fcSileSiesta

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

Bases: sisl.io.siesta.SileSiesta

Force constant file

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 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_force([displacement, na])	Reads all displacement forces by multiplying with the displacement value
read_force_constant([na])	Reads the force-constant stored in the FC 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

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_force(displacement=None, na=None)

Reads all displacement forces by multiplying with the displacement value

Since the force constant file does not contain the non-displaced configuration this will only return forces on the displaced configurations minus the forces from the non-displaced configuration.

This may be used in conjunction with phonopy by noticing that Siesta FC-runs does the displacements in reverse order (-x/+x vs. +x/-x). In this case one should reorder the elements like this:

>>> fc = np.roll(fc, 1, axis=2)

Parameters

• displacement (float, optional) – the used displacement in the calculation, since Siesta 4.1-b4 this value is written in the FC file and hence not required. If prior Siesta versions are used and this is not supplied the 0.04 Bohr displacement will be assumed.

• na (int, optional) – number of atoms in geometry (for returning correct number of atoms), since Siesta 4.1-b4 this value is written in the FC file and hence not required. If prior Siesta versions are used then the file is expected to only contain 1-atom displacement.

Returns

numpy.ndarray – force constant matrix times the displacement, see read_force_constant for details regarding data layout.

Return type

(displaced atoms, d[xyz], [-+], total atoms, xyz)

read_force_constant(na=None)

Reads the force-constant stored in the FC file

Parameters

na (int, optional) – number of atoms in the unit-cell, if not specified it will guess on only one atom displacement.

Returns

numpy.ndarray – force constant matrix containing all forces. The 2nd dimension contains contains the directions, 3rd dimension contains -/+ displacements.

Return type

(displacement, d[xyz], [-+], atoms, xyz)

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.