sisl.io.tbtrans.phtncSilePHtrans
- class sisl.io.tbtrans.phtncSilePHtrans(filename, mode='r', lvl=0, access=1, *args, **kwargs)
Bases:
tbtncSileTBtrans
PHtrans file object
Methods
ADOS
([elec, E, kavg, atoms, orbitals, sum, norm])Spectral density of states (DOS) (1/eV).
Adensity_matrix
(elec, E[, kavg, isc, ...])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
(E[, kavg, isc, orbitals, uc])Atomic COHP curve of the Green function
atom_COHP_from_orbital
(COHP[, uc])Calculate the atomic COHP curve from the orbital COHP
atom_COOP
(E[, kavg, isc, orbitals, uc])Atomic COOP curve of the Green function
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
close
()density_matrix
(E[, kavg, isc, orbitals, ...])Density matrix from the Green function at energy
E
(1/eV)dir_file
([filename, filename_base])File of the current Sile
eta
([elec])The imaginary part used when calculating the self-energies in eV (or for the device
fano
([elec_from, elec_to, kavg, zero_T])The Fano-factor for the calculation (requires calculated transmission eigenvalues)
info
([elec])Information about the calculated quantities available for extracting in this file
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
([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, E[, kavg, isc, orbitals])Orbital resolved COHP analysis of the spectral function
orbital_ACOOP
(elec, E[, kavg, isc, orbitals])Orbital COOP analysis of the spectral function
orbital_COHP
(E[, kavg, isc, orbitals])Orbital resolved COHP analysis of the Green function
orbital_COOP
(E[, kavg, isc, orbitals])Orbital COOP analysis of the Green function
orbital_current
(elec, E[, kavg, isc, only, ...])Orbital current originating from elec as a sparse matrix
phonon_temperature
(elec)Phonon bath temperature [Kelvin]
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_data
(*args, **kwargs)Read specific type of data.
read_geometry
(*args, **kwargs)Returns Geometry object from this file
Returns SuperCell object from this file
reflection
([elec, kavg, from_single])Reflection into electrode elec
transmission
([elec_from, elec_to, kavg])Transmission from elec_from to elec_to.
transmission_bulk
([elec, kavg])Bulk transmission for the elec electrode
transmission_eig
([elec_from, elec_to, kavg])Transmission eigenvalues from elec_from to elec_to.
vector_current
(elec, E[, kavg, only, orbitals])Vector for each atom describing the mean path for the current travelling through the atom
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.
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
- ADOS(elec=0, E=None, kavg=True, atoms=None, orbitals=None, sum=True, norm='none') ndarray
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, 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).
- Adensity_matrix(elec, E, kavg=True, isc=None, orbitals=None, geometry=None) csr_matrix
Spectral function density matrix at energy
E
(1/eV)The 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
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, optional) – whether the returned density matrix is k-averaged, or an explicit (unweighed) k-point is returned
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.
See also
density_matrix
Green function density matrix
- Returns
object containing the Geometry and the density matrix elements
- Return type
- BDOS(elec=0, E=None, kavg=True, sum=True, norm='none') ndarray
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.
- DOS(E=None, kavg=True, atoms=None, orbitals=None, sum=True, norm='none') ndarray
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)
- 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)
- atom_ACOHP(elec, E, kavg=True, isc=None, orbitals=None, uc=False) csr_matrix
Atomic COHP curve of the spectral function
- Parameters
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 ofshape = (self.na, self.na)
, else, it will return a sparse matrix ofshape = (self.na, self.na * self.n_s)
. One may figure out the connections viasc_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) csr_matrix
Atomic COOP curve of the spectral function
- Parameters
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 ofshape = (self.na, self.na)
, else, it will return a sparse matrix ofshape = (self.na, self.na * self.n_s)
. One may figure out the connections viasc_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(E, kavg=True, isc=None, orbitals=None, uc=False) csr_matrix
Atomic COHP curve of the Green function
- Parameters
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 ofshape = (self.na, self.na)
, else, it will return a sparse matrix ofshape = (self.na, self.na * self.n_s)
. One may figure out the connections viasc_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_ACOHP
atomic COHP analysis of the spectral function
atom_COOP
atomic COOP analysis of the Green function
- atom_COHP_from_orbital(COHP, uc=False) csr_matrix
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
ororbital_ACOHP
uc (bool, optional) – whether the returned COHP are only in the unit-cell. If
True
this will return a sparse matrix ofshape = (self.na, self.na)
, else, it will return a sparse matrix ofshape = (self.na, self.na * self.n_s)
. One may figure out the connections viasc_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(E, kavg=True, isc=None, orbitals=None, uc=False) csr_matrix
Atomic COOP curve of the Green function
- Parameters
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 ofshape = (self.na, self.na)
, else, it will return a sparse matrix ofshape = (self.na, self.na * self.n_s)
. One may figure out the connections viasc_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_ACOOP
atomic COOP analysis of the spectral function
atom_COHP
atomic COHP analysis of the Green function
- atom_COOP_from_orbital(COOP, uc=False) csr_matrix
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
ororbital_ACOOP
uc (bool, optional) – whether the returned COOP are only in the unit-cell. If
True
this will return a sparse matrix ofshape = (self.na, self.na)
, else, it will return a sparse matrix ofshape = (self.na, self.na * self.n_s)
. One may figure out the connections viasc_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) ndarray
Atomic current of atoms
Short hand function for calling
orbital_current
andatom_current_from_orbital
.- Parameters
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) ndarray
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
- bond_current(elec, E, kavg=True, isc=None, only='out', orbitals=None, uc=False) csr_matrix
Bond-current between atoms (sum of orbital currents)
Short hand function for calling
orbital_current
andbond_current_from_orbital
.- Parameters
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 ({"+"/"out", "-"/"in", "all"/"both"}) – If +/out is supplied only the positive orbital currents are used (going out) for -/in, only the negative orbital currents are used (going in), else return 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 ofshape = (self.na, self.na * self.n_s)
. One may figure out the connections viasc_index
.
Examples
>>> Jij = tbt.orbital_current(0, -1.0, only="out") # 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='out', uc=False) csr_matrix
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="out"
: only \(J_{\nu\mu} > 0\) are summed onto the corresponding atom,only="in"
: only \(J_{\nu\mu} < 0\) are summed onto the corresponding atom,only="both"
: 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 ({"+"/"out", "-"/"in", "all"/"both"}) – If +/out is supplied only the positive orbital currents are used (outgoing) for -/in, only the negative orbital currents are used (incoming), 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 ofshape = (self.na, self.na)
, else, it will return a sparse matrix ofshape = (self.na, self.na * self.n_s)
. One may figure out the connections viasc_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
- property cell
Unit cell in file
- chemical_potential = None
- close()
- current = None
- current_parameter = None
- density_matrix(E, kavg=True, isc=None, orbitals=None, geometry=None) csr_matrix
Density matrix from the Green function at energy
E
(1/eV)The 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\[\rho_{\mathbf G}(E, \mathbf r) = -\frac{1}{\pi}\sum_{\nu\mu}\phi_\nu(\mathbf r)\phi_\mu(\mathbf r) \Im[\mathbf G_{\nu\mu}(E)]\]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
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, optional) – whether the returned density matrix is k-averaged, or an explicit (unweighed) k-point is returned
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.
See also
Adensity_matrix
spectral function density matrix
- Returns
object containing the Geometry and the density matrix elements
- Return type
- dir_file(filename=None, filename_base='')
File of the current Sile
- property elecs
List of electrodes
- electron_temperature = None
- eta(elec=None)
The imaginary part used when calculating the self-energies in eV (or for the device
- fano(elec_from=0, elec_to=1, kavg=True, zero_T=1e-06) ndarray
The Fano-factor for the calculation (requires calculated transmission eigenvalues)
Calculate the Fano factor defined as (or through the shot-noise):
\[\begin{split}F(E) &= \frac{\sum_{k,n} T_{k,n}(E)[1 - T_{k,n}(E)] w_k}{\sum_{k,n} T_{k,n}(E) w_k} \\ &= S(E, V) / S_P(E, V)\end{split}\]Notes
The default zero_T may change in the future. This calculation will only work for non-polarized calculations since the divisor needs to be the spin-sum. The current implementation uses the full transmission as the divisor.
Examples
For a spin-polarized calculation one should calculate the Fano factor as:
>>> up = get_sile('siesta.TBT_UP.nc') >>> down = get_sile('siesta.TBT_DN.nc') >>> fano = up.fano() * up.transmission() + down.fano() * down.transmission() >>> fano /= up.transmission() + down.transmission()
- Parameters
elec_to (str, int, optional) – the absorbing electrode (different from elec_from)
kavg (bool, int, optional) – whether the returned Fano factor is k-averaged, or an explicit (unweighed) k-point is returned. In any case the divisor will always be the k-averaged transmission.
zero_T (float, optional) – any transmission eigen value lower than this value will be treated as exactly 0.
See also
shot_noise
shot-noise term (zero temperature limit)
noise_power
temperature dependent noise power
- 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 calculated quantities 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 = None
- 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
- noise_power = None
- norm(atoms=None, orbitals=None, norm='none') int
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.
- property o_dev
Orbital indices (0-based) of device orbitals (sorted)
See also
pivot
retrieve the device orbitals, non-sorted
- orbital_ACOHP(elec, E, kavg=True, isc=None, orbitals=None) csr_matrix
Orbital resolved COHP analysis of the 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
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.
See also
orbital_COHP
orbital resolved COHP analysis of the Green function
atom_COHP_from_orbital
atomic COHP analysis from an orbital COHP
atom_COHP
atomic COHP analysis of the Green function
atom_ACOHP
atomic COHP analysis of the spectral function
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
orbital_ACOOP
orbital resolved COOP analysis of the spectral function
atom_ACOOP
atomic COOP analysis of the spectral function
- orbital_ACOOP(elec, E, kavg=True, isc=None, orbitals=None) csr_matrix
Orbital COOP analysis of the 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
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.
Examples
>>> ACOOP = tbt.orbital_ACOOP(0, -1.0) # COOP @ E = -1 eV from ``0`` 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
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_ACOOP
atomic COOP analysis of the spectral function
orbital_COHP
orbital resolved COHP analysis of the Green function
atom_COHP_from_orbital
atomic COHP analysis from an orbital COHP
atom_COHP
atomic COHP analysis of the Green function
orbital_ACOHP
orbital resolved COHP analysis of the spectral function
atom_ACOHP
atomic COHP analysis of the spectral function
- orbital_COHP(E, kavg=True, isc=None, orbitals=None) csr_matrix
Orbital resolved COHP analysis of the Green 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:
\[\mathrm{COHP}^{\mathbf G}_{\nu\mu} = \frac{-1}{2\pi} \Im\big[(\mathbf G - \mathbf G^\dagger)_{\nu\mu} \mathbf H_{\mu\nu} \big]\]- Parameters
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.
Examples
>>> COHP = tbt.orbital_COHP(-1.0) # COHP @ E = -1 eV >>> COHP[10, 11] # COHP value between the 11th and 12th orbital
See also
atom_COHP_from_orbital
atomic COHP analysis from an orbital COHP
atom_COHP
atomic COHP analysis of the Green function
orbital_ACOHP
orbital resolved COHP analysis of the spectral function
atom_ACOHP
atomic COHP analysis of the spectral function
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
orbital_ACOOP
orbital resolved COOP analysis of the spectral function
atom_ACOOP
atomic COOP analysis of the spectral function
- orbital_COOP(E, kavg=True, isc=None, orbitals=None) csr_matrix
Orbital COOP analysis of the Green function
This will return a sparse matrix, see
scipy.sparse.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:
\[\mathrm{COOP}^{\mathbf G}_{\nu\mu} = \frac{-1}{2\pi} \Im\big[(\mathbf G - \mathbf G^\dagger)_{\nu\mu} \mathbf S_{\mu\nu} \big]\]The sum of the COOP DOS is equal to the DOS:
\[\mathrm{DOS}_{\nu} = \sum_\mu \mathrm{COOP}^{\mathbf G}_{\nu\mu}\]One can calculate the (diagonal) balanced COOP analysis, see JPCM 15 (2003), 7751-7761 for details. The DBCOOP is given by:
\[\begin{split}D &= \sum_\nu \mathrm{COOP}^{\mathbf G}_{\nu\nu} \\ \mathrm{DBCOOP}^{\mathbf G}_{\nu\mu} &= \mathrm{COOP}^{\mathbf G}_{\nu\mu} / D\end{split}\]The BCOOP can be looked up in the reference above.
- Parameters
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.
Examples
>>> COOP = tbt.orbital_COOP(-1.0) # COOP @ E = -1 eV >>> COOP[10, 11] # COOP value between the 11th and 12th orbital >>> COOP.sum(1).A[tbt.o_dev, 0] == tbt.DOS(sum=False)[tbt.Eindex(-1.0)] >>> D = COOP.diagonal().sum() >>> DBCOOP = COOP / D
See also
atom_COOP_from_orbital
transfer an orbital COOP to atomic COOP
atom_COOP
atomic COOP analysis of the Green function
orbital_ACOOP
orbital resolved COOP analysis of the spectral function
atom_ACOOP
atomic COOP analysis of the spectral function
orbital_COHP
orbital resolved COHP analysis of the Green function
atom_COHP_from_orbital
atomic COHP analysis from an orbital COHP
atom_COHP
atomic COHP analysis of the Green function
orbital_ACOHP
orbital resolved COHP analysis of the spectral function
atom_ACOHP
atomic COHP analysis of the spectral function
- orbital_current(elec, E, kavg=True, isc=None, only='all', orbitals=None) csr_matrix
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
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"/"both", "+"/"out", "-"/"in"}) – which orbital currents to return, all, positive (outgoing) or negative (incoming) values only. Default to
"all"
because it can then be used in the subsequent default arguments forbond_current_from_orbital
andatom_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 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_data(*args, **kwargs)
Read specific type of data.
This is a generic routine for reading different parts of the data-file.
- 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) ndarray
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
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
- to_json()
- transmission(elec_from=0, elec_to=1, kavg=True) ndarray
Transmission from elec_from to elec_to.
The transmission between two electrodes may be retrieved from the Sile.
The transmission is calculated as:
\[T(E) = \mathrm{Tr}[\mathbf{G}\boldsymbol\Gamma_{\mathrm{from}}\mathbf{G}^\dagger\boldsymbol\Gamma_{\mathrm{to}}]\]where all quantities are energy dependent.
- Parameters
See also
transmission_eig
the transmission decomposed in eigenchannels
transmission_bulk
the total transmission in a periodic lead
reflection
total reflection back into the electrode
- transmission_bulk(elec=0, kavg=True) ndarray
Bulk transmission for the elec electrode
The bulk transmission is equivalent to creating a 2 terminal device with electrode elec tiled 3 times.
- Parameters
See also
transmission
the total transmission
transmission_eig
the transmission decomposed in eigenchannels
reflection
total reflection back into the electrode
- transmission_eig(elec_from=0, elec_to=1, kavg=True) ndarray
Transmission eigenvalues from elec_from to elec_to.
- Parameters
See also
transmission
the total transmission
transmission_bulk
the total transmission in a periodic lead
- vector_current(elec, E, kavg=True, only='out', orbitals=None) ndarray
Vector for each atom describing the mean path for the current travelling through the atom
See
vector_current_from_bond
for details.- Parameters
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 ({"+"/"out", "-"/"in", "all"/"both"}) – By default only sum outgoing vector currents (
"out"
). The incoming vector currents may be retrieved by"in"
, while the average incoming and outgoing direction can be obtained with"both"
. In the last case the vector currents are divided by 2 to ensure the length of the vector is compatible 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
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) ndarray
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
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