outSileSiesta

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

Output file

This enables reading the output quantities from the Siesta output.

Attributes

base_file	File of the current Sile
file	File of the current Sile
job_completed	True if the full file has been read and “Job completed” was found.

Methods

__init__(self, filename[, mode, comment])	Initialize self.
dir_file(self[, filename])	File of the current Sile
exist(self)	Query whether the file exists
read(self, \*args, \*\*kwargs)	Generic read method which should be overloaded in child-classes
read_data(self, \*args, \*\*kwargs)	Read specific content in the Siesta out file
read_force(self[, last, all])	Reads the forces from the Siesta output file
read_geometry(self[, last, all])	Reads the geometry from the Siesta output file
read_moment(self[, orbital, quantity, last, all])	Reads the moments from the Siesta output file These will only be present in case of spin-orbit coupling.
read_species(self)	Reads the species from the top of the output file.
read_stress(self[, key, last, all])	Reads the stresses from the Siesta output file
write(self, \*args, \*\*kwargs)	Generic write method which should be overloaded in child-classes

property base_file

File of the current Sile

dir_file(self, filename=None)

File of the current Sile

exist(self)

Query whether the file exists

property file

File of the current Sile

property job_completed

True if the full file has been read and “Job completed” was found.

read(self, *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_data(self, *args, **kwargs)

Read specific content in the Siesta out file

The currently implemented things are denoted in the parameters list. Note that the returned quantities are in the order of keywords, so:

>>> read_data(geometry=True, force=True)
<geometry>, <force>
>>> read_data(force=True, geometry=True)
<force>, <geometry>

Parameters

geometry: bool

return the last geometry in the outSileSiesta

force: bool

return the last force in the outSileSiesta

moment: bool

return the last moments in the outSileSiesta (only for spin-orbit coupling calculations)

read_force(self, last=True, all=False)

Reads the forces from the Siesta output file

Parameters

last: bool, optional

only read the last force

all: bool, optional

return a list of all forces (like an MD) If True last is ignored

Returns

forces: np.ndarray or None

returns None if the forces are not found in the output, otherwise forces will be returned

read_geometry(self, last=True, all=False)

Reads the geometry from the Siesta output file

Parameters

last: bool, optional

only read the last geometry

all: bool, optional

return a list of all geometries (like an MD) If True last is ignored

Returns

geometries: list or Geometry or None

if all is False only one geometry will be returned (or None). Otherwise a list of geometries corresponding to the MD-runs.

read_moment(self, orbital=False, quantity='S', last=True, all=False)

Reads the moments from the Siesta output file These will only be present in case of spin-orbit coupling.

Parameters

orbital: bool, False

return a table with orbitally resolved moments.

quantity: str, ‘S’

return the spin-moments or the L moments

last: bool, True

only read the last force

all: bool, False

return a list of all forces (like an MD) If True last is ignored

read_species(self)

Reads the species from the top of the output file.

If wanting the species this HAS to be the first routine called.

It returns an array of Atom objects which may easily be indexed.

read_stress(self, key='static', last=True, all=False)

Reads the stresses from the Siesta output file

Parameters

key{‘static’, ‘total’}

which stress to read from the output.

last: bool, optional

only read the last stress

all: bool, optional

return a list of all stresses (like an MD) If True last is ignored

Returns

stresses: np.ndarray or None

returns None if the stresses are not found in the output, otherwise stresses will be returned

write(self, *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.