sisl.io.xyzSile

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

Bases: Sile

XYZ file object

Methods

dir_file([filename, filename_base])

File of the current Sile

read(*args, **kwargs)

Generic read method which should be overloaded in child-classes

read_geometry([atoms, sc])

Returns Geometry object from the XYZ file

write(*args, **kwargs)

Generic write method which should be overloaded in child-classes

write_geometry(geometry[, fmt, comment])

Writes the geometry to the contained file

base_file

File of the current Sile

file

File of the current Sile

__init__(filename, mode='r', comment=None, *args, **kwargs)
property base_file

File of the current Sile

dir_file(filename=None, filename_base='')

File of the current Sile

property file

File of the current Sile

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(atoms=None, sc=None)[source]

Returns Geometry object from the XYZ file

Parameters
  • atoms (Atoms, optional) – the atoms to be associated with the Geometry

  • sc (SuperCell, optional) – the supercell to be associated with the geometry

to_json()
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', comment=None)[source]

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

  • comment (str, optional) – if None, a sisl made comment that can be used for parsing the unit-cell is used else this comment will be written at the 2nd line.