sisl.io.siesta.aniSileSiesta
- class sisl.io.siesta.aniSileSiesta(filename, *args, **kwargs)
Bases:
xyzSile
,SileSiesta
Plotting
Plotting functions for the
aniSileSiesta
class.plot.geometry
([data_atoms, ...])Calls
read_geometry
and creates aGeometryPlot
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
Returns a Atoms object from the XYZ file
read_geometry
([atoms, lattice])Returns Geometry object from the XYZ file
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
File of the current Sile
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 aGeometryPlot
from its output.- Parameters:
data_atoms (
Atoms
, optional) – the atoms to be associated with the Geometrylattice (
Lattice
, optional) – the lattice to be associated with the geometryaxes – 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
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
Returns Geometry object from the XYZ file
- Parameters:
atoms (
Atoms
, optional) – the atoms to be associated with the Geometrylattice (
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
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)
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
aniSileSiesta
class.