xsfSile

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

Bases: sisl.io.Sile

XSF file for XCrySDen

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 xsfSile after initialization
_step_md()	Step the MD counter
_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([data])	Returns Geometry object from the XSF file
write(*args, **kwargs)	Generic write method which should be overloaded in child-classes
write_geometry(geometry[, fmt, data])	Writes the geometry to the contained file
write_grid(*args, **kwargs)	Store grid(s) data to an XSF file
write_supercell(sc[, fmt])	Writes the supercell 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

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(data=False)

Returns Geometry object from the XSF file

Parameters

data (bool, optional) – in case the XSF file has auxiliary data, return that as well.

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='.8f', data=None)

Writes the geometry to the contained file

Parameters

• geometry (Geometry) – the geometry to be written

• fmt (str, optional) – used format for the precision of the data

• data ((geometry.na, 3), optional) – auxiliary data associated with the geometry to be saved along side. Internally in XCrySDen this data is named Forces

write_grid(*args, **kwargs)

Store grid(s) data to an XSF file

Examples

>>> g1 = Grid(0.1, sc=2.)
>>> g2 = Grid(0.1, sc=2.)
>>> get_sile('output.xsf', 'w').write_grid(g1, g2)

Parameters

• *args (Grid) – a list of data-grids to be written to the XSF file. Each argument gets the field name ?grid_<> where <> starts with the integer 0, and ? is real_/imag_ for complex valued grids.

• geometry (Geometry, optional) – the geometry stored in the file, defaults to args[0].geometry

• fmt (str, optional) – floating point format for data (.5e)

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

write_supercell(sc, fmt='.8f')

Writes the supercell to the contained file

Parameters

• sc (SuperCell) – the supercell to be written

• fmt (str, optional) – used format for the precision of the data