sisl.Atom

class sisl.Atom(*args, **kwargs)

Bases: _Dispatchs

Atomic information, mass, name number of orbitals and ranges

Object to handle atomic mass, name, number of orbitals and orbital range.

The Atom object handles the atomic species with information such as

• atomic number

• mass

• number of orbitals

• radius of each orbital

The Atom object is pickle-able.

Parameters

• Z (int or str) – key lookup for the atomic specie, Atom[key]

• orbitals (list of Orbital or float, optional) – all orbitals associated with this atom. Default to one orbital.

• mass (float, optional) – the atomic mass, if not specified uses the mass from PeriodicTable

• tag (str, optional) – arbitrary designation for user handling similar atoms with different settings (defaults to the label of the atom)

Methods

copy([Z, orbitals, mass, tag])	Return copy of this object
equal(other[, R, psi])	True if other is the same as this atomic specie
index(orbital)	Return the index of the orbital in the atom object
iter([group])	Loop on all orbitals in this atom
maxR()	Return the maximum range of orbitals.
radius([method])	Return the atomic radii of the atom (in Ang)
remove(orbitals)	Return the same atom without a specific set of orbitals
scale(scale)	Scale the atomic radii and return an equivalent atom.
sub(orbitals)	Return the same atom with only a subset of the orbitals present
toSphere([center])	Return a sphere with the maximum orbital radius equal
Z	Atomic number
mass	Atomic mass
no	Number of orbitals on this atom
orbitals	List of orbitals
symbol	Return short atomic name (Au==79).
tag	Tag for atom
to	A dispatcher for classes, using __get__ it converts into ObjectDispatcher upon invocation from an object, or a TypeDispatcher when invoked from a class

property Z: ndarray[Any, dtype[int32]]

Atomic number

__init__(Z, orbitals=None, mass=None, tag=None, **kwargs)

copy(Z=None, orbitals=None, mass=None, tag=None)

Return copy of this object

equal(other, R=True, psi=False)

True if other is the same as this atomic specie

Parameters

• other (Atom) – the other object to check againts

• R (bool, optional) – if True the equality check also checks the orbital radii, else they are not compared

• psi (bool, optional) – if True, also check the wave-function component of the orbitals, see Orbital.psi

index(orbital)

Return the index of the orbital in the atom object

iter(group=False)

Loop on all orbitals in this atom

Parameters

group (bool, optional) – if two orbitals share the same radius one may be able to group two orbitals together

Returns

current orbital, if group is True this is a list of orbitals, otherwise a single orbital is returned

Return type

Orbital

property mass: ndarray[Any, dtype[float64]]

Atomic mass

maxR()

Return the maximum range of orbitals.

property no: int

Number of orbitals on this atom

property orbitals

List of orbitals

radius(method='calc')

Return the atomic radii of the atom (in Ang)

See PeriodicTable.radius for details on the argument.

remove(orbitals)

Return the same atom without a specific set of orbitals

Parameters

orbitals (array_like) – indices of the orbitals to remove

Returns

without the specified orbitals

Return type

Atom

See also

sub

retain a selected set of orbitals

scale(scale)

Scale the atomic radii and return an equivalent atom.

Parameters

scale (float) – the scale factor for the atomic radii

sub(orbitals)

Return the same atom with only a subset of the orbitals present

Parameters

orbitals (array_like) – indices of the orbitals to retain

Returns

with only the subset of orbitals

Return type

Atom

Raises

ValueError – if the number of orbitals removed is too large or some indices are outside the allowed range

property symbol

Return short atomic name (Au==79).

property tag: str

Tag for atom

to

A dispatcher for classes, using __get__ it converts into ObjectDispatcher upon invocation from an object, or a TypeDispatcher when invoked from a class

This is a class-placeholder allowing a dispatcher to be a class attribute and converted into an ObjectDispatcher when invoked from an object.

If it is called on the class, it will return a TypeDispatcher.

This class should be an attribute of a class. It heavily relies on the __get__ special method.

Parameters

• name (str) – name of the attribute in the class

• dispatchs (dict, optional) – dictionary of dispatch methods

• obj_getattr (callable, optional) – method with 2 arguments, an obj and the attr which may be used to control how the attribute is called.

• instance_dispatcher (AbstractDispatcher, optional) – control how instance dispatchers are handled through __get__ method. This controls the dispatcher used if called from an instance.

• type_dispatcher (AbstractDispatcher, optional) – control how class dispatchers are handled through __get__ method. This controls the dispatcher used if called from a class.

Examples

>>> class A:
...   new = ClassDispatcher("new", obj_getattr=lambda obj, attr: getattr(obj.sub, attr))

The above defers any attributes to the contained A.sub attribute.

toSphere(center=None)

Return a sphere with the maximum orbital radius equal

Returns

a sphere with radius equal to the maximum radius of the orbitals

Return type

Sphere