outSileSiesta

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

Bases: sisl.io.siesta.SileSiesta

Output file from Siesta

This enables reading the output quantities from the Siesta output.

Attributes

__dict__
__doc__
__module__
__weakref__	list of weak references to the object (if defined)
_job_completed
_write_default
_write_default_only
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

_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()
_read_geometry_atomic(line[, species])	Wrapper for reading the geometry as in the outcoor output
_read_geometry_outcoor(line[, species])	Wrapper for reading the geometry as in the outcoor output
_read_supercell_outcell()	Wrapper for reading the unit-cell from the outcoor block
_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_data(*args, **kwargs)	Read specific content in the Siesta out file
read_force([last, all, total, max])	Reads the forces from the Siesta output file
read_geometry([last, all])	Reads the geometry from the Siesta output file
read_moment([orbitals, quantity, last, all])	Reads the moments from the Siesta output file These will only be present in case of spin-orbit coupling.
read_scf([key, iscf, imd, as_dataframe])	Parse SCF information and return a table of SCF information depending on what is requested
read_species()	Reads the species from the top of the output file.
read_stress([key, last, all])	Reads the stresses from the Siesta output file
write(*args, **kwargs)	Generic write method which should be overloaded in child-classes

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

property job_completed

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

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_data(*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, optional) – read geometry, args are passed to read_geometry

• force (bool, optional) – read force, args are passed to read_force

• stress (bool, optional) – read stress, args are passed to read_stress

• moment (bool, optional) – read moment, args are passed to read_moment (only for spin-orbit calculations)

read_force(last=True, all=False, total=False, max=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

• total (bool, optional) – return the total forces instead of the atomic forces.

• max (bool, optional) –

  whether only the maximum atomic force should be returned for each step.

  Setting it to True is equivalent to max(outSile.read_force()) in case atomic forces are written in the output file (WriteForces .true. in the fdf file)

  Note that this is not the same as doing max(outSile.read_force(total=True)) since the forces returned in that case are averages on each axis.

Returns

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

The shape of the array will be different depending on the type of forces requested:

• atomic (default): (nMDsteps, nAtoms, 3)

• total: (nMDsteps, 3)

• max: (nMDsteps, )

If all is False, the first dimension does not exist. In the case of max, the returned value will therefore be just a float, not an array.

If total and max are both True, they are returned separately as a tuple: (total, max)

Return type

numpy.ndarray or None

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

Return type

list or Geometry or None

read_moment(orbitals=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

• orbitals (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_scf(key='scf', iscf=- 1, imd=None, as_dataframe=False)

Parse SCF information and return a table of SCF information depending on what is requested

Parameters

• key ({'scf', 'ts-scf'}) – parse SCF information from Siesta SCF or TranSiesta SCF

• iscf (int, optional) – which SCF cycle should be stored. If -1 only the final SCF step is stored, for None all SCF cycles are returned. When iscf values queried are not found they will be truncated to the nearest SCF step.

• imd (int or None, optional) – whether only a particular MD step is queried, if None, all MD steps are parsed and returned. A negative number wraps for the last MD steps.

• as_dataframe (boolean, optional) – whether the information should be returned as a pandas.DataFrame. The advantage of this format is that everything is indexed and therefore you know what each value means.You can also perform operations very easily on a dataframe.

read_species()

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(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

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

Return type

numpy.ndarray or None

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.