deltancSileTBtrans¶
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class
sisl.io.tbtrans.
deltancSileTBtrans
(filename, mode='r', lvl=0, access=1, *args, **kwargs)[source]¶ TBtrans \(\delta\) file object
The \(\delta\) file object is an extension enabled in TBtrans which allows changing the Hamiltonian in transport problems.
\[\mathbf H'(\mathbf k) = \mathbf H(\mathbf k) + \delta\mathbf H(E, \mathbf k) + \delta\mathbf\Sigma(E, \mathbf k)\]This file may either be used directly as the \(\delta\mathbf H\) or the \(\delta\mathbf\Sigma\).
When writing \(\delta\) terms using
write_delta
one may addk
orE
arguments to make the \(\delta\) dependent onk
and/orE
.Refer to the TBtrans manual on how to use this feature.
Examples
>>> H = Hamiltonian(geom.graphene(), dtype=np.complex128) >>> H[0, 0] = 1j >>> dH = get_sile('deltaH.dH.nc', 'w') >>> dH.write_delta(H) >>> H[1, 1] = 1. >>> dH.write_delta(H, k=[0, 0, 0]) # Gamma only >>> H[0, 0] += 1. >>> dH.write_delta(H, E=1.) # only at 1 eV >>> H[1, 1] += 1.j >>> dH.write_delta(H, E=1., k=[0, 0, 0]) # only at 1 eV and Gamma-point
Attributes
base_file
File of the current Sile file
File of the current Sile Methods
__init__
(filename[, mode, lvl, access])Initialize self. close
()dir_file
([filename])File of the current Sile exist
()Query whether the file exists iter
([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 read_delta
(**kwargs)Reads a delta model from the file read_geometry
(*args, **kwargs)Returns the Geometry object from this file read_supercell
()Returns the SuperCell object from this file write
(*args, **kwargs)Generic write method which should be overloaded in child-classes write_delta
(delta, **kwargs)Writes a \(\delta\) Hamiltonian to the file write_geometry
(geometry)Creates the NetCDF file and writes the geometry information write_supercell
(sc)Creates the NetCDF file and writes the supercell information -
base_file
¶ File of the current Sile
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close
()¶
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dir_file
(filename=None)¶ File of the current Sile
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exist
()¶ Query whether the file exists
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file
¶ File of the current Sile
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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 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.
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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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.
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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.
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write_delta
(delta, **kwargs)[source]¶ Writes a \(\delta\) Hamiltonian to the file
This term may be of
- level-1: no E or k dependence
- level-2: k-dependent
- level-3: E-dependent
- level-4: k- and E-dependent
Parameters: - delta : SparseOrbitalBZSpin
the model to be saved in the NC file
- k : array_like, optional
a specific k-point \(\delta\) term. I.e. only save the \(\delta\) term for the given k-point. May be combined with E for a specific k and energy point.
- E : float, optional
an energy dependent \(\delta\) term. I.e. only save the \(\delta\) term for the given energy. May be combined with k for a specific k and energy point.
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