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.

\[\mathbf H'(\mathbf k) = \mathbf H(\mathbf k) + \delta\mathbf H(E, \mathbf k) + \delta\boldsymbol\Sigma(E, \mathbf k)\]

This file may either be used directly as the \(\delta\mathbf H\) or the \(\delta\boldsymbol\Sigma\).

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

base_directory([relative_to])	Retrieve the base directory of the file, relative to the path relative_to
close()
dir_file([filename, filename_base])	File of the current Sile
has_level(ilvl)	Query whether the file has level ilvl content
iter([group, dimension, variable, levels, root])	Iterator on all groups, variables and dimensions.
merge(fname, *deltas, **kwargs)	Merge several delta files into one Sile which contains the sum of the content
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_lattice()	Returns the Lattice object from this file
write(*args, **kwargs)	Generic write method which should be overloaded in child-classes
write_delta(delta, **kwargs)	Writes a \(\delta\) term to the file
write_geometry(geometry)	Creates the NetCDF file and writes the geometry information
write_lattice(lattice)	Creates the NetCDF file and writes the supercell information
base_file	File of the current Sile
file	File of the current Sile
plot	Handles all plotting possibilities for a class

__init__(filename, mode='r', lvl=0, access=1, *args, **kwargs)

Just to pass away the args and kwargs

base_directory(relative_to='.')

Retrieve the base directory of the file, relative to the path relative_to

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

has_level(ilvl)

Query whether the file has level ilvl content

Parameters:

ilvl (int) – the level to be queried, one of 1, 2, 3 or 4

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

classmethod merge(fname, *deltas, **kwargs)

Merge several delta files into one Sile which contains the sum of the content

In cases where implementors use several different delta files it is necessary to merge them into a single delta file before use in TBtrans. This method does exactly that.

Notes

The code checks whether fname is different from all deltas and that all deltas are the same class.

Parameters:

• fname (str, Path) – the output name of the merged file

• *deltas (deltancSileTBtrans, str, Path) – all the delta files that should be merged

• **kwargs – arguments passed directly to the init of cls(fname, **kwargs)

plot

Handles all plotting possibilities for a class

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.

read_delta(**kwargs)

Reads a delta model from the file

read_geometry(*args, **kwargs)

Returns the Geometry object from this file

read_lattice()

Returns the Lattice object from this file

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)

Writes a \(\delta\) term 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.

Notes

The input options for TBtrans determine whether this is a self-energy term or a Hamiltonian term.

write_geometry(geometry)

Creates the NetCDF file and writes the geometry information

write_lattice(lattice)

Creates the NetCDF file and writes the supercell information