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
Attributes
__dict__
__doc__
__module__
__weakref__
list of weak references to the object (if defined)
_write_default
_write_default_only
File of the current Sile
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_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
-
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”
-
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
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property