sisl.io.vasp.chgSileVASP

class sisl.io.vasp.chgSileVASP(filename, *args, **kwargs)

Bases: carSileVASP

Charge density plus geometry

This file-object handles the charge-density from VASP

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
`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 this Sile
`read_grid`([index, dtype])	Reads the charge density from the file and returns with a grid (plus geometry)
`read_lattice`()	Returns Lattice object from this Sile
`write`(args, *kwargs)	Generic write method which should be overloaded in child-classes
`write_geometry`(geometry[, dynamic, ...])	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

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:

[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 – reordered geometry

Return type:

Geometry

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(ret_dynamic: bool = False) → Geometry

Returns Geometry object from this Sile

Possibly also return the dynamics (if present).

Parameters:

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

Returns:

Geometry – the contained geometry
numpy.ndarray – which Cartesian directions are allowed to move (only if ret_dynamic)

Return type:

Geometry

read_grid(index=0, dtype=<class 'numpy.float64'>, **kwargs) → Grid[source]

Reads the charge density from the file and returns with a grid (plus geometry)

Parameters:

index (int or array_like, optional) – the index of the grid to read. For a spin-polarized VASP calculation 0 and 1 are allowed, UP/DOWN. For non-collinear 0, 1, 2 or 3 is allowed which equals, TOTAL, x, y, z charge density with the Cartesian directions equal to the charge magnetization. For array-like they refer to the fractional contributions for each corresponding index.
dtype (dtype, optional) – grid stored dtype
spin (optional) – same as index argument. spin argument has precedence.

Returns:

charge density grid with associated geometry

Return type:

Grid

read_lattice() → Lattice

Returns Lattice object from this Sile

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, dynamic=True, group_species: bool = False)

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) – 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