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

Plotting

`plot`	Plotting functions for the `deltancSileTBtrans` class.
`plot.geometry`(*args[, ...])	Calls `read_geometry` and creates a `GeometryPlot` from its output.

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

Attributes

`base_file`	File of the current Sile
`file`	File of the current Sile

base_directory(relative_to='.'): Retrieve the base directory of the file, relative to the path relative_to

close()

dir_file(filename=None, filename_base=''): File of the current Sile

has_level(ilvl)[source]

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:

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

classmethod merge(fname, *deltas, **kwargs)[source]

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.geometry(*args, data_kwargs={}, axes: Axes = ['x', 'y', 'z'], atoms: AtomsIndex = None, atoms_style: Sequence[AtomsStyleSpec] = [], atoms_scale: float = 1.0, atoms_colorscale: Colorscale | None = None, drawing_mode: Literal['scatter', 'balls', None] = None, bind_bonds_to_ats: bool = True, points_per_bond: int = 20, bonds_style: StyleSpec = {}, bonds_scale: float = 1.0, bonds_colorscale: Colorscale | None = None, show_atoms: bool = True, show_bonds: bool = True, show_cell: Literal['box', 'axes', False] = 'box', cell_style: StyleSpec = {}, nsc: tuple[int, int, int] = (1, 1, 1), atoms_ndim_scale: tuple[float, float, float] = (16, 16, 1), bonds_ndim_scale: tuple[float, float, float] = (1, 1, 10), dataaxis_1d: np.ndarray | Callable | None = None, arrows: Sequence[AtomArrowSpec] = (), backend='plotly') → GeometryPlot

Calls read_geometry and creates a GeometryPlot from its output.

Parameters:

axes – The axes to project the geometry to.
atoms – The atoms to plot. If None, all atoms are plotted.
atoms_style – List of style specifications for the atoms. See the showcase notebooks for examples.
atoms_scale – Scaling factor for the size of all atoms.
atoms_colorscale – Colorscale to use for the atoms in case the color attribute is an array of values. If None, the default colorscale is used for each backend.
drawing_mode – The method used to draw the atoms.
bind_bonds_to_ats – Whether to display only bonds between atoms that are being displayed.
points_per_bond – When the points are drawn using points instead of lines (e.g. in some frameworks to draw multicolor bonds), the number of points used per bond.
bonds_style – Style specification for the bonds. See the showcase notebooks for examples.
bonds_scale – Scaling factor for the width of all bonds.
bonds_colorscale – Colorscale to use for the bonds in case the color attribute is an array of values. If None, the default colorscale is used for each backend.
show_atoms – Whether to display the atoms.
show_bonds – Whether to display the bonds.
show_cell – Mode to display the cell. If False, the cell is not displayed.
cell_style – Style specification for the cell. See the showcase notebooks for examples.
nsc – Number of unit cells to display in each direction.
atoms_ndim_scale – Scaling factor for the size of the atoms for different dimensionalities (1D, 2D, 3D).
bonds_ndim_scale – Scaling factor for the width of the bonds for different dimensionalities (1D, 2D, 3D).
dataaxis_1d – Only meaningful for 1D plots. The data to plot on the Y axis.
arrows – List of arrow specifications to display. See the showcase notebooks for examples.
backend – The backend to use to generate the figure.