sisl.io.vasp.locpotSileVASP
- class sisl.io.vasp.locpotSileVASP(filename, mode='r', comment=None, *args, **kwargs)
Bases:
sisl.io.vasp.carSileVASP
Electrostatic (or total) potential plus geometry
This file-object handles the electrostatic(total) potential from VASP
Methods
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 the CONTCAR/POSCAR file
read_grid
([index, dtype])Reads the potential (in eV) from the file and returns with a grid (plus geometry)
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
File of the current Sile
File of the current Sile
- __init__(filename, mode='r', comment=None, *args, **kwargs)
- property base_file
File of the current Sile
- 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: .. 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”
- 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)
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_grid(index=0, dtype=<class 'numpy.float64'>)[source]
Reads the potential (in eV) from the file and returns with a grid (plus geometry)
- Parameters
index (int or array_like, optional) – the index of the potential 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 total potential with the Cartesian directions equal to the potential for the magnetization directions. For array-like they refer to the fractional contributions for each corresponding index.
dtype (numpy.dtype, optional) – grid stored dtype
- Returns
Grid
- Return type
potential with associated geometry
- read_supercell()
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)
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
See also
geometry_group
method used to group atoms together according to their species