xvSileSiesta

class sisl.io.siesta.xvSileSiesta(filename, mode='r', comment=None, *args, **kwargs)

Geometry file

Attributes

base_file	File of the current Sile
file	File of the current Sile

Methods

__init__(self, filename[, mode, comment])	Initialize self.
dir_file(self[, filename])	File of the current Sile
exist(self)	Query whether the file exists
read(self, \*args, \*\*kwargs)	Generic read method which should be overloaded in child-classes
read_data(self)	Returns an array with the velocities from the XV file
read_geometry(self[, velocity, species_Z])	Returns a Geometry object from the XV file
read_supercell(self)	Returns SuperCell object from the XV file
read_velocity(self)	Returns an array with the velocities from the XV file
write(self, \*args, \*\*kwargs)	Generic write method which should be overloaded in child-classes
write_geometry(self, geom[, fmt, velocity])	Writes the geometry to the contained file

property base_file

File of the current Sile

dir_file(self, filename=None)

File of the current Sile

exist(self)

Query whether the file exists

property file

File of the current Sile

read(self, *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(self)

Returns an array with the velocities from the XV file

Returns

velocity :

read_geometry(self, velocity=False, species_Z=False)

Returns a Geometry object from the XV file

Parameters

species_Zbool, optional

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

velocitybool, optional

also return the velocities in the file

Returns

Geometry

velocityonly if velocity is true.

read_supercell(self)

Returns SuperCell object from the XV file

read_velocity(self)

Returns an array with the velocities from the XV file

Returns

velocity :

write(self, *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(self, geom, fmt='.9f', velocity=None)

Writes the geometry to the contained file

Parameters

geomGeometry

geometry to write in the XV file

fmtstr, optional

the precision used for writing the XV file

velocitynumpy.ndarray, optional

velocities to write in the XV file (will be zero if not specified). Units input must be in Ang/fs.