sisl.io.siesta.xvSileSiesta

class sisl.io.siesta.xvSileSiesta(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_data()	Returns an array with the velocities from the XV file
read_geometry([ret_velocity, species_as_Z])	Returns a Geometry object from the XV file
read_lattice()	Returns Lattice object from the XV file
read_velocity()	Returns an array with the velocities from the XV file
write(*args, **kwargs)	Generic write method which should be overloaded in child-classes
write_geometry(geometry[, fmt, velocity])	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_data() → ndarray

Returns an array with the velocities from the XV file

Return type:

ndarray

read_geometry(ret_velocity: bool = False, species_as_Z: bool = False) → Geometry

Returns a Geometry object from the XV file

Parameters:

• ret_velocity (bool) – also return the velocities in the file

• species_as_Z (bool) – if True the atomic numbers are the species indices (useful when reading the ChemicalSpeciesLabel block simultaneously).

Returns:

• geometry (Geometry) – the geometry in the XV file

• velocity (numpy.ndarray) – only if ret_velocity is true.

Return type:

Geometry

read_lattice() → Lattice

Returns Lattice object from the XV file

Return type:

Lattice

read_velocity() → ndarray

Returns an array with the velocities from the XV file

Return type:

ndarray

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', velocity=None)

Writes the geometry to the contained file

Parameters:

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

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

• velocity (ndarray, optional) – velocities to write in the XV file (will be zero if not specified). Units input must be in Ang/fs.