Atom¶

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)

Attributes

`R`	Orbital radius
`__dict__`
`__doc__`
`__hash__`
`__module__`
`__weakref__`	list of weak references to the object (if defined)
`no`	Number of orbitals on this atom
`q0`	Orbital initial charges
`symbol`	Return short atomic name (Au==79).

Methods

`__delattr__`	Implement delattr(self, name).
`__dir__`	Default dir() implementation.
`__eq__`(b)	Return true if the saved quantities are the same
`__format__`	Default object formatter.
`__ge__`	Return self>=value.
`__getattribute__`	Return getattr(self, name).
`__getitem__`(key)	The orbital corresponding to index key
`__getstate__`()	Return the state of this object
`__gt__`	Return self>value.
`__init__`(Z[, orbitals, mass, tag])	Initialize self.
`__init_subclass__`	This method is called when a class is subclassed.
`__iter__`()	Loop on all orbitals in this atom
`__le__`	Return self<=value.
`__len__`()	Return number of orbitals in this atom
`__lt__`	Return self<value.
`__ne__`(b)	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).
`__setstate__`(d)	Re-create the state of this object
`__sizeof__`	Size of object in memory, in bytes.
`__str__`()	Return str(self).
`__subclasshook__`	Abstract classes can override this to customize issubclass().
`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

property R¶: Orbital radius

copy(Z=None, orbitals=None, mass=None, tag=None)[source]¶: Return copy of this object

equal(other, R=True, psi=False)[source]¶

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)[source]¶: Return the index of the orbital in the atom object

iter(group=False)[source]¶

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

maxR()[source]¶: Return the maximum range of orbitals.

property no¶: Number of orbitals on this atom

property q0¶: Orbital initial charges

radius(method='calc')[source]¶

Return the atomic radii of the atom (in Ang)

See PeriodicTable.radius for details on the argument.

remove(orbitals)[source]¶

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