phtsencSilePHtrans¶
-
class
sisl.io.tbtrans.
phtsencSilePHtrans
(filename, mode='r', lvl=0, access=1, *args, **kwargs)[source]¶ PHtrans file object
Attributes
Sampled energy-points in file
Atomic indices (0-based) of device atoms
Atomic indices (0-based) of device atoms
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
Weights of k-points in file
Weights of k-points in file
Atomic coordinates in file
Atomic coordinates in file
Methods
Eindex
(self, E)Return the closest energy index corresponding to the energy
E
__init__
(self, filename[, mode, lvl, access])Initialize self.
a2p
(self, atom[, elec])Return the pivoting orbital indices (0-based) for the atoms, possibly on an electrode
btd
(self)Block-sizes for the BTD method in the device region
chemical_potential
(self, elec)Return the chemical potential associated with the electrode elec
close
(self)dir_file
(self[, filename])File of the current Sile
eta
(self, elec)The imaginary part used when calculating the self-energies in eV
exist
(self)Query whether the file exists
iter
(self[, group, dimension, variable, …])Iterator on all groups, variables and dimensions.
kindex
(self, k)Return the index of the k-point that is closests to the queried k-point (in reduced coordinates)
mu
(self, elec)Return the chemical potential associated with the electrode elec
n_btd
(self)Number of blocks in the BTD partioning in the device region
o2p
(self, orbital[, elec])Return the pivoting indices (0-based) for the orbitals, possibly on an electrode
pivot
(self[, elec, in_device, sort])Return the pivoting indices for a specific electrode
read
(self, \*args, \*\*kwargs)Generic read method which should be overloaded in child-classes
read_geometry
(self, \*args, \*\*kwargs)Returns Geometry object from this file
read_supercell
(self)Returns SuperCell object from this file
scattering_matrix
(self, elec, E[, k, sort])Return the scattering matrix from the electrode elec
self_energy
(self, elec, E[, k, sort])Return the self-energy from the electrode elec
self_energy_average
(self, elec, E[, sort])Return the k-averaged average self-energy from the electrode elec
write
(self, \*args, \*\*kwargs)Generic write method which should be overloaded in child-classes
write_geometry
(self, \*args, \*\*kwargs)This is not meant to be used
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property
E
¶ Sampled energy-points in file
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Eindex
(self, E)¶ Return the closest energy index corresponding to the energy
E
- Parameters
- Efloat or int
if
int
, return it-self, else return the energy index which is closests to the energy.
-
a2p
(self, atom, elec=None)¶ Return the pivoting orbital indices (0-based) for the atoms, possibly on an electrode
This is equivalent to:
>>> p = self.o2p(self.geom.a2o(atom, True))
- Parameters
- atomarray_like or int
atomic indices (0-based)
- elecstr or int or None
electrode to return pivoting indices of (if None it is the device pivoting indices).
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property
a_buf
¶ Atomic indices (0-based) of device atoms
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property
a_dev
¶ Atomic indices (0-based) of device atoms
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property
base_file
¶ File of the current Sile
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btd
(self)¶ Block-sizes for the BTD method in the device region
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property
cell
¶ Unit cell in file
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chemical_potential
(self, elec)¶ Return the chemical potential associated with the electrode elec
-
close
(self)¶
-
dir_file
(self, filename=None)¶ File of the current Sile
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property
elecs
¶ List of electrodes
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eta
(self, elec)¶ The imaginary part used when calculating the self-energies in eV
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exist
(self)¶ Query whether the file exists
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property
file
¶ File of the current Sile
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property
geom
¶ The associated geometry from this file
-
property
geometry
¶ The associated geometry from this file
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iter
(self, group=True, dimension=True, variable=True, levels=-1, root=None)¶ Iterator on all groups, variables and dimensions.
This iterator iterates through all groups, variables and dimensions in the
Dataset
The generator sequence will _always_ be:
Group
Dimensions in group
Variables in group
As the dimensions are generated before the variables it is possible to copy groups, dimensions, and then variables such that one always ensures correct dependencies in the generation of a new
SileCDF
.- Parameters
- group
bool
(True) whether the iterator yields Group instances
- dimension
bool
(True) whether the iterator yields Dimension instances
- variable
bool
(True) whether the iterator yields Variable instances
- levels
int
(-1) number of levels to traverse, with respect to
root
variable, i.e. number of sub-groups this iterator will return.- root
str
(None) the base root to start iterating from.
- group
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
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property
k
¶ Sampled k-points in file
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kindex
(self, k)¶ Return the index of the k-point that is closests to the queried k-point (in reduced coordinates)
- Parameters
- karray_like of float
the queried k-point in reduced coordinates \(]-0.5;0.5]\).
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property
kpt
¶ Sampled k-points in file
-
property
lasto
¶ Last orbital of corresponding atom
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mu
(self, elec)¶ Return the chemical potential associated with the electrode elec
-
property
nE
¶ Number of energy-points in file
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n_btd
(self)¶ Number of blocks in the BTD partioning in the device region
-
property
na
¶ Returns number of atoms in the cell
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property
na_b
¶ Number of atoms in the buffer region
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property
na_buffer
¶ Number of atoms in the buffer region
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property
na_d
¶ Number of atoms in the device region
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property
na_dev
¶ Number of atoms in the device region
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property
na_u
¶ Returns number of atoms in the cell
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property
ne
¶ Number of energy-points in file
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property
nk
¶ Number of k-points in file
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property
nkpt
¶ Number of k-points in file
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property
no
¶ Returns number of orbitals in the cell
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property
no_d
¶ Number of orbitals in the device region
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property
no_u
¶ Returns number of orbitals in the cell
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o2p
(self, orbital, elec=None)¶ Return the pivoting indices (0-based) for the orbitals, possibly on an electrode
- Parameters
- orbitalarray_like or int
orbital indices (0-based)
- elecstr or int or None
electrode to return pivoting indices of (if None it is the device pivoting indices).
-
property
o_dev
¶ Orbital indices (0-based) of device orbitals
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pivot
(self, elec=None, in_device=False, sort=False)¶ Return the pivoting indices for a specific electrode
- Parameters
- elecstr or int
the corresponding electrode to return the self-energy from
- in_devicebool, optional
If
True
the pivoting table will be translated to the device region orbitals- sortbool, optional
Whether the returned indices are sorted. Mostly useful if the self-energies are returned sorted as well.
Examples
>>> se = tbtsencSileTBtrans(...) >>> 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]
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read
(self, *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_geometry
(self, *args, **kwargs)¶ Returns Geometry object from this file
-
read_supercell
(self)¶ Returns SuperCell object from this file
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scattering_matrix
(self, elec, E, k=0, sort=False)¶ Return the scattering matrix from the electrode elec
The scattering matrix is calculated as:
\[\Gamma(E) = i [\Sigma(E) - \Sigma^\dagger(E)]\]- Parameters
- elecstr or int
the corresponding electrode to return the scattering matrix from
- Efloat or int
energy to retrieve the scattering matrix at, if a floating point the closest energy value will be found and returned, if an integer it will correspond to the exact index
- karray_like or int
k-point to retrieve, if an integer it is the k-index in the file
- sortbool, optional
if
True
the returned scattering matrix will be sorted (equivalent to pivoting the scattering matrix)
-
self_energy
(self, elec, E, k=0, sort=False)¶ Return the self-energy from the electrode elec
- Parameters
- elecstr or int
the corresponding electrode to return the self-energy from
- Efloat or int
energy to retrieve the self-energy at, if a floating point the closest energy value will be found and returned, if an integer it will correspond to the exact index
- karray_like or int
k-point to retrieve, if an integer it is the k-index in the file
- sortbool, optional
if
True
the returned self-energy will be sorted (equivalent to pivoting the self-energy)
-
self_energy_average
(self, elec, E, sort=False)¶ Return the k-averaged average self-energy from the electrode elec
- Parameters
- elecstr or int
the corresponding electrode to return the self-energy from
- Efloat or int
energy to retrieve the self-energy at, if a floating point the closest energy value will be found and returned, if an integer it will correspond to the exact index
- sortbool, optional
if
True
the returned self-energy will be sorted but not necessarily consecutive in the device region.
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property
wk
¶ Weights of k-points in file
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property
wkpt
¶ Weights of k-points in file
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write
(self, *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.
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write_geometry
(self, *args, **kwargs)¶ This is not meant to be used
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property
xa
¶ Atomic coordinates in file
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property
xyz
¶ Atomic coordinates in file
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property