sisl.io.siesta.hsxSileSiesta

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

Bases: SileBinSiesta

Hamiltonian and overlap matrix file

This file does not contain all information regarding the system.

To ensure no errors are being raised one should pass a Geometry with correct number of atoms and correct number of supercells. The number of orbitals will be updated in the returned matrices geometry.

>>> hsx = hsxSileSiesta("siesta.HSX")
>>> HS = hsx.read_hamiltonian() # may fail
>>> HS = hsx.read_hamiltonian(geometry=<>) # should run correctly if above satisfied

Users are adviced to use the tshsSileSiesta instead since that correctly contains all information.

Plotting

`plot`	Plotting functions for the `hsxSileSiesta` class.
`plot.geometry`(*[, ...])	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_basis`(**kwargs)	Reads basis set and geometry information from the HSX file
`read_fermi_level`(**kwargs)	Reads the fermi level in the file
`read_geometry`(**kwargs)	Read the geometry from the file
`read_hamiltonian`(**kwargs)	Returns the electronic structure from the siesta.TSHS file
`read_lattice`(**kwargs)	Read the lattice from the file
`read_overlap`(**kwargs)	Returns the electronic structure from the siesta.TSHS file
`write`(args, *kwargs)	Generic write method which should be overloaded in child-classes

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_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.