cubeSile

class sisl.io.cube.cubeSile(filename, mode='r', comment=None, *args, **kwargs)

Bases: sisl.io.Sile

CUBE file object

Attributes

__dict__
__doc__
__module__
__weakref__	list of weak references to the object (if defined)
_write_default
_write_default_only
base_file	File of the current Sile
file	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 Sile 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
read(*args, **kwargs)	Generic read method which should be overloaded in child-classes
read_geometry()	Returns Geometry object from the CUBE file
read_grid([imag])	Returns Grid object from the CUBE file
read_supercell([na])	Returns SuperCell object from the CUBE file
write(*args, **kwargs)	Generic write method which should be overloaded in child-classes
write_geometry(geometry[, fmt, size, origo])	Writes Geometry object attached to this grid
write_grid(grid[, fmt, imag])	Write Grid to the contained file
write_supercell(sc[, fmt, size, origo])	Writes SuperCell object attached to this grid

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

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()

Returns Geometry object from the CUBE file

read_grid(imag=None)

Returns Grid object from the CUBE file

Parameters

imag (str or Sile or Grid) – the imaginary part of the grid. If the geometries does not match an error will be raised.

read_supercell(na=False)

Returns SuperCell object from the CUBE file

Parameters

na (bool, optional) – whether to also return the number of atoms in the geometry

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, fmt='15.10e', size=None, origo=None, *args, **kwargs)

Writes Geometry object attached to this grid

Parameters

• geometry (Geometry) – geometry to be written

• fmt (str, optional) – floating point format for stored values

• size ((3, ), optional) – shape of the stored grid ([1, 1, 1])

• origo ((3, ), optional) – origo of the cell ([0, 0, 0])

write_grid(grid, fmt='.5e', imag=False, *args, **kwargs)

Write Grid to the contained file

Parameters

• grid (Grid) – the grid to be written in the CUBE file

• fmt (str, optional) – format used for precision output

• imag (bool, optional) – write only imaginary part of the grid, default to only writing the real part.

• buffersize (int, optional) – size of the buffer while writing the data, (6144)

write_supercell(sc, fmt='15.10e', size=None, origo=None, *args, **kwargs)

Writes SuperCell object attached to this grid

Parameters

• sc (SuperCell) – supercell to be written

• fmt (str, optional) – floating point format for stored values

• size ((3, ), optional) – shape of the stored grid ([1, 1, 1])

• origo ((3, ), optional) – origo of the cell ([0, 0, 0])