sisl.io.siesta.pdosSileSiesta
- class sisl.io.siesta.pdosSileSiesta(filename, *args, **kwargs)
Bases:
SileSiesta
Projected DOS file with orbital information
Data file containing the PDOS as calculated by Siesta.
Plotting
Plotting functions for the
pdosSileSiesta
class.plot.geometry
(*[, axes, ...])Calls
read_geometry
and creates aGeometryPlot
from its output.plot.pdos
(*[, groups, ...])Creates a
PDOSData
object and then plots aPdosPlot
from it.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_data
([as_dataarray])Returns data associated with the PDOS file
Returns the fermi-level
Read the geometry with coordinates and correct orbital counts
write
(*args, **kwargs)Generic write method which should be overloaded in child-classes
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(*, 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:
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.
- plot.pdos(*, groups: Sequence[OrbitalStyleQuery] = [{'name': 'DOS'}], Erange: tuple[float, float] = (-2, 2), E_axis: Literal['x', 'y'] = 'x', line_mode: Literal['line', 'scatter', 'area_line'] = 'line', line_scale: float = 1.0, backend: str = 'plotly') PdosPlot
Creates a
PDOSData
object and then plots aPdosPlot
from it.- Parameters:
groups – List of orbital specifications to filter and accumulate the PDOS. The contribution of each group will be displayed in a different line. See showcase notebook for examples.
Erange – The energy range to plot.
E_axis – Axis to project the energies.
line_mode – Mode used to draw the PDOS lines.
line_scale – Scaling factor for the width of all lines.
backend – The backend to generate the figure.
See also
PdosPlot
The plot class used to generate the plot.
PDOSData
The class to which data is converted.
- 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_data(as_dataarray: bool = False)[source]
Returns data associated with the PDOS file
For spin-polarized calculations the returned values are up/down, orbitals, energy. For non-collinear calculations the returned values are sum/x/y/z, orbitals, energy.
- Parameters:
as_dataarray (
bool
, optional) – If True the returned PDOS is axarray.DataArray
with energy, spin and orbital information as coordinates in the data. The geometry, unit and Fermi level are stored as attributes in the DataArray.- Returns:
geom (
Geometry
) – instance with positions, atoms and orbitals.E (
numpy.ndarray
) – the energies at which the PDOS has been evaluated at (if Fermi-level present in file energies are shifted to \(E - E_F = 0\)).PDOS (
numpy.ndarray
) – an array of DOS with dimensions(nspin, geom.no, len(E))
(with different spin-components) or(geom.no, len(E))
(spin-symmetric).all (
xarray.DataArray
) – if as_dataarray is True, only this data array is returned, in this case all data can be post-processed using thexarray
selection routines.
- 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
pdosSileSiesta
class.