sisl.io.xyzSile

class sisl.io.xyzSile(filename, *args, **kwargs)

Bases: Sile

XYZ file object

Methods

base_directory([relative_to])

Retrieve the base directory of the file, relative to the path relative_to

close()

dir_file([filename, filename_base])

File of the current Sile

read(*args, **kwargs)

Generic read method which should be overloaded in child-classes

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 in extxyz format

base_file

File of the current Sile

file

File of the current Sile

plot

Handles all plotting possibilities for a class

read_basis

read_geometry

read_lattice

__init__(filename, mode='r', *args, **kwargs)

Just to pass away the args and kwargs

base_directory(relative_to='.')

Retrieve the base directory of the file, relative to the path relative_to

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

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_basis = <sisl.io._multiple.SileBound object>[source]
Return type:

Atoms

read_geometry = <sisl.io._multiple.SileBound object>[source]
Parameters:

lattice (Lattice | None)

Return type:

Geometry

read_lattice = <sisl.io._multiple.SileBound object>[source]
Return type:

Lattice

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: Geometry, fmt: str = '.8f', comment: str | None = None)[source]

Writes the geometry to the contained file in extxyz format

Parameters:

  • geometry (Geometry) – the geometry to be written

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

  • comment (str | None) – 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.