sisl.io.siesta.structSileSiesta

class sisl.io.siesta.structSileSiesta(filename, *args, **kwargs)

Bases: SileSiesta

Geometry file

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([atoms, species_as_Z])	Returns a Geometry object from the STRUCT file
read_lattice()	Returns Lattice object from the STRUCT file
write(*args, **kwargs)	Generic write method which should be overloaded in child-classes
write_geometry(geometry[, fmt])	Writes the geometry to the contained file
base_file	File of the current Sile
file	File of the current Sile
plot	Handles all plotting possibilities for a class

__init__(filename, mode='r', *args, **kwargs)

Just to pass away the args and kwargs

base_directory(relative_to='.')

Retrieve the base directory of the file, relative to the path relative_to

property base_file

File of the current Sile

close()

dir_file(filename=None, filename_base='')

File of the current Sile

property file

File of the current Sile

plot

Handles all plotting possibilities for a class

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(atoms: Atoms | Geometry | None = None, species_as_Z: bool = False) → Geometry

Returns a Geometry object from the STRUCT file

Parameters:

• atoms (Optional[Atoms, Geometry]) – an object containing the basis information, is useful to overwrite the atoms object contained in the geometry.

• species_as_Z (bool) – Deprecated, it does nothing!

Return type:

Geometry

read_lattice() → Lattice

Returns Lattice object from the STRUCT file

Return type:

Lattice

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 = '.9f')

Writes the geometry to the contained file

Parameters:

• geometry (Geometry) – geometry to write in the STRUCT file

• fmt (str) – the precision used for writing the coordinates in the file