sisl.io.siesta.tshsSileSiesta

class sisl.io.siesta.tshsSileSiesta(filename, mode='r', *args, **kwargs)

Bases: onlysSileSiesta

Geometry, Hamiltonian and overlap matrix file

Plotting

`plot`	Plotting functions for the `tshsSileSiesta` class.
`plot.geometry`([data_atoms, ...])	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
`dir_file`([filename, filename_base])	File of the current Sile
`read`(args, *kwargs)	Generic read method which should be overloaded in child-classes
`read_fermi_level`()	Query the Fermi-level contained in the file
`read_geometry`([atoms])	Returns Geometry object from a TranSiesta file
`read_hamiltonian`([geometry])	Electronic structure from the siesta.TSHS file
`read_lattice`()	Returns a Lattice object from a TranSiesta file
`read_overlap`(**kwargs)	Returns the overlap matrix from the TranSiesta file
`write`(args, *kwargs)	Generic write method which should be overloaded in child-classes
`write_hamiltonian`(H, **kwargs)	Writes the Hamiltonian to a siesta.TSHS file

Attributes

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

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

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

plot.geometry(data_atoms: Atoms | Geometry | None = None, *, 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.

See also

GeometryPlot: The plot class used to generate the plot.
read_geometry: The method called to get the data.

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_fermi_level() → float

Query the Fermi-level contained in the file

Returns:: float – fermi-level of the system

read_geometry(atoms: Atoms | Geometry | None = None): Returns Geometry object from a TranSiesta file

read_hamiltonian(geometry=None, **kwargs) → Hamiltonian[source]

Electronic structure from the siesta.TSHS file

The TSHS file format does not contain exact orbital information. When reading the Hamiltonian directly using this class one will find wrong orbital information. In such cases it may be beneficial to pass the geometry argument to override the contained geometry.

The orbital order is unaltered but the atomic and orbital information will be somewhat arbitrary.

Parameters:: geometry (Geometry, optional) – override the contained geometry in the returned Hamiltonian. Useful when reading files directly using this class.

Examples

Reading the Hamiltonian using the tshsSileSiesta backend through the fdf sile. Since the fdf file will try and read the basis sets using other files than the TSHS.

>>> H = sisl.get_sile("RUN.fdf").read_hamiltonian(order="TSHS")

An equivalent, but different way would be:

>>> geom = sisl.get_sile("RUN.fdf").read_geometry()
>>> H = sisl.get_sile("siesta.TSHS").read_hamiltonian(geometry=geom)

read_lattice() → Lattice: Returns a Lattice object from a TranSiesta file

read_overlap(**kwargs) → Overlap: Returns the overlap matrix from the TranSiesta 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_hamiltonian(H, **kwargs)[source]: Writes the Hamiltonian to a siesta.TSHS file

property base_file: File of the current Sile

property file: File of the current Sile

plot: Plotting functions for the tshsSileSiesta class.

property version: int: The version of the file