sisl.io.xyzSile

class sisl.io.xyzSile(filename, *args, **kwargs)

Bases: Sile

XYZ file object

Plotting

plot

Plotting functions for the xyzSile class.

plot.geometry([data_atoms, lattice, ...])

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

read(*args, **kwargs)

Generic read method which should be overloaded in child-classes

read_basis()

Returns a Atoms object from the XYZ file

read_geometry([atoms, lattice])

Returns Geometry object from the XYZ file

read_lattice()

Returns a Lattice object from the XYZ file

write(*args, **kwargs)

Generic write method which should be overloaded in child-classes

write_geometry(geometry[, fmt, comment])

Writes the geometry to the contained file in extxyz format

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

plot.geometry(data_atoms=None, lattice: Lattice | 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:

  • data_atoms (Atoms, optional) – the atoms to be associated with the Geometry

  • lattice (Lattice, optional) – the lattice to be associated with the geometry

  • 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() → Atoms[source]

Returns a Atoms object from the XYZ file

Notes

This method defaults to return the first item(s).

This method enables slicing for handling multiple values (see [...|default]).

This is an optional handler enabling returning multiple elements if read_basis[...|0] allows this.

>>> single = obj.read_basis() # returns the default entry of read_basis[...|0]

To retrieve the first two elements that read_basis will return

>>> first_two = obj.read_basis[:2]()

Retrieving the last two is done equivalently:

>>> last_two = obj.read_basis[-2:]()

While one can store the sliced function tmp = obj.read_basis[:] one will loose the slice after each call.

read_geometry(atoms=None, lattice: Lattice | None = None) → Geometry[source]

Returns Geometry object from the XYZ file

Parameters:

  • atoms (Atoms, optional) – the atoms to be associated with the Geometry

  • lattice (Lattice, optional) – the lattice to be associated with the geometry

Notes

This method defaults to return the first item(s).

This method enables slicing for handling multiple values (see [...|default]).

This is an optional handler enabling returning multiple elements if read_geometry[...|0] allows this.

>>> single = obj.read_geometry() # returns the default entry of read_geometry[...|0]

To retrieve the first two elements that read_geometry will return

>>> first_two = obj.read_geometry[:2]()

Retrieving the last two is done equivalently:

>>> last_two = obj.read_geometry[-2:]()

While one can store the sliced function tmp = obj.read_geometry[:] one will loose the slice after each call.

read_lattice() → Lattice[source]

Returns a Lattice object from the XYZ file

Notes

This method defaults to return the first item(s).

This method enables slicing for handling multiple values (see [...|default]).

This is an optional handler enabling returning multiple elements if read_lattice[...|0] allows this.

>>> single = obj.read_lattice() # returns the default entry of read_lattice[...|0]

To retrieve the first two elements that read_lattice will return

>>> first_two = obj.read_lattice[:2]()

Retrieving the last two is done equivalently:

>>> last_two = obj.read_lattice[-2:]()

While one can store the sliced function tmp = obj.read_lattice[:] one will loose the slice after each call.

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_geometry(geometry: Geometry, fmt: str = '.8f', comment: str | None = None)[source]

Writes the geometry to the contained file in extxyz format

Parameters:

  • geometry – the geometry to be written

  • fmt – used format for the precision of the data

  • comment – if None, a sisl made comment that can be used for parsing the unit-cell is used else this comment will be written at the 2nd line.

property base_file

File of the current Sile

property file

File of the current Sile

plot

Plotting functions for the xyzSile class.