xvSileSiesta

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

Bases: sisl.io.siesta.SileSiesta

Geometry file

Attributes

__dict__
__doc__
__module__
__weakref__	list of weak references to the object (if defined)
_write_default
_write_default_only
base_file	File of the current Sile
file	File of the current Sile

Methods

_ArgumentParser_args_single()	Default arguments for the Sile
__delattr__	Implement delattr(self, name).
__dir__	Default dir() implementation.
__enter__()	Opens the output file and returns it self
__eq__	Return self==value.
__exit__(type, value, traceback)
__format__	Default object formatter.
__ge__	Return self>=value.
__getattr__(name)	Override to check the handle
__getattribute__	Return getattr(self, name).
__gt__	Return self>value.
__hash__	Return hash(self).
__init__(filename[, mode, comment])	Initialize self.
__init_subclass__	This method is called when a class is subclassed.
__iter__()	Iterator for file
__le__	Return self<=value.
__lt__	Return self<value.
__ne__	Return self!=value.
__new__	Create and return a new object.
__reduce__	Helper for pickle.
__reduce_ex__	Helper for pickle.
__repr__	Return repr(self).
__setattr__	Implement setattr(self, name, value).
__sizeof__	Size of object in memory, in bytes.
__str__()	Return a representation of the Sile
__subclasshook__	Abstract classes can override this to customize issubclass().
_base_file(f)	Make f refer to the file with the appropriate base directory
_base_setup(*args, **kwargs)	Setup the Sile after initialization
_open()
_setup(*args, **kwargs)	Setup the Sile after initialization
_write(*args, **kwargs)	Wrapper to default the write statements
dir_file([filename])	File of the current Sile
exist()	Query whether the file exists
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([velocity, species_Z])	Returns a Geometry object from the XV file
read_supercell()	Returns SuperCell 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(geom[, fmt, velocity])	Writes the geometry to the contained file

property base_file

File of the current Sile

dir_file(filename=None)

File of the current Sile

exist()

Query whether the file exists

property file

File of the current Sile

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()

Returns an array with the velocities from the XV file

Returns

Return type

velocity

read_geometry(velocity=False, species_Z=False)

Returns a Geometry object from the XV file

Parameters

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

• velocity (bool, optional) – also return the velocities in the file

Returns

• Geometry

• velocity (only if velocity is true.)

read_supercell()

Returns SuperCell object from the XV file

read_velocity()

Returns an array with the velocities from the XV file

Returns

Return type

velocity

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

Writes the geometry to the contained file

Parameters

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

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

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