sisl.io.siesta.hsxSileSiesta

class sisl.io.siesta.hsxSileSiesta

Bases: SileBinSiesta

Hamiltonian and overlap matrix file

Historically there are several HSX file versions output from Siesta.

Since Siesta 5.3, the HSX file format is containing all the information present in the TranSiesta specific TSHS file-format, plus more information. As such, the TSHS file format is deprecated and will not be used anymore. Therefore users should adapt their workflows to be done with HSX files.

Basically, one should never work with HSX files from Siesta <= 4, since they are not information complete.

Notes

At some point we will deprecate the older HSX file versions (<= 4).

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.HSX file
`read_lattice`(**kwargs)	Read the lattice from the file
`read_overlap`(**kwargs)	Returns the electronic structure from the siesta.HSX file
`write`(args, *kwargs)	Generic write method which should be overloaded in child-classes
`write_hamiltonian`(H, **kwargs)	Writes the Hamiltonian to a siesta.HSX 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_kwargs={}, axes=['x', 'y', 'z'], atoms=None, atoms_style=[], atoms_scale=1.0, atoms_colorscale=None, drawing_mode=None, bind_bonds_to_ats=True, points_per_bond=20, bonds_style={}, bonds_scale=1.0, bonds_colorscale=None, show_atoms=True, show_bonds=True, show_cell='box', cell_style={}, nsc=(1, 1, 1), atoms_ndim_scale=(16, 16, 1), bonds_ndim_scale=(1, 1, 10), dataaxis_1d=None, arrows=(), backend='plotly')

Calls read_geometry and creates a GeometryPlot from its output.

Parameters:

axes (Axes) – The axes to project the geometry to.
atoms (AtomsIndex) – The atoms to plot. If None, all atoms are plotted.
atoms_style (Sequence[AtomsStyleSpec]) – List of style specifications for the atoms. See the showcase notebooks for examples.
atoms_scale (float) – Scaling factor for the size of all atoms.
atoms_colorscale (Optional[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 (Literal['scatter', 'balls', None]) – The method used to draw the atoms.
bind_bonds_to_ats (bool) – Whether to display only bonds between atoms that are being displayed.
points_per_bond (int) – 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 (StyleSpec) – Style specification for the bonds. See the showcase notebooks for examples.
bonds_scale (float) – Scaling factor for the width of all bonds.
bonds_colorscale (Optional[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 (bool) – Whether to display the atoms.
show_bonds (bool) – Whether to display the bonds.
show_cell (Literal['box', 'axes', False]) – Mode to display the cell. If False, the cell is not displayed.
cell_style (StyleSpec) – Style specification for the cell. See the showcase notebooks for examples.
nsc (tuple[int, int, int]) – Number of unit cells to display in each direction.
atoms_ndim_scale (tuple[float, float, float]) – Scaling factor for the size of the atoms for different dimensionalities (1D, 2D, 3D).
bonds_ndim_scale (tuple[float, float, float]) – Scaling factor for the width of the bonds for different dimensionalities (1D, 2D, 3D).
dataaxis_1d (Optional[Union[np.ndarray, Callable]]) – Only meaningful for 1D plots. The data to plot on the Y axis.
arrows (Sequence[AtomArrowSpec]) – List of arrow specifications to display. See the showcase notebooks for examples.
backend – The backend to use to generate the figure.

Return type:

GeometryPlot