sisl.io.vasp.locpotSileVASP

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

Bases: carSileVASP

Electrostatic (or total) potential plus geometry

This file-object handles the electrostatic(total) potential from VASP

Methods

`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 the CONTCAR/POSCAR file
`read_grid`([index, dtype])	Reads the potential (in eV) from the file and returns with a grid (plus geometry)
`read_lattice`()	Returns Lattice 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
`base_file`	File of the current Sile
`file`	File of the current Sile

class InfoAttr(attr, regex, parser, doc='', updatable=False, default=None, found=False)

Bases: object

Holder for parsing lines and extracting information from text files

This consists of:

attr:

the name of the attribute This will be the sile.info. access point.

regex:

the regular expression used to match a line. If a str, it will be compiled as is to a regex pattern. regex.match(line) will be used to check if the value should be updated.

parser:

if regex.match(line) returns a match that is true, then this parser will be executed. The parser must be a function accepting two arguments:

def parser(attr, match)

where attr is this object, and match is the match done on the line. (Note that match.string will return the full line used to match against).

updatable:

control whether a new match on the line will update using parser. If false, only the first match will update the value

default:

the default value of the attribute

found:

whether the value has been found in the file.

__init__(attr, regex, parser, doc='', updatable=False, default=None, found=False)

attr

copy()

doc

documentation(): Returns a documentation string for this object

found

parser

process(line)

regex

updatable

value

__init__(filename, mode='r', *args, **kwargs): Just to pass away the args and kwargs

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: .. 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

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=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'>, **kwargs)[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
spin (optional) – same as index argument. spin argument has precedence.

Returns

Grid

Return type

potential with associated geometry

read_lattice(): Returns Lattice 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