carSileVASP¶

class sisl.io.vasp.carSileVASP(filename, mode='r', comment=None, *args, **kwargs)¶

Bases: sisl.io.vasp.SileVASP

*CAR VASP files for defining geomtries

This file-object handles both POSCAR and CONTCAR files

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 carSile 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
`geometry_group`(geometry[, ret_index])	Order atoms in geometry according to species such that all of one specie is consecutive
`read`(args, *kwargs)	Generic read method which should be overloaded in child-classes
`read_geometry`([ret_dynamic])	Returns Geometry object from the CONTCAR/POSCAR file
`read_supercell`()	Returns SuperCell object from the CONTCAR/POSCAR file
`write`(args, *kwargs)	Generic write method which should be overloaded in child-classes
`write_geometry`(geometry[, dynamic, …])	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

static geometry_group(geometry, ret_index=False)¶

Order atoms in geometry according to species such that all of one specie is consecutive

When creating VASP input files (poscarSileVASP for instance) the equivalent POTCAR file needs to contain the pseudos for each specie as they are provided in blocks.

I.e. for a geometry like this: .. code:

[Atom(6), Atom(4), Atom(6)]

the resulting POTCAR needs to contain the pseudo for Carbon twice.

This method will re-order atoms according to the species”

Parameters

geometry (Geometry) – geometry to be re-ordered
ret_index (bool, optional) – return sorted indices

Returns

geometry

Return type

reordered geometry

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(ret_dynamic=False)[source]¶

Returns Geometry object from the CONTCAR/POSCAR file

Possibly also return the dynamics (if present).

Parameters: ret_dynamic (bool, optional) – also return selective dynamics (if present), if not, None will be returned.

read_supercell()[source]¶: Returns SuperCell object from the CONTCAR/POSCAR file

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, dynamic=True, group_species=False)[source]¶

Writes the geometry to the contained file

Parameters

geometry (Geometry) – geometry to be written to the file
dynamic (None, bool or list, optional) – define which atoms are dynamic in the VASP run (default is True, which means all atoms are dynamic). If None, the resulting file will not contain any dynamic flags
group_species (bool, optional) – before writing geometry first re-order species to have species in consecutive blocks (see geometry_group)

Examples

>>> car = carSileVASP('POSCAR', 'w')
>>> geom = geom.graphene()
>>> geom.write(car) # regular car without Selective Dynamics
>>> geom.write(car, dynamic=False) # fix all atoms
>>> geom.write(car, dynamic=[False, (True, False, True)]) # fix 1st and y coordinate of 2nd