sisl.io.siesta.tbtrans_proj module¶
Sile object for reading TBtrans binary projection files
-
class
sisl.io.siesta.tbtrans_proj.
tbtprojncSileSiesta
(filename, mode='r', lvl=0, access=1, _open=True)[source]¶ Bases:
sisl.io.siesta.tbtrans.tbtncSileSiesta
TBtrans projection 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
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 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
toto
.Tbulk
(elec[, avg])Return the bulk transmission in the elec
electrodeTeig
(elec_from, elec_to[, avg])Return the transmission eigenvalues from from
toto
.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
toto
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 NetCDF4Dataset
typeisDimension
(obj)Return true if obj
is an instance of the NetCDF4Dimension
typeisGroup
(obj)Return true if obj
is an instance of the NetCDF4Group
typeisRoot
(obj)Return true if obj
is an instance of the NetCDF4Dataset
typeisVariable
(obj)Return true if obj
is an instance of the NetCDF4Variable
typeiter
([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 fileread_sc
()Returns SuperCell
object from a .TBT.nc filetransmission
(elec_from, elec_to[, avg])Return the transmission from from
toto
.transmission_bulk
(elec[, avg])Return the bulk transmission in the elec
electrodetransmission_eig
(elec_from, elec_to[, avg])Return the transmission eigenvalues from from
toto
.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
(**kwargs)Write the TBT.AV.nc equivalent of this TBtrans output Creates/Opens a SileCDF
Opens a SileCDF with
mode
and compression levellvl
. Ifmode
is in read-mode (r) the compression level is ignored.The final
access
parameter sets how the file should be open and subsequently accessed.- means direct file access for every variable read
- 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
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 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
toto
.Tbulk
(elec[, avg])Return the bulk transmission in the elec
electrodeTeig
(elec_from, elec_to[, avg])Return the transmission eigenvalues from from
toto
.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
toto
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 NetCDF4Dataset
typeisDimension
(obj)Return true if obj
is an instance of the NetCDF4Dimension
typeisGroup
(obj)Return true if obj
is an instance of the NetCDF4Group
typeisRoot
(obj)Return true if obj
is an instance of the NetCDF4Dataset
typeisVariable
(obj)Return true if obj
is an instance of the NetCDF4Variable
typeiter
([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 fileread_sc
()Returns SuperCell
object from a .TBT.nc filetransmission
(elec_from, elec_to[, avg])Return the transmission from from
toto
.transmission_bulk
(elec[, avg])Return the bulk transmission in the elec
electrodetransmission_eig
(elec_from, elec_to[, avg])Return the transmission eigenvalues from from
toto
.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
(**kwargs)Write the TBT.AV.nc equivalent of this TBtrans output
-
class
sisl.io.siesta.tbtrans_proj.
phtprojncSileSiesta
(filename, mode='r', lvl=0, access=1, _open=True)[source]¶ Bases:
sisl.io.siesta.tbtrans_proj.tbtprojncSileSiesta
PHtrans projection 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
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 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
toto
.Tbulk
(elec[, avg])Return the bulk transmission in the elec
electrodeTeig
(elec_from, elec_to[, avg])Return the transmission eigenvalues from from
toto
.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
toto
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 NetCDF4Dataset
typeisDimension
(obj)Return true if obj
is an instance of the NetCDF4Dimension
typeisGroup
(obj)Return true if obj
is an instance of the NetCDF4Group
typeisRoot
(obj)Return true if obj
is an instance of the NetCDF4Dataset
typeisVariable
(obj)Return true if obj
is an instance of the NetCDF4Variable
typeiter
([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 fileread_sc
()Returns SuperCell
object from a .TBT.nc filetransmission
(elec_from, elec_to[, avg])Return the transmission from from
toto
.transmission_bulk
(elec[, avg])Return the bulk transmission in the elec
electrodetransmission_eig
(elec_from, elec_to[, avg])Return the transmission eigenvalues from from
toto
.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
(**kwargs)Write the TBT.AV.nc equivalent of this TBtrans output Creates/Opens a SileCDF
Opens a SileCDF with
mode
and compression levellvl
. Ifmode
is in read-mode (r) the compression level is ignored.The final
access
parameter sets how the file should be open and subsequently accessed.- means direct file access for every variable read
- 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
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 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
toto
.Tbulk
(elec[, avg])Return the bulk transmission in the elec
electrodeTeig
(elec_from, elec_to[, avg])Return the transmission eigenvalues from from
toto
.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
toto
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 NetCDF4Dataset
typeisDimension
(obj)Return true if obj
is an instance of the NetCDF4Dimension
typeisGroup
(obj)Return true if obj
is an instance of the NetCDF4Group
typeisRoot
(obj)Return true if obj
is an instance of the NetCDF4Dataset
typeisVariable
(obj)Return true if obj
is an instance of the NetCDF4Variable
typeiter
([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 fileread_sc
()Returns SuperCell
object from a .TBT.nc filetransmission
(elec_from, elec_to[, avg])Return the transmission from from
toto
.transmission_bulk
(elec[, avg])Return the bulk transmission in the elec
electrodetransmission_eig
(elec_from, elec_to[, avg])Return the transmission eigenvalues from from
toto
.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
(**kwargs)Write the TBT.AV.nc equivalent of this TBtrans output