sisl.io.tbtrans.deltancSileTBtrans

class sisl.io.tbtrans.deltancSileTBtrans(filename, mode='r', lvl=0, access=1, *args, **kwargs)

Bases: SileCDFTBtrans

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 add k or E arguments to make the $$\delta$$ dependent on k and/or E.

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


Methods

 dir_file([filename, filename_base]) File of the current Sile 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 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 Creates the NetCDF file and writes the supercell information base_file File of the current Sile file File of the current Sile
__init__(filename, mode='r', lvl=0, access=1, *args, **kwargs)
property base_file

File of the current Sile

close()
dir_file(filename=None, filename_base='')

File of the current Sile

property file

File of the current Sile

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:

1. Group

2. Dimensions in group

3. 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

plot

Handles all plotting possibilities for a class

Parameters

kwargs – keyword arguments will try and search for the attribute read_<> and call it with the remaining **kwargs as arguments.

Reads a delta model from the file

Returns the Geometry object from this file

Returns the SuperCell object from this file

to_json()
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.

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.

write_geometry(geometry)[source]

Creates the NetCDF file and writes the geometry information

write_supercell(sc)[source]

Creates the NetCDF file and writes the supercell information