sisl.io.siesta.tbtrans module¶
Sile object for reading TBtrans binary files
-
class
sisl.io.siesta.tbtrans.
tbtncSileSiesta
(filename, mode='r', lvl=0, access=1, _open=True)[source]¶ Bases:
sisl.io.siesta.sile.SileCDFSIESTA
TBtrans file object
This
SileCDF
implements the TBtrans output*.TBT.nc
sile which contains calculated 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
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 -
ADOS
(elec, E=None, avg=True, atom=None)[source]¶ Return the DOS of the spectral function from
elec
(1/eV).Parameters: elec: ``str``
electrode originating spectral function
E :
int
(None
)optionally only return the DOS of atoms at a given energy point
avg: ``bool`` (`True`)
whether the returned DOS is k-averaged
atom :
array_like
,int
(_all_)only return for a given set of atoms (Python based indices)
-
ArgumentParser
(parser=None, *args, **kwargs)¶
-
BDOS
(elec, E=None, avg=True)[source]¶ Return the bulk DOS of
elec
(1/eV).Parameters: elec: ``str``
electrode where the bulk DOS is returned
E :
int
(None
)optionally only return the DOS of atoms at a given energy point
avg: ``bool`` (`True`)
whether the returned DOS is k-averaged
-
BulkDOS
(elec, E=None, avg=True)¶ Return the bulk DOS of
elec
(1/eV).Parameters: elec: ``str``
electrode where the bulk DOS is returned
E :
int
(None
)optionally only return the DOS of atoms at a given energy point
avg: ``bool`` (`True`)
whether the returned DOS is k-averaged
-
DOS
(E=None, avg=True, atom=None)[source]¶ Return the Green function DOS (1/eV).
Parameters: E :
int
(None
)optionally only return the DOS of atoms at a given energy point
avg: ``bool`` (`True`)
whether the returned DOS is k-averaged
atom :
array_like
,int
(_all_)only return for a given set of atoms (Python based indices)
-
DOS_A
(elec, E=None, avg=True, atom=None)¶ Return the DOS of the spectral function from
elec
(1/eV).Parameters: elec: ``str``
electrode originating spectral function
E :
int
(None
)optionally only return the DOS of atoms at a given energy point
avg: ``bool`` (`True`)
whether the returned DOS is k-averaged
atom :
array_like
,int
(_all_)only return for a given set of atoms (Python based indices)
-
DOS_Gf
(E=None, avg=True, atom=None)¶ Return the Green function DOS (1/eV).
Parameters: E :
int
(None
)optionally only return the DOS of atoms at a given energy point
avg: ``bool`` (`True`)
whether the returned DOS is k-averaged
atom :
array_like
,int
(_all_)only return for a given set of atoms (Python based indices)
-
DOS_bulk
(elec, E=None, avg=True)¶ Return the bulk DOS of
elec
(1/eV).Parameters: elec: ``str``
electrode where the bulk DOS is returned
E :
int
(None
)optionally only return the DOS of atoms at a given energy point
avg: ``bool`` (`True`)
whether the returned DOS is k-averaged
-
E
¶ Sampled energy-points in file
-
Elecs
¶ List of electrodes
-
Electrodes
¶ List of electrodes
-
T
(elec_from, elec_to, avg=True)¶ Return the transmission from
from
toto
.The transmission between two electrodes may be retrieved from the
Sile
.Parameters: elec_from: ``str``
the originating electrode
elec_to: ``str``
the absorbing electrode (different from
elec_from
)avg: ``bool`` (`True`)
whether the returned transmission is k-averaged
-
Tbulk
(elec, avg=True)¶ Return the bulk transmission in the
elec
electrodeParameters: elec: ``str``
the bulk electrode
avg: ``bool`` (`True`)
whether the returned transmission is k-averaged
-
Teig
(elec_from, elec_to, avg=True)¶ Return the transmission eigenvalues from
from
toto
.The transmission eigenvalues between two electrodes may be retrieved from the
Sile
.Parameters: elec_from: ``str``
the originating electrode
elec_to: ``str``
the absorbing electrode (different from
elec_from
)avg: ``bool`` (`True`)
whether the returned eigenvalues are k-averaged
-
a2p
(atom)[source]¶ Return the pivoting indices (0-based) for the atoms
Parameters: atom :
array_like
,int
atomic indices (0-based)
-
a_d
¶ Atomic indices (1-based) of device atoms
-
a_dev
¶ Atomic indices (1-based) of device atoms
-
atom_current
(elec, E, avg=True, activity=True)[source]¶ Return the atom-current of atoms.
This should not be confused with the bond-currents.
Parameters: elec: ``str``
the electrode of originating electrons
E: float or int
the energy or energy index of the atom current.
avg: ``bool`` (`True`)
whether the atom current returned is k-averaged
activity: ``bool`` (`True`)
whether the activity current is returned. This is defined using these two equations:
\[J_I^{|a|} &=\frac{1}{2} \sum_J \big| \sum_{\nu\in I}\sum_{\mu\in J} J_{\nu\mu} \big| J_I^{|o|} &=\frac{1}{2} \sum_J \sum_{\nu\in I}\sum_{\mu\in J} \big| J_{\nu\mu} \big|\]If
activity = False
it returns\[J_I^{|a|}\]and if
activity = True
it returns\[J_I^{\mathcal A} = \sqrt{ J_I^{|a|} J_I^{|o|} }\]
-
atom_current_from_orbital
(Jij, activity=True)[source]¶ Return the atom-current of atoms.
This takes a sparse matrix with size
self.geom.no, self.geom.no_s
as argument with the associated orbital currents.Please note that this returns the atomic current by folding all orbital currents into the unit-cell.
Parameters: Jij: ``scipy.sparse.*_matrix``
the orbital currents as retrieved from
orbital_current
activity: ``bool`` (`True`)
whether the activity current is returned. This is defined using these two equations:
\[J_I^{|a|} &=\frac{1}{2} \sum_J \big| \sum_{\nu\in I}\sum_{\mu\in J} J_{\nu\mu} \big| J_I^{|o|} &=\frac{1}{2} \sum_J \sum_{\nu\in I}\sum_{\mu\in J} \big| J_{\nu\mu} \big|\]If
activity = False
it returns\[J_I^{|a|}\]and if
activity = True
it returns\[J_I^{\mathcal A} = \sqrt{ J_I^{|a|} J_I^{|o|} }\]
-
bond_current
(elec, E, avg=True, isc=None, sum='+', uc=False)[source]¶ Return the bond-current between atoms (sum of orbital currents)
Parameters: elec :
str
the electrode of originating electrons
E : float or int
A
float
for energy in eV,int
for explicit energy index Unlikeorbital_current
this may not beNone
as the down-scaling of the orbital currents may not be equivalent for all energy points.avg :
bool
(True
)whether the bond current returned is k-averaged
isc :
array_like
([0, 0, 0]
)the returned bond currents from the unit-cell (
[0, 0, 0]
) to the given supercell. If[None, None, None]
is passed all bond currents are returned.sum :
str
('+'
)this value may be “+”/”-“/”all” If “+” is supplied only the positive orbital currents are used, for “-”, only the negative orbital currents are used, else return the sum of both.
uc :
bool
(False
)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 viaGeometry.sc_index
.
-
bond_current_from_orbital
(Jij, sum='+', uc=None)[source]¶ Return the bond-current between atoms (sum of orbital currents) by passing the orbital currents.
Parameters: Jij :
scipy.sparse.*_matrix
the orbital currents as retrieved from
orbital_current
sum :
str
('+'
)this value may be “+”/”-“/”all” If “+” is supplied only the positive orbital currents are used, for “-”, only the negative orbital currents are used, else return both.
uc :
bool
(Jij.shape[0] == Jij.shape[1]
)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 viaGeometry.sc_index
.
-
cell
¶ Unit cell in file
-
current
(elec_from, elec_to, avg=True)[source]¶ Return the current from
from
toto
using the weights in the file.
-
elecs
¶ List of electrodes
-
electrodes
¶ List of electrodes
-
electronic_temperature
(elec)[source]¶ Return temperature of the electrode electronic distribution in Kelvin
-
geom
¶ Returns the associated geometry from the TBT file
-
kpt
¶ Sampled k-points in file
-
lasto
¶ Last orbital of corresponding atom
-
mu
(elec)¶ Return the chemical potential associated with the electrode
elec
-
nE
¶ Number of energy-points in file
-
na
¶ Returns number of atoms in the cell
-
na_d
¶ Number of atoms in the device region
-
na_dev
¶ Number of atoms in the device region
-
na_u
¶ Returns number of atoms in the cell
-
ne
¶ Number of energy-points in file
-
nkpt
¶ 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
-
o2p
(orbital)[source]¶ Return the pivoting indices (0-based) for the orbitals
Parameters: orbital :
array_like
,int
orbital indices (0-based)
-
orbital_current
(elec, E, avg=True, isc=None)[source]¶ Return the orbital current originating from
elec
.This will return a sparse matrix (
scipy.sparse.csr_matrix
). The sparse matrix may be interacted with like a normal matrix although it enables extremely big matrices.Parameters: elec: str
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.avg: bool, optional
whether the orbital current returned is k-averaged, default to True
isc: array_like (`[0, 0, 0]`)
the returned bond currents from the unit-cell (
[0, 0, 0]
) to the given supercell, the default is only orbital currents in the unitcell.
-
pivot
¶ Pivot table of device orbitals to obtain input sorting
-
pvt
¶ Pivot table of device orbitals to obtain input sorting
-
read_data
(*args, **kwargs)[source]¶ Read specific type of data.
This is a generic routine for reading different parts of the data-file.
Parameters: geom: ``bool``
return the geometry
atom_current: ``bool``
return the atomic current flowing through an atom (the activity current)
vector_current: ``bool``
return the orbital currents as vectors
-
transmission
(elec_from, elec_to, avg=True)[source]¶ Return the transmission from
from
toto
.The transmission between two electrodes may be retrieved from the
Sile
.Parameters: elec_from: ``str``
the originating electrode
elec_to: ``str``
the absorbing electrode (different from
elec_from
)avg: ``bool`` (`True`)
whether the returned transmission is k-averaged
-
transmission_bulk
(elec, avg=True)[source]¶ Return the bulk transmission in the
elec
electrodeParameters: elec: ``str``
the bulk electrode
avg: ``bool`` (`True`)
whether the returned transmission is k-averaged
-
transmission_eig
(elec_from, elec_to, avg=True)[source]¶ Return the transmission eigenvalues from
from
toto
.The transmission eigenvalues between two electrodes may be retrieved from the
Sile
.Parameters: elec_from: ``str``
the originating electrode
elec_to: ``str``
the absorbing electrode (different from
elec_from
)avg: ``bool`` (`True`)
whether the returned eigenvalues are k-averaged
-
vector_current
(elec, E, avg=True)[source]¶ Return the atom-current with vector components of atoms.
Parameters: elec: ``str``
the electrode of originating electrons
E: float or int
the energy or energy index of the vector current. Unlike
orbital_current
this may not beNone
as the down-scaling of the orbital currents may not be equivalent for all energy points.avg: ``bool`` (`True`)
whether the vector current returned is k-averaged
-
vector_current_from_orbital
(Jij)[source]¶ Return the atom-current with vector components of atoms.
This takes a sparse matrix with size
self.geom.no, self.geom.no_s
as argument with the associated orbital currents.Parameters: Jij: ``scipy.sparse.*_matrix``
the orbital currents as retrieved from
orbital_current
-
wkpt
¶ Weights of k-points in file
-
write_tbtav
(**kwargs)[source]¶ Write the TBT.AV.nc equivalent of this TBtrans output
This will create/overwrite the file with the ending TBT.AV.nc and thus will not take notice of any older files.
-
xa
¶ Atomic coordinates in file
-
xyz
¶ Atomic coordinates in file
-
class
sisl.io.siesta.tbtrans.
phtncSileSiesta
(filename, mode='r', lvl=0, access=1, _open=True)[source]¶ Bases:
sisl.io.siesta.tbtrans.tbtncSileSiesta
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
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.
dHncSileSiesta
(filename, mode='r', lvl=0, access=1, _open=True)[source]¶ Bases:
sisl.io.siesta.sile.SileCDFSIESTA
TBtrans delta-H file object
Attributes
file
Filename of the current Sile
Methods
ArgumentParser
([parser])Returns the arguments that may be available for this Sile ArgumentParser_out
([parser])Appends additional arguments based on the output of the file 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. read
(*args, **kwargs)Generic read method which should be overloaded in child-classes write
(*args, **kwargs)Generic write method which should be overloaded in child-classes write_es
(ham, **kwargs)Writes Hamiltonian model to file write_geom
(geom)Creates the NetCDF file and writes the geometry information 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
file
Filename of the current Sile
Methods
ArgumentParser
([parser])Returns the arguments that may be available for this Sile ArgumentParser_out
([parser])Appends additional arguments based on the output of the file 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. read
(*args, **kwargs)Generic read method which should be overloaded in child-classes write
(*args, **kwargs)Generic write method which should be overloaded in child-classes write_es
(ham, **kwargs)Writes Hamiltonian model to file write_geom
(geom)Creates the NetCDF file and writes the geometry information -
write_es
(ham, **kwargs)[source]¶ Writes Hamiltonian model to file
Parameters: ham :
Hamiltonian
modelthe model to be saved in the NC file
spin : int, 0
the spin-index of the Hamiltonian object that is stored.