sisl.io.siesta.tbtrans_av module

Sile object for reading TBtrans AV binary files

class sisl.io.siesta.tbtrans_av.tbtavncSileSiesta(filename, mode='r', lvl=0, access=1, _open=True)

Bases: sisl.io.siesta.tbtrans.tbtncSileSiesta

TBtrans average file object

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

Although the TBtrans code is in fortran and the resulting NetCDF file variables are in fortran indexing (1-based), everything is returned as Python indexing (0-based) when scripting.

This is vital when using this Sile.

Note that when using the command-line utility sdata the indexing is fortran based because the data handlers are meant for _easy_ use.

Attributes

E	Sampled energy-points in file
Elecs	List of electrodes
Electrodes	List of electrodes
a_d	Atomic indices (1-based) of device atoms
a_dev	Atomic indices (1-based) of device atoms
cell	Unit cell in file
elecs	List of electrodes
electrodes	List of electrodes
file	Filename of the current Sile
geom	Returns the associated geometry from the TBT file
kpt	Sampled k-points in file
lasto	Last orbital of corresponding atom
nE	Number of energy-points in file
na	Returns number of atoms in the cell
na_d	Number of atoms in the device region
na_dev	Number of atoms in the device region
na_u	Returns number of atoms in the cell
ne	Number of energy-points in file
nkpt	Always return 1, this is to signal other routines
no	Returns number of orbitals in the cell
no_d	Number of orbitals in the device region
no_u	Returns number of orbitals in the cell
pivot	Pivot table of device orbitals to obtain input sorting
pvt	Pivot table of device orbitals to obtain input sorting
wkpt	Weights of k-points in file
xa	Atomic coordinates in file
xyz	Atomic coordinates in file

Methods

ADOS(elec[, E, avg, atom])	Return the DOS of the spectral function from elec (1/eV).
ArgumentParser([parser])
ArgumentParser_out([parser])	Appends additional arguments based on the output of the file
BDOS(elec[, E, avg])	Return the bulk DOS of elec (1/eV).
BulkDOS(elec[, E, avg])	Return the bulk DOS of elec (1/eV).
DOS([E, avg, atom])	Return the Green function DOS (1/eV).
DOS_A(elec[, E, avg, atom])	Return the DOS of the spectral function from elec (1/eV).
DOS_Gf([E, avg, atom])	Return the Green function DOS (1/eV).
DOS_bulk(elec[, E, avg])	Return the bulk DOS of elec (1/eV).
Eindex(E)	Return the closest energy index corresponding to the energy E
T(elec_from, elec_to[, avg])	Return the transmission from from to to.
Tbulk(elec[, avg])	Return the bulk transmission in the elec electrode
Teig(elec_from, elec_to[, avg])	Return the transmission eigenvalues from from to to.
a2p(atom)	Return the pivoting indices (0-based) for the atoms
atom_current(elec, E[, avg, activity])	Return the atom-current of atoms.
atom_current_from_orbital(Jij[, activity])	Return the atom-current of atoms.
bond_current(elec, E[, avg, isc, sum, uc])	Return the bond-current between atoms (sum of orbital currents)
bond_current_from_orbital(Jij[, sum, uc])	Return the bond-current between atoms (sum of orbital currents) by passing the orbital currents.
chemical_potential(elec)	Return the chemical potential associated with the electrode elec
current(elec_from, elec_to[, avg])	Return the current from from to to using the weights in the file.
electronic_temperature(elec)	Return temperature of the electrode electronic distribution in Kelvin
isDataset(obj)	Return true if obj is an instance of the NetCDF4 Dataset type
isDimension(obj)	Return true if obj is an instance of the NetCDF4 Dimension type
isGroup(obj)	Return true if obj is an instance of the NetCDF4 Group type
isRoot(obj)	Return true if obj is an instance of the NetCDF4 Dataset type
isVariable(obj)	Return true if obj is an instance of the NetCDF4 Variable type
iter([group, dimension, variable, levels, root])	Iterator on all groups, variables and dimensions.
kT(elec)	Return temperature of the electrode electronic distribution in eV
mu(elec)	Return the chemical potential associated with the electrode elec
o2p(orbital)	Return the pivoting indices (0-based) for the orbitals
orbital_current(elec, E[, avg, isc])	Return the orbital current originating from elec.
read(*args, **kwargs)	Generic read method which should be overloaded in child-classes
read_data(*args, **kwargs)	Read specific type of data.
read_geom(*args, **kwargs)	Returns Geometry object from a .TBT.nc file
read_sc()	Returns SuperCell object from a .TBT.nc file
transmission(elec_from, elec_to[, avg])	Return the transmission from from to to.
transmission_bulk(elec[, avg])	Return the bulk transmission in the elec electrode
transmission_eig(elec_from, elec_to[, avg])	Return the transmission eigenvalues from from to to.
vector_current(elec, E[, avg])	Return the atom-current with vector components of atoms.
vector_current_from_orbital(Jij)	Return the atom-current with vector components of atoms.
write(*args, **kwargs)	Generic write method which should be overloaded in child-classes
write_geom(*args, **kwargs)	This is not meant to be used
write_tbtav(*args, **kwargs)	Wrapper for writing the k-averaged TBT.AV.nc file.

Creates/Opens a SileCDF

Opens a SileCDF with mode and compression level lvl. If mode is in read-mode (r) the compression level is ignored.

The final access parameter sets how the file should be open and subsequently accessed.

0. means direct file access for every variable read
1. means stores certain variables in the object.

Attributes

E	Sampled energy-points in file
Elecs	List of electrodes
Electrodes	List of electrodes
a_d	Atomic indices (1-based) of device atoms
a_dev	Atomic indices (1-based) of device atoms
cell	Unit cell in file
elecs	List of electrodes
electrodes	List of electrodes
file	Filename of the current Sile
geom	Returns the associated geometry from the TBT file
kpt	Sampled k-points in file
lasto	Last orbital of corresponding atom
nE	Number of energy-points in file
na	Returns number of atoms in the cell
na_d	Number of atoms in the device region
na_dev	Number of atoms in the device region
na_u	Returns number of atoms in the cell
ne	Number of energy-points in file
nkpt	Always return 1, this is to signal other routines
no	Returns number of orbitals in the cell
no_d	Number of orbitals in the device region
no_u	Returns number of orbitals in the cell
pivot	Pivot table of device orbitals to obtain input sorting
pvt	Pivot table of device orbitals to obtain input sorting
wkpt	Weights of k-points in file
xa	Atomic coordinates in file
xyz	Atomic coordinates in file

Methods

ADOS(elec[, E, avg, atom])	Return the DOS of the spectral function from elec (1/eV).
ArgumentParser([parser])
ArgumentParser_out([parser])	Appends additional arguments based on the output of the file
BDOS(elec[, E, avg])	Return the bulk DOS of elec (1/eV).
BulkDOS(elec[, E, avg])	Return the bulk DOS of elec (1/eV).
DOS([E, avg, atom])	Return the Green function DOS (1/eV).
DOS_A(elec[, E, avg, atom])	Return the DOS of the spectral function from elec (1/eV).
DOS_Gf([E, avg, atom])	Return the Green function DOS (1/eV).
DOS_bulk(elec[, E, avg])	Return the bulk DOS of elec (1/eV).
Eindex(E)	Return the closest energy index corresponding to the energy E
T(elec_from, elec_to[, avg])	Return the transmission from from to to.
Tbulk(elec[, avg])	Return the bulk transmission in the elec electrode
Teig(elec_from, elec_to[, avg])	Return the transmission eigenvalues from from to to.
a2p(atom)	Return the pivoting indices (0-based) for the atoms
atom_current(elec, E[, avg, activity])	Return the atom-current of atoms.
atom_current_from_orbital(Jij[, activity])	Return the atom-current of atoms.
bond_current(elec, E[, avg, isc, sum, uc])	Return the bond-current between atoms (sum of orbital currents)
bond_current_from_orbital(Jij[, sum, uc])	Return the bond-current between atoms (sum of orbital currents) by passing the orbital currents.
chemical_potential(elec)	Return the chemical potential associated with the electrode elec
current(elec_from, elec_to[, avg])	Return the current from from to to using the weights in the file.
electronic_temperature(elec)	Return temperature of the electrode electronic distribution in Kelvin
isDataset(obj)	Return true if obj is an instance of the NetCDF4 Dataset type
isDimension(obj)	Return true if obj is an instance of the NetCDF4 Dimension type
isGroup(obj)	Return true if obj is an instance of the NetCDF4 Group type
isRoot(obj)	Return true if obj is an instance of the NetCDF4 Dataset type
isVariable(obj)	Return true if obj is an instance of the NetCDF4 Variable type
iter([group, dimension, variable, levels, root])	Iterator on all groups, variables and dimensions.
kT(elec)	Return temperature of the electrode electronic distribution in eV
mu(elec)	Return the chemical potential associated with the electrode elec
o2p(orbital)	Return the pivoting indices (0-based) for the orbitals
orbital_current(elec, E[, avg, isc])	Return the orbital current originating from elec.
read(*args, **kwargs)	Generic read method which should be overloaded in child-classes
read_data(*args, **kwargs)	Read specific type of data.
read_geom(*args, **kwargs)	Returns Geometry object from a .TBT.nc file
read_sc()	Returns SuperCell object from a .TBT.nc file
transmission(elec_from, elec_to[, avg])	Return the transmission from from to to.
transmission_bulk(elec[, avg])	Return the bulk transmission in the elec electrode
transmission_eig(elec_from, elec_to[, avg])	Return the transmission eigenvalues from from to to.
vector_current(elec, E[, avg])	Return the atom-current with vector components of atoms.
vector_current_from_orbital(Jij)	Return the atom-current with vector components of atoms.
write(*args, **kwargs)	Generic write method which should be overloaded in child-classes
write_geom(*args, **kwargs)	This is not meant to be used
write_tbtav(*args, **kwargs)	Wrapper for writing the k-averaged TBT.AV.nc file.

nkpt

Always return 1, this is to signal other routines

write_tbtav(*args, **kwargs)

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

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

Parameters:

from : tbtncSileSiesta

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

class sisl.io.siesta.tbtrans_av.phtavncSileSiesta(filename, mode='r', lvl=0, access=1, _open=True)

Bases: sisl.io.siesta.tbtrans_av.tbtavncSileSiesta

PHtrans file object

Attributes

E	Sampled energy-points in file
Elecs	List of electrodes
Electrodes	List of electrodes
a_d	Atomic indices (1-based) of device atoms
a_dev	Atomic indices (1-based) of device atoms
cell	Unit cell in file
elecs	List of electrodes
electrodes	List of electrodes
file	Filename of the current Sile
geom	Returns the associated geometry from the TBT file
kpt	Sampled k-points in file
lasto	Last orbital of corresponding atom
nE	Number of energy-points in file
na	Returns number of atoms in the cell
na_d	Number of atoms in the device region
na_dev	Number of atoms in the device region
na_u	Returns number of atoms in the cell
ne	Number of energy-points in file
nkpt	Always return 1, this is to signal other routines
no	Returns number of orbitals in the cell
no_d	Number of orbitals in the device region
no_u	Returns number of orbitals in the cell
pivot	Pivot table of device orbitals to obtain input sorting
pvt	Pivot table of device orbitals to obtain input sorting
wkpt	Weights of k-points in file
xa	Atomic coordinates in file
xyz	Atomic coordinates in file

Methods

ADOS(elec[, E, avg, atom])	Return the DOS of the spectral function from elec (1/eV).
ArgumentParser([parser])
ArgumentParser_out([parser])	Appends additional arguments based on the output of the file
BDOS(elec[, E, avg])	Return the bulk DOS of elec (1/eV).
BulkDOS(elec[, E, avg])	Return the bulk DOS of elec (1/eV).
DOS([E, avg, atom])	Return the Green function DOS (1/eV).
DOS_A(elec[, E, avg, atom])	Return the DOS of the spectral function from elec (1/eV).
DOS_Gf([E, avg, atom])	Return the Green function DOS (1/eV).
DOS_bulk(elec[, E, avg])	Return the bulk DOS of elec (1/eV).
Eindex(E)	Return the closest energy index corresponding to the energy E
T(elec_from, elec_to[, avg])	Return the transmission from from to to.
Tbulk(elec[, avg])	Return the bulk transmission in the elec electrode
Teig(elec_from, elec_to[, avg])	Return the transmission eigenvalues from from to to.
a2p(atom)	Return the pivoting indices (0-based) for the atoms
atom_current(elec, E[, avg, activity])	Return the atom-current of atoms.
atom_current_from_orbital(Jij[, activity])	Return the atom-current of atoms.
bond_current(elec, E[, avg, isc, sum, uc])	Return the bond-current between atoms (sum of orbital currents)
bond_current_from_orbital(Jij[, sum, uc])	Return the bond-current between atoms (sum of orbital currents) by passing the orbital currents.
chemical_potential(elec)	Return the chemical potential associated with the electrode elec
current(elec_from, elec_to[, avg])	Return the current from from to to using the weights in the file.
electronic_temperature(elec)	Return temperature of the electrode electronic distribution in Kelvin
isDataset(obj)	Return true if obj is an instance of the NetCDF4 Dataset type
isDimension(obj)	Return true if obj is an instance of the NetCDF4 Dimension type
isGroup(obj)	Return true if obj is an instance of the NetCDF4 Group type
isRoot(obj)	Return true if obj is an instance of the NetCDF4 Dataset type
isVariable(obj)	Return true if obj is an instance of the NetCDF4 Variable type
iter([group, dimension, variable, levels, root])	Iterator on all groups, variables and dimensions.
kT(elec)	Return temperature of the electrode electronic distribution in eV
mu(elec)	Return the chemical potential associated with the electrode elec
o2p(orbital)	Return the pivoting indices (0-based) for the orbitals
orbital_current(elec, E[, avg, isc])	Return the orbital current originating from elec.
read(*args, **kwargs)	Generic read method which should be overloaded in child-classes
read_data(*args, **kwargs)	Read specific type of data.
read_geom(*args, **kwargs)	Returns Geometry object from a .TBT.nc file
read_sc()	Returns SuperCell object from a .TBT.nc file
transmission(elec_from, elec_to[, avg])	Return the transmission from from to to.
transmission_bulk(elec[, avg])	Return the bulk transmission in the elec electrode
transmission_eig(elec_from, elec_to[, avg])	Return the transmission eigenvalues from from to to.
vector_current(elec, E[, avg])	Return the atom-current with vector components of atoms.
vector_current_from_orbital(Jij)	Return the atom-current with vector components of atoms.
write(*args, **kwargs)	Generic write method which should be overloaded in child-classes
write_geom(*args, **kwargs)	This is not meant to be used
write_tbtav(*args, **kwargs)	Wrapper for writing the k-averaged TBT.AV.nc file.

Creates/Opens a SileCDF

Opens a SileCDF with mode and compression level lvl. If mode is in read-mode (r) the compression level is ignored.

The final access parameter sets how the file should be open and subsequently accessed.

0. means direct file access for every variable read
1. means stores certain variables in the object.

Attributes

E	Sampled energy-points in file
Elecs	List of electrodes
Electrodes	List of electrodes
a_d	Atomic indices (1-based) of device atoms
a_dev	Atomic indices (1-based) of device atoms
cell	Unit cell in file
elecs	List of electrodes
electrodes	List of electrodes
file	Filename of the current Sile
geom	Returns the associated geometry from the TBT file
kpt	Sampled k-points in file
lasto	Last orbital of corresponding atom
nE	Number of energy-points in file
na	Returns number of atoms in the cell
na_d	Number of atoms in the device region
na_dev	Number of atoms in the device region
na_u	Returns number of atoms in the cell
ne	Number of energy-points in file
nkpt	Always return 1, this is to signal other routines
no	Returns number of orbitals in the cell
no_d	Number of orbitals in the device region
no_u	Returns number of orbitals in the cell
pivot	Pivot table of device orbitals to obtain input sorting
pvt	Pivot table of device orbitals to obtain input sorting
wkpt	Weights of k-points in file
xa	Atomic coordinates in file
xyz	Atomic coordinates in file

Methods

ADOS(elec[, E, avg, atom])	Return the DOS of the spectral function from elec (1/eV).
ArgumentParser([parser])
ArgumentParser_out([parser])	Appends additional arguments based on the output of the file
BDOS(elec[, E, avg])	Return the bulk DOS of elec (1/eV).
BulkDOS(elec[, E, avg])	Return the bulk DOS of elec (1/eV).
DOS([E, avg, atom])	Return the Green function DOS (1/eV).
DOS_A(elec[, E, avg, atom])	Return the DOS of the spectral function from elec (1/eV).
DOS_Gf([E, avg, atom])	Return the Green function DOS (1/eV).
DOS_bulk(elec[, E, avg])	Return the bulk DOS of elec (1/eV).
Eindex(E)	Return the closest energy index corresponding to the energy E
T(elec_from, elec_to[, avg])	Return the transmission from from to to.
Tbulk(elec[, avg])	Return the bulk transmission in the elec electrode
Teig(elec_from, elec_to[, avg])	Return the transmission eigenvalues from from to to.
a2p(atom)	Return the pivoting indices (0-based) for the atoms
atom_current(elec, E[, avg, activity])	Return the atom-current of atoms.
atom_current_from_orbital(Jij[, activity])	Return the atom-current of atoms.
bond_current(elec, E[, avg, isc, sum, uc])	Return the bond-current between atoms (sum of orbital currents)
bond_current_from_orbital(Jij[, sum, uc])	Return the bond-current between atoms (sum of orbital currents) by passing the orbital currents.
chemical_potential(elec)	Return the chemical potential associated with the electrode elec
current(elec_from, elec_to[, avg])	Return the current from from to to using the weights in the file.
electronic_temperature(elec)	Return temperature of the electrode electronic distribution in Kelvin
isDataset(obj)	Return true if obj is an instance of the NetCDF4 Dataset type
isDimension(obj)	Return true if obj is an instance of the NetCDF4 Dimension type
isGroup(obj)	Return true if obj is an instance of the NetCDF4 Group type
isRoot(obj)	Return true if obj is an instance of the NetCDF4 Dataset type
isVariable(obj)	Return true if obj is an instance of the NetCDF4 Variable type
iter([group, dimension, variable, levels, root])	Iterator on all groups, variables and dimensions.
kT(elec)	Return temperature of the electrode electronic distribution in eV
mu(elec)	Return the chemical potential associated with the electrode elec
o2p(orbital)	Return the pivoting indices (0-based) for the orbitals
orbital_current(elec, E[, avg, isc])	Return the orbital current originating from elec.
read(*args, **kwargs)	Generic read method which should be overloaded in child-classes
read_data(*args, **kwargs)	Read specific type of data.
read_geom(*args, **kwargs)	Returns Geometry object from a .TBT.nc file
read_sc()	Returns SuperCell object from a .TBT.nc file
transmission(elec_from, elec_to[, avg])	Return the transmission from from to to.
transmission_bulk(elec[, avg])	Return the bulk transmission in the elec electrode
transmission_eig(elec_from, elec_to[, avg])	Return the transmission eigenvalues from from to to.
vector_current(elec, E[, avg])	Return the atom-current with vector components of atoms.
vector_current_from_orbital(Jij)	Return the atom-current with vector components of atoms.
write(*args, **kwargs)	Generic write method which should be overloaded in child-classes
write_geom(*args, **kwargs)	This is not meant to be used
write_tbtav(*args, **kwargs)	Wrapper for writing the k-averaged TBT.AV.nc file.