sisl.io.siesta.aniSileSiesta

class sisl.io.siesta.aniSileSiesta

Bases: xyzSile, SileSiesta

Plotting

`plot`	Plotting functions for the `aniSileSiesta` 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
`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=None, *, 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:

data_atoms (Atoms, optional) – the atoms to be associated with the Geometry
lattice (Lattice, optional) – the lattice to be associated with the geometry
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

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()

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.

Return type:: Atoms

read_geometry(atoms=None, lattice=None)

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

Return type:

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()

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.

Return type:: Lattice

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, fmt='.8f', comment=None)

Writes the geometry to the contained file in extxyz format

Parameters:

geometry (Geometry) – the geometry to be written
fmt (str) – used format for the precision of the data
comment (str | None) – 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 aniSileSiesta class.