sisl.io.gulp.gotSileGULP
- class sisl.io.gulp.gotSileGULP(filename, *args, **kwargs)
Bases:
SileGULP
GULP output file object
- Parameters:
Plotting
Plotting functions for the
gotSileGULP
class.plot.geometry
(*[, data_kwargs, ...])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_dynamical_matrix
(**kwargs)Returns a GULP dynamical matrix model for the output of GULP
read_geometry
(**kwargs)Reads a geometry and creates the GULP dynamical geometry
read_lattice
([key])Reads a Lattice and creates the GULP cell
read_lattice_nsc
([key])Reads the dimensions of the supercell
set_dyn_key
(key)Overwrites internal key lookup value for the dynamical matrix vectors
Overwrites internal key lookup value for the dynamical matrix vectors
set_geometry_key
(key)Overwrites internal key lookup value for the geometry vectors
set_key
(segment, key)Sets the segment lookup key
set_lattice_key
(key)Overwrites internal key lookup value for the cell vectors
set_supercell_key
(key)Overwrites internal key lookup value for the cell vectors
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(*, data_kwargs={}, 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.
- 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_dynamical_matrix(**kwargs) DynamicalMatrix [source]
Returns a GULP dynamical matrix model for the output of GULP
- Parameters:
cutoff (
float
, optional) – absolute values below the cutoff are considered 0. Defaults to 0. eV/Ang**2.hermitian (
bool
, optional) – if true (default), the returned dynamical matrix will be hermitiandtype (
np.dtype (np.float64)
) – default data-type of the matrixorder (
list
ofstr
, optional) – the order of which to try and read the dynamical matrix By default this is['got'/'gout', 'FC']
. Note thatFC
corresponds to thefcSileGULP
file (FORCE_CONSTANTS_2ND
).
- set_dyn_key(key)
Overwrites internal key lookup value for the dynamical matrix vectors
- set_dynamical_matrix_key(key)[source]
Overwrites internal key lookup value for the dynamical matrix vectors
- set_supercell_key(key)
Overwrites internal key lookup value for the cell vectors
- 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
gotSileGULP
class.