Atom

class sisl.Atom(Z, orbital=None, mass=None, tag=None, **kwargs)

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

Zint or str

key lookup for the atomic specie, Atom[key]

orbitallist of Orbital or float, optional

all orbitals associated with this atom. Default to one orbital.

massfloat, optional

the atomic mass, if not specified uses the mass from PeriodicTable

tagstr, optional

arbitrary designation for user handling similar atoms with different settings (defaults to the label of the atom)

Attributes

Zint

atomic number

noint

Number of orbitals on this atom

Rnumpy.ndarray

Orbital radius

q0numpy.ndarray

Orbital initial charges

massfloat

mass of Atom

Attributes

R	Orbital radius
no	Number of orbitals on this atom
q0	Orbital initial charges
symbol	Return short atomic name (Au==79).

Methods

__init__(self, Z[, orbital, mass, tag])	Initialize self.
copy(self[, Z, orbital, mass, tag])	Return copy of this object
equal(self, other[, R, psi])	True if other is the same as this atomic specie
index(self, orbital)	Return the index of the orbital in the atom object
iter(self[, group])	Loop on all orbitals in this atom
maxR(self)	Return the maximum range of orbitals.
radius(self[, method])	Return the atomic radii of the atom (in Ang)
remove(self, orbitals)	Return the same atom without a specific set of orbitals
scale(self, scale)	Scale the atomic radii and return an equivalent atom.
sub(self, orbitals)	Return the same atom with only a subset of the orbitals present
toSphere(self[, center])	Return a sphere with the maximum orbital radius equal

property R

Orbital radius

copy(self, Z=None, orbital=None, mass=None, tag=None)

Return copy of this object

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

True if other is the same as this atomic specie

Parameters

otherAtom

the other object to check againts

Rbool, optional

if True the equality check also checks the orbital radii, else they are not compared

psibool, optional

if True, also check the wave-function component of the orbitals, see Orbital.psi

index(self, orbital)

Return the index of the orbital in the atom object

iter(self, group=False)

Loop on all orbitals in this atom

Parameters

groupbool, optional

if two orbitals share the same radius one may be able to group two orbitals together

Returns

Orbital

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

maxR(self)

Return the maximum range of orbitals.

property no

Number of orbitals on this atom

property q0

Orbital initial charges

radius(self, method='calc')

Return the atomic radii of the atom (in Ang)

See PeriodicTable.radius for details on the argument.

remove(self, orbitals)

Return the same atom without a specific set of orbitals

Parameters

orbitalsarray_like

indices of the orbitals to remove

Returns

Atom

without the specified orbitals

See also

sub

retain a selected set of orbitals

scale(self, scale)

Scale the atomic radii and return an equivalent atom.

Parameters

scalefloat

the scale factor for the atomic radii

sub(self, orbitals)

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

Parameters

orbitalsarray_like

indices of the orbitals to retain

Returns

Atom

with only the subset of orbitals

Raises

ValueErrorif the number of orbitals removed is too large or some indices are outside the allowed range

property symbol

Return short atomic name (Au==79).

toSphere(self, center=None)

Return a sphere with the maximum orbital radius equal

Returns

~sisl.shape.Sphere

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