sisl.io.fhiaims.inSileFHIaims
- class sisl.io.fhiaims.inSileFHIaims(filename, *args, **kwargs)
Bases:
SileFHIaims
FHI-aims
geometry.in
file objectPlotting
Plotting functions for the
inSileFHIaims
class.plot.geometry
([ret_velocity, ...])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
read_geometry
([ret_velocity, ret_moment])Reads Geometry object from the file
Reads supercell object from the file
Reads initial moment in the file
Reads velocity in the file
write
(*args, **kwargs)Generic write method which should be overloaded in child-classes
write_geometry
(geometry[, fmt, as_frac, ...])Writes the geometry to the contained file
write_lattice
(lattice[, fmt])Writes the supercell to the contained file
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(ret_velocity: bool = False, ret_moment: bool = False, *, 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:
ret_velocity (
bool
, optional) – also return the velocities in the file, if not present, it will return a 0 arrayret_moment (
bool
, optional) – also return the moments specified in the file, if not present, it will return a 0 arrayaxes – 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_geometry(ret_velocity: bool = False, ret_moment: bool = False) Geometry [source]
Reads Geometry object from the file
- Parameters:
- Returns:
geometry (
Geometry
) – geometry found in filevelocity (
numpy.ndarray
) – array of velocities in Ang/ps for each atom, will only be returned if ret_velocity is truemoment (
numpy.ndarray
) – array of initial moments of each atom, will only be returned if ret_moment is true
- 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', as_frac: bool = False, velocity=None, moment=None)[source]
Writes the geometry to the contained file
- Parameters:
geometry – the geometry to be written
fmt – used format for the precision of the data
as_frac – whether coordinates are written as fractional coordinates
velocity (
array_like
, optional) – also write the velocity fields in [Ang/ps]moment (
array_like
, optional) – also write an initial moment for each atom
- write_lattice(lattice: Lattice, fmt: str = '.8f')[source]
Writes the supercell to the contained file
- Parameters:
lattice – the supercell to be written
fmt – used format for the precision of the data
- property base_file
File of the current Sile
- property file
File of the current Sile
- plot
Plotting functions for the
inSileFHIaims
class.