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
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 charge density from the file and returns with a grid (plus geometry)
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
File of the current Sile
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”
- 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 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 (numpy.dtype, optional) – grid stored dtype
spin (optional) – same as index argument. spin argument has precedence.
- Returns
Grid
- Return type
charge density grid 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
See also
geometry_group
method used to group atoms together according to their species