`transmission_eig`(elec_mol_proj_from, ...[, kavg])	Transmission eigenvalues from elec_mol_proj_from to elec_mol_proj_to
`vector_current`(elec, E[, kavg, only, orbitals])	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_tbtav`(args, *kwargs)	Convert this to a TBT.AV.nc file, i.e. all k dependent quantites are averaged out.
`E`	Sampled energy-points in file
`a_buf`	Atomic indices (0-based) of device atoms
`a_dev`	Atomic indices (0-based) of device atoms (sorted)
`atom_COHP`
`atom_COOP`
`base_file`	File of the current Sile
`cell`	Unit cell in file
`current`
`current_parameter`
`density_matrix`
`elecs`	List of electrodes
`fano`
`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
`molecules`	List of regions where state projections may happen
`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
`noise_power`
`o_dev`	Orbital indices (0-based) of device orbitals (sorted)
`orbital_COHP`
`orbital_COOP`
`shot_noise`
`wk`	Weights of k-points in file
`wkpt`	Weights of k-points in file
`xa`	Atomic coordinates in file
`xyz`	Atomic coordinates in file

ADOS(elec_mol_proj, E=None, kavg=True, atoms=None, orbitals=None, sum=True, norm='none')[source]

Projected spectral density of states (DOS) (1/eV)

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

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

where \(|i\rangle\) may be a sum of states. The normalization constant (\(N\)) is defined in the routine norm and depends on the arguments.

Parameters

elec_mol_proj (str or tuple) – originating projected spectral function (<electrode>.<molecule>.<projection>)
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
atoms (array_like of int or bool, optional) – only return for a given set of atoms (default to all). NOT allowed with orbital keyword
orbitals (array_like of int or bool, optional) – only return for a given set of orbitals (default to all) NOT allowed with atoms 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).

Adensity_matrix(elec_mol_proj, E, kavg=True, isc=None, orbitals=None, geometry=None)[source]

Projected spectral function density matrix at energy E (1/eV)

The projected density matrix can be used to calculate the LDOS in real-space.

The \(\mathrm{LDOS}(E, \mathbf r)\) may be calculated using the density routine. Basically the LDOS in real-space may be calculated as

\[\rho_{\mathbf A_{\mathfrak{el}}}(E, \mathbf r) = \frac{1}{2\pi}\sum_{\nu\mu}\phi_\nu(\mathbf r)\phi_\mu(\mathbf r) \Re[\mathbf A_{\mathfrak{el}, \nu\mu}(E)]\]

where \(\phi\) are the orbitals. Note that the broadening used in the TBtrans calculations ensures the broadening of the density, i.e. it should not be necessary to perform energy averages over the density matrices.

Parameters

elec_mol_proj (str or tuple) – the projected electrode of originating electrons
E (float or int) – the energy or the energy index of density matrix. 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 density matrix is k-averaged, an explicit k-point or a selection of k-points
isc (array_like, optional) – the returned density matrix from unit-cell ([None, None, None]) to the given supercell, the default is all density matrix elements for the supercell. To only get unit cell orbital currents, pass [0, 0, 0].
orbitals (array-like or dict, optional) – only retain density matrix elements for a subset of orbitals, all other are set to 0.
geometry (Geometry, optional) – geometry that will be associated with the density matrix. By default the geometry contained in this file will be used. However, then the atomic species are probably incorrect, nor will the orbitals contain the basis-set information required to generate the required density in real-space.

Returns

DensityMatrix

Return type

the object containing the Geometry and the density matrix elements

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, optional) – whether the returned DOS is k-averaged, or an explicit (unweighed) k-point is returned
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, atoms=None, orbitals=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, optional) – whether the returned DOS is k-averaged, or an explicit (unweighed) k-point is returned
atoms (array_like of int or bool, optional) – only return for a given set of atoms (default to all). NOT allowed with orbitals keyword. If True it will use all atoms in the device. False is equivalent to None.
orbitals (array_like of int or bool, optional) – only return for a given set of orbitals (default to all) NOT allowed with atoms keyword. If True it will use all orbitals in the device. False is equivalent to None.
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

property E: Sampled energy-points in file

Eindex(E)

Return the closest energy index corresponding to the energy E

Parameters: E (float or int or str) – if int, return it-self, else return the energy index which is closests to the energy. For a str it will be parsed to a float and treated as such.

__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

Parameters

elec (str or int) – electrode to retrieve indices for
bulk (bool, optional) – whether the returned indices are only in the pristine electrode, or the down-folding region (electrode + downfolding region, not in device)

a_elec(elec)

Electrode atomic indices for the full geometry (sorted)

Parameters: elec (str or int) – electrode to retrieve indices for

atom_ACOHP(elec, E, kavg=True, isc=None, orbitals=None, uc=False)

Atomic COHP curve of the spectral function

Parameters

elec (str or int) – the electrode of the spectral function
E (float or int) – the energy or the energy index of COHP. If an integer is passed it is the index, otherwise the index corresponding to Eindex(E) is used.
kavg (bool, int, optional) – whether the returned COHP is k-averaged, or an explicit (unweighed) k-point is returned
isc (array_like, optional) – the returned COHP from unit-cell ([None, None, None]) to the given supercell, the default is all COHP for the supercell. To only get unit cell orbital currents, pass [0, 0, 0].
orbitals (array-like or dict, optional) – only retain COHP matrix elements for a subset of orbitals, all other are set to 0.
uc (bool, optional) – whether the returned COHP 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 sc_index.

See also

orbital_COHP: orbital resolved COHP analysis of the Green function
atom_COHP_from_orbital: transfer an orbital COHP to atomic COHP
atom_COHP: atomic COHP analysis of the Green function
atom_ACOOP: atomic COOP analysis of the spectral function

atom_ACOOP(elec, E, kavg=True, isc=None, orbitals=None, uc=False)

Atomic COOP curve of the spectral function

Parameters

elec (str or int) – the electrode of the spectral function
E (float or int) – the energy or the energy index of COOP. If an integer is passed it is the index, otherwise the index corresponding to Eindex(E) is used.
kavg (bool, int, optional) – whether the returned COOP is k-averaged, or an explicit (unweighed) k-point is returned
isc (array_like, optional) – the returned COOP from unit-cell ([None, None, None]) to the given supercell, the default is all COOP for the supercell. To only get unit cell orbital currents, pass [0, 0, 0].
orbitals (array-like or dict, optional) – only retain COOP matrix elements for a subset of orbitals, all other are set to 0.
uc (bool, optional) – whether the returned COOP 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 sc_index.

See also

orbital_COOP: orbital resolved COOP analysis of the Green function
atom_COOP_from_orbital: transfer an orbital COOP to atomic COOP
atom_COOP: atomic COOP analysis of the Green function
atom_ACOHP: atomic COHP analysis of the spectral function

atom_COHP = None

atom_COHP_from_orbital(COHP, uc=False)

Calculate the atomic COHP curve from the orbital COHP

The atomic COHP are a sum over all orbital COHP:

\[\mathrm{COHP}_{\alpha\beta} = \sum_{\nu\in\alpha}\sum_{\mu\in\beta} \mathrm{COHP}_{\nu\mu}\]

Parameters

COHP (scipy.sparse.csr_matrix) – the orbital COHP as retrieved from orbital_COHP or orbital_ACOHP
uc (bool, optional) – whether the returned COHP 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 sc_index.

See also

orbital_COHP: orbital resolved COHP analysis of the Green function
orbital_ACOHP: orbital resolved COHP analysis of the spectral function
atom_COHP: atomic COHP analysis of the Green function

atom_COOP = None

atom_COOP_from_orbital(COOP, uc=False)

Calculate the atomic COOP curve from the orbital COOP

The atomic COOP are a sum over all orbital COOP:

\[\mathrm{COOP}_{\alpha\beta} = \sum_{\nu\in\alpha}\sum_{\mu\in\beta} \mathrm{COOP}_{\nu\mu}\]

Parameters

COOP (scipy.sparse.csr_matrix) – the orbital COOP as retrieved from orbital_COOP or orbital_ACOOP
uc (bool, optional) – whether the returned COOP 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 sc_index.

See also

orbital_COOP: orbital resolved COOP analysis of the Green function
orbital_ACOOP: orbital resolved COOP analysis of the spectral function
atom_COOP: atomic COOP analysis of the Green function

atom_current(elec, E, kavg=True, activity=True, orbitals=None)

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, optional) – whether the returned atomic current is k-averaged, or an explicit (unweighed) k-point is returned
activity (bool, optional) – whether the activity current is returned, see atom_current_from_orbital for details.
orbitals (array-like or dict, optional) – only retain orbital currents for a subset of orbitals before calculating bond-current Passed directly to orbital_current.

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)

property base_file: File of the current Sile

bloch(elec)

Bloch-expansion coefficients for an electrode

Parameters: elec (str or int) – bloch expansions of electrode

bond_current(elec, E, kavg=True, isc=None, only='+', orbitals=None, 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, optional) – whether the returned bond current is k-averaged, or an explicit (unweighed) k-point is returned
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.
only ({'+', '-', '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. Please see discussion in orbital_current.
orbitals (array-like or dict, optional) – only retain orbital currents for a subset of orbitals before calculating bond-current Passed directly to orbital_current.
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 sc_index.

Examples

>>> Jij = tbt.orbital_current(0, -1.0, only='+') # 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

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)

bond_current_from_orbital(Jij, only='+', 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

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

Parameters

Jij (scipy.sparse.csr_matrix) – the orbital currents as retrieved from orbital_current
only ({'+', '-', '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 sc_index.

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

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)

btd(elec=None)

Block-sizes for the BTD method in the device/electrode region

Parameters: elec (str or int, optional) – the BTD block sizes for the device (if none), otherwise the downfolding BTD block sizes for the electrode

property cell: Unit cell in file

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

close()

current = None

current_parameter = None

density_matrix = None

dir_file(filename=None, filename_base=''): File of the current Sile

eigenstate(molecule, k=None, all=True)[source]

Return the eigenstate on the projected molecule

The eigenstate object will contain the geometry as the parent object. The eigenstate will be in the Lowdin basis:

\[|\psi'_i\rangle = \mathbf S^{1/2} |\psi_i\rangle\]

Parameters

molecule (str) – name of the molecule to retrieve the eigenstate from
k (optional) – k-index for retrieving a specific k-point (default to all)
all (bool, optional) – whether all states should be returned

Return type

EigenstateElectron

property elecs: List of electrodes

electron_temperature(elec)

Electron bath temperature [Kelvin]

Parameters: elec (str or int) – electrode to extract the temperature from

See also

kT: bath temperature in [eV]

eta(elec=None)

The imaginary part used when calculating the self-energies in eV (or for the device

Parameters: elec (str, int, optional) – electrode to extract the eta value from. If not specified (or None) the device region eta will be returned.

fano = None

property file: File of the current Sile

property geom: The associated geometry from this file

property geometry: The associated geometry from this file

info(molecule=None)[source]

Information about the calculated quantities available for extracting in this file

Parameters: molecule (str or int) – the molecule to request information from

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

property k: Sampled k-points in file

kT(elec)

Electron bath temperature [eV]

Parameters: elec (str or int) – electrode to extract the temperature from

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

property molecules: List of regions where state projections may happen

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

Parameters: elec (str or int, optional) – if None the number of blocks in the device region BTD matrix. Else the number of BTD blocks in the electrode down-folding.

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)

Parameters: elec (str or int) – Number of downfolding atoms for electrode elec

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)

Parameters: elec (str or int) – Number of downfolding orbitals for electrode elec

no_e(elec)

Number of orbitals in the downfolded region of the electrode in the device

Parameters: elec (str or int) – Specify the electrode to query number of downfolded orbitals

property no_u: Returns number of orbitals in the cell

noise_power = None

norm(atoms=None, orbitals=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 orbitals is an argument a conversion of orbitals 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 atoms is specified, this is equivalent to the ‘atom’ option.

Parameters

atoms (array_like of int or bool, optional) – only return for a given set of atoms (default to all). NOT allowed with orbitals keyword
orbitals (array_like of int or bool, optional) – only return for a given set of orbitals (default to all) NOT allowed with atoms keyword
norm ({'none', 'atom', 'orbital', 'all'}) – how the normalization of the summed DOS is performed (see norm routine)

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.

Parameters

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

property o_dev

Orbital indices (0-based) of device orbitals (sorted)

See also

pivot: retrieve the device orbitals, non-sorted

orbital_ACOHP(elec_mol_proj, E, kavg=True, isc=None, orbitals=None)[source]

Orbital COHP analysis of the projected spectral function

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

The COHP analysis can be written as:

\[\mathrm{COHP}^{\mathbf A}_{\nu\mu} = \frac{1}{2\pi} \Re\big[\mathbf A_{\nu\mu} \mathbf H_{\nu\mu} \big]\]

Parameters

elec_mol_proj (str or tuple) – the electrode of the projected spectral function
E (float or int) – the energy or the energy index of COHP. 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 COHP is k-averaged, an explicit k-point or a selection of k-points
isc (array_like, optional) – the returned COHP from unit-cell ([None, None, None]) to the given supercell, the default is all COHP for the supercell. To only get unit cell orbital currents, pass [0, 0, 0].
orbitals (array-like or dict, optional) – only retain COHP matrix elements for a subset of orbitals, all other are set to 0.

See also

atom_COHP_from_orbital: atomic COHP analysis from an orbital COHP
atom_ACOHP: atomic COHP analysis of the projected spectral function
atom_COOP_from_orbital: transfer an orbital COOP to atomic COOP
orbital_ACOOP: orbital resolved COOP analysis of the projected spectral function
atom_ACOOP: atomic COOP analysis of the projected spectral function

orbital_ACOOP(elec_mol_proj, E, kavg=True, isc=None, orbitals=None)[source]

Orbital COOP analysis of the projected spectral function

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

The COOP analysis can be written as:

\[\mathrm{COOP}^{\mathbf A}_{\nu\mu} = \frac{1}{2\pi} \Re\big[\mathbf A_{\nu\mu} \mathbf S_{\mu\nu} \big]\]

The sum of the COOP DOS is equal to the DOS:

\[\mathrm{ADOS}_{\nu} = \sum_\mu \mathrm{COOP}^{\mathbf A}_{\nu\mu}\]

One can calculate the (diagonal) balanced COOP analysis, see JPCM 15 (2003), 7751-7761 for details. The DBCOOP is given by:

\[\begin{split}D &= \sum_\nu \mathrm{COOP}^{\mathbf A}_{\nu\nu} \\ \mathrm{DBCOOP}^{\mathbf A}_{\nu\mu} &= \mathrm{COOP}^{\mathbf A}_{\nu\mu} / D\end{split}\]

The BCOOP can be looked up in the reference above.

Parameters

elec_mol_proj (str or tuple) – the electrode of the spectral function
E (float or int) – the energy or the energy index of COOP. 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 COOP is k-averaged, an explicit k-point or a selection of k-points
isc (array_like, optional) – the returned COOP from unit-cell ([None, None, None]) to the given supercell, the default is all COOP for the supercell. To only get unit cell orbital currents, pass [0, 0, 0].
orbitals (array-like or dict, optional) – only retain COOP matrix elements for a subset of orbitals, all other are set to 0.

Examples

>>> ACOOP = tbt.orbital_ACOOP('Left.C60.HOMO', -1.0) # COOP @ E = -1 eV from ``Left.C60.HOMO`` spectral function
>>> ACOOP[10, 11] # COOP value between the 11th and 12th orbital
>>> ACOOP.sum(1).A[tbt.o_dev, 0] == tbt.ADOS(0, sum=False)[tbt.Eindex(-1.0)]
>>> D = ACOOP.diagonal().sum()
>>> ADBCOOP = ACOOP / D

See also

atom_COOP_from_orbital: transfer an orbital COOP to atomic COOP
atom_ACOOP: atomic COOP analysis of the projected spectral function
atom_COHP_from_orbital: atomic COHP analysis from an orbital COHP
orbital_ACOHP: orbital resolved COHP analysis of the projected spectral function
atom_ACOHP: atomic COHP analysis of the projected spectral function

orbital_COHP = None

orbital_COOP = None

orbital_current(elec, E, kavg=True, isc=None, only='all', orbitals=None)

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.

When requesting orbital-currents it is vital to consider how the data needs to be analysed before extracting the data. For instance, if only local currents are interesting one should use only='+'. While if one is interested in the transmission between subset of orbitals, only='all' is the correct method.

For inexperienced users it is adviced to try out all three values of only to ensure the correct physics is obtained.

This becomes even more important when the orbital currents are calculated with magnetic fields. With \(\mathbf B\) fields local current loops may form and current does not necessarily flow along the transport direction.

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, optional) – whether the returned orbital current is k-averaged, or an explicit (unweighed) k-point is returned
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].
only ({'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.
orbitals (array-like or dict, optional) – only retain orbital currents for a subset of orbitals.

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

>>> Jij = tbt.orbital_current(0, -1.0,
...     orbitals={tbt.geometry.atoms[0]: [0, 1]})

only retain currents from 1st and 2nd orbitals on first atom type (all atoms of that type in the entire structure.

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)

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 geometry self.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

Parameters: elec (str or int) – the corresponding electrode to get the pivoting indices for

projections(molecule)[source]

List of projections on molecule

Parameters: molecule (str) – name of molecule to retrieve projections on

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

reflection(elec=0, kavg=True, from_single=False)

Reflection into electrode elec

The reflection into electrode elec is calculated as:

\[R(E) = T_{\mathrm{bulk}}(E) - \sum_{\mathrm{to}} T_{\mathrm{elec}\to\mathrm{to}}(E)\]

Another way of calculating the reflection is via:

\[R(E) = T_{\mathrm{bulk}}(E) - \big\{i \mathrm{Tr}[(\mathbf G-\mathbf G^\dagger)\boldsymbol\Gamma_{\mathrm{elec}}] - \mathrm{Tr}[\mathbf G\boldsymbol\Gamma_{\mathrm{elec}}\mathbf G^\dagger\boldsymbol\Gamma_{\mathrm{elec}}]\big\}\]

Both are identical, however, numerically they may be different. Particularly when the bulk transmission is very large compared to the transmission to the other electrodes one should prefer the first equation.

Parameters

elec (str, int, optional) – the backscattered electrode
kavg (bool, int, optional) – whether the returned reflection is k-averaged, or an explicit (unweighed) k-point is returned
from_single (bool, optional) – whether the reflection is calculated using the Green function and a single scattering matrix Eq. (2) above (true), otherwise Eq. (1) will be used (false).

See also

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

shot_noise = None

transmission(elec_mol_proj_from, elec_mol_proj_to, kavg=True)[source]

Transmission from mol_proj_elec_from to mol_proj_elec_to

Parameters

elec_mol_proj_from (str or tuple) – the originating scattering projection (<electrode>.<molecule>.<projection>)
elec_mol_proj_to (str or tuple) – the absorbing scattering projection (<electrode>.<molecule>.<projection>)
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: projected transmission decomposed in eigenchannels

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, optional) – whether the returned transmission are k-averaged, or an explicit (unweighed) k-point is returned

See also

transmission: the total transmission
transmission_eig: the transmission decomposed in eigenchannels
reflection: total reflection back into the electrode

transmission_eig(elec_mol_proj_from, elec_mol_proj_to, kavg=True)[source]

Transmission eigenvalues from elec_mol_proj_from to elec_mol_proj_to

Parameters

elec_mol_proj_from (str or tuple) – the originating scattering projection (<electrode>.<molecule>.<projection>)
elec_mol_proj_to (str or tuple) – the absorbing scattering projection (<electrode>.<molecule>.<projection>)
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: projected transmission

vector_current(elec, E, kavg=True, only='+', orbitals=None)

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 or 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, optional) – whether the returned vector current is k-averaged, or an explicit (unweighed) k-point is returned
only ({'+', '-', '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.
orbitals (array-like or dict, optional) – only retain orbital currents for a subset of orbitals before calculating bond-current Passed directly to orbital_current.

Returns

array of vectors per atom in the Geometry (only non-zero for device atoms)

Return type

numpy.ndarray

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

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)

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.

write_tbtav(*args, **kwargs)

Convert this to a TBT.AV.nc file, i.e. all k dependent quantites are averaged out.

This command will overwrite any previous file with the ending TBT.AV.nc and thus will not take notice of any older files.

Parameters: file (str) – output filename

property xa: Atomic coordinates in file

property xyz: Atomic coordinates in file