deltancSileTBtrans

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

Bases: sisl.io.tbtrans.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

Attributes

__dict__
__doc__
__module__
__weakref__	list of weak references to the object (if defined)
_cmp_args	Returns the compression arguments for the NetCDF file
_write_default
_write_default_only
base_file	File of the current Sile
file	File of the current Sile

Methods

_ArgumentParser_args_single()	Default arguments for the Sile
__delattr__	Implement delattr(self, name).
__dir__	Default dir() implementation.
__enter__()	Opens the output file and returns it self
__eq__	Return self==value.
__exit__(type, value, traceback)
__format__	Default object formatter.
__ge__	Return self>=value.
__getattr__(name)	Override to check the handle
__getattribute__	Return getattr(self, name).
__gt__	Return self>value.
__hash__	Return hash(self).
__init__(filename[, mode, lvl, access])	Initialize self.
__init_subclass__	This method is called when a class is subclassed.
__iter__([group, dimension, variable, …])	Iterator on all groups, variables and dimensions.
__le__	Return self<=value.
__lt__	Return self<value.
__ne__	Return self!=value.
__new__	Create and return a new object.
__reduce__	Helper for pickle.
__reduce_ex__	Helper for pickle.
__repr__	Return repr(self).
__setattr__	Implement setattr(self, name, value).
__sizeof__	Size of object in memory, in bytes.
__str__()	Return a representation of the Sile
__subclasshook__	Abstract classes can override this to customize issubclass().
_add_lvl(ilvl)	Simply adds and returns a group if it does not exist it will be created
_base_file(f)	Make f refer to the file with the appropriate base directory
_base_setup(*args, **kwargs)	Setup the Sile after initialization
_crt_dim(n, name, l)
_crt_grp(n, name)
_crt_var(n, name, *args, **kwargs)
_dimension(name[, tree])	Local method for obtaing the dimension in a certain tree
_dimensions(n, name[, tree])	Retrieve method to get the NetCDF variable
_get_lvl(ilvl)
_get_lvl_k_E(**kwargs)	Return level, k and E indices, in that order.
_read_class(cls, **kwargs)	Reads a class model from a file
_setup(*args, **kwargs)	Setup the Sile after initialization
_value(name[, tree])	Local method for obtaining the data from the SileCDF.
_variable(name[, tree])	Local method for obtaining the data from the SileCDF.
_variables(n, name[, tree])	Retrieve method to get the NetCDF variable
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

property base_file

File of the current Sile

close()

dir_file(filename=None)

File of the current Sile

exist()

Query whether the file exists

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

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_supercell()

Returns the SuperCell 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 \(\delta\) 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)

Creates the NetCDF file and writes the geometry information

write_supercell(sc)

Creates the NetCDF file and writes the supercell information