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.

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_basis(**kwargs) Atoms[source]

Reads basis set and geometry information from the HSX file

read_fermi_level(**kwargs) float[source]

Reads the fermi level in the file

Only valid for files created by Siesta >=5.

read_geometry(**kwargs) Geometry[source]

Read the geometry from the file

This will always work on new files Siesta >=5, but only sometimes on older versions of the HSX file format.

read_hamiltonian(**kwargs) Hamiltonian[source]

Returns the electronic structure from the siesta.TSHS file

read_lattice(**kwargs) Lattice[source]

Read the lattice from the file

This will always work on new files Siesta >=5, but only sometimes on older versions of the HSX file format.

read_overlap(**kwargs) Overlap[source]

Returns the electronic structure from the siesta.TSHS 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.

property base_file

File of the current Sile

property file

File of the current Sile

plot

Plotting functions for the hsxSileSiesta class.

property version: int

The version of the file