pyiron_atomistics.atomistics.structure.atom.Atom

class pyiron_atomistics.atomistics.structure.atom.Atom(symbol='X', position=(0, 0, 0), tag=None, momentum=None, mass=None, magmom=None, charge=None, atoms=None, index=None, pse=None, element=None, **qwargs)

Bases: Atom

Class for representing a single atom derived from the ASE atom class.

Parameters:

• symbol (str/pyiron_atomistics.atomistics.structure.periodic_table.ChemcicalElement) – Symbol or elecment object

• position (list/numpy.ndarray) – Position of atom in cartesian coordinates

• tag (str) – Tag assigned to structure

• momentum (float) – Momentum

• mass (float) – Atomic mass in a.u.

• magmom (float) – Magnetic moment in Bohn Magneton

• charge (float) – Charge in e

• atoms (ase.atoms.Atoms) – Assigned atoms

• index (int) – Assigned index

__init__(symbol='X', position=(0, 0, 0), tag=None, momentum=None, mass=None, magmom=None, charge=None, atoms=None, index=None, pse=None, element=None, **qwargs)

Methods

__init__([symbol, position, tag, momentum, ...])
cut_reference_to_atoms()	Cut reference to atoms object.
delete(name)	Delete name attribute.
get(name)	Get name attribute, return default if not explicitly set.
get_raw(name)	Get name attribute, return None if not explicitly set.
set(name, value)	Set name attribute to value.

Attributes

data
atoms
index
a	A-coordinate
b	B-coordinate
c	C-coordinate
charge	Initial atomic charge
magmom	Initial magnetic moment
mass	Gives the atomic mass of the atom
momentum	XYZ-momentum
number	The atomic number of the atom
position	XYZ-coordinates
scaled_position
symbol	The chemical symbol of the atom
tag	Integer tag
x	X-coordinate
y	Y-coordinate
z	Z-coordinate

property a

A-coordinate

property b

B-coordinate

property c

C-coordinate

property charge

Initial atomic charge

cut_reference_to_atoms()

Cut reference to atoms object.

delete(name)

Delete name attribute.

get(name)

Get name attribute, return default if not explicitly set.

get_raw(name)

Get name attribute, return None if not explicitly set.

property magmom

Initial magnetic moment

property mass

Gives the atomic mass of the atom

Returns:

The atomic mass in a.u.

Return type:

float

property momentum

XYZ-momentum

property number

The atomic number of the atom

Returns:

The atomic number according to the periodic table

Return type:

int

property position

XYZ-coordinates

set(name, value)

Set name attribute to value.

property symbol

The chemical symbol of the atom

Returns:

The chemical symbol of the atom

Return type:

str

property tag

Integer tag

property x

X-coordinate

property y

Y-coordinate

property z

Z-coordinate