sisl.io.gulp.gotSileGULP

class sisl.io.gulp.gotSileGULP(filename, *args, **kwargs)

Bases: SileGULP

GULP output file object

Parameters:
  • filename (str) – filename of the file

  • mode (str, optional) – opening mode of file, default to read-only

  • base (str, optional) – base directory of the file

Plotting

plot

Plotting functions for the gotSileGULP class.

plot.geometry(*[, data_kwargs, ...])

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_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

set_dynamical_matrix_key(key)

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

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_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 a GeometryPlot 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 hermitian

  • dtype (np.dtype (np.float64)) – default data-type of the matrix

  • order (list of str, optional) – the order of which to try and read the dynamical matrix By default this is ['got'/'gout', 'FC']. Note that FC corresponds to the fcSileGULP file (FORCE_CONSTANTS_2ND).

read_geometry(**kwargs) Geometry[source]

Reads a geometry and creates the GULP dynamical geometry

read_lattice(key=None, **kwargs) Lattice[source]

Reads a Lattice and creates the GULP cell

read_lattice_nsc(key=None)[source]

Reads the dimensions of the supercell

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_geometry_key(key)[source]

Overwrites internal key lookup value for the geometry vectors

set_key(segment, key)[source]

Sets the segment lookup key

set_lattice_key(key)[source]

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

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.