ASE Manual Release 3.6.1.2825 CAMd - CampOS Wiki

ASE Manual, Release 3.6.1.2828
• get_center_of_mass()
• get_distance()
• get_volume()
• has()
• edit()
• identical_to()
7.1.7 List of all Methods
class ase.atoms.Atoms(symbols=None, positions=None, numbers=None, tags=None, momenta=None,
masses=None, magmoms=None, charges=None,
scaled_positions=None, cell=None, pbc=None, celldisp=None, constraint=None,
calculator=None, info=None)
Atoms object.
The Atoms object can represent an isolated molecule, or a periodically repeated structure. It has a unit cell
and there may be periodic boundary conditions along any of the three unit cell axes.
Information about the atoms (atomic numbers and position) is stored in ndarrays. Optionally, there can be
information about tags, momenta, masses, magnetic moments and charges.
In order to calculate energies, forces and stresses, a calculator object has to attached to the atoms object.
Parameters:
symbols: str (formula) or list of str Can be a string formula, a list of symbols or a list of Atom objects.
Examples: ‘H2O’, ‘COPt12’, [’H’, ‘H’, ‘O’], [Atom(‘Ne’, (x, y, z)), ...].
positions: list of xyz-positions Atomic positions. Anything that can be converted to an ndarray of shape
(n, 3) will do: [(x1,y1,z1), (x2,y2,z2), ...].
scaled_positions: list of scaled-positions Like positions, but given in units of the unit cell. Can not be set
at the same time as positions.
numbers: list of int Atomic numbers (use only one of symbols/numbers).
tags: list of int Special purpose tags.
momenta: list of xyz-momenta Momenta for all atoms.
masses: list of float Atomic masses in atomic units.
magmoms: list of float or list of xyz-values Magnetic moments. Can be either a single value for each
atom for collinear calculations or three numbers for each atom for non-collinear calculations.
charges: list of float Atomic charges.
cell: 3x3 matrix Unit cell vectors. Can also be given as just three numbers for orthorhombic cells. Default
value: [1, 1, 1].
celldisp: Vector Unit cell displacement vector. To visualize a displaced cell around the center of mass of a
Systems of atoms. Default value = (0,0,0)
pbc: one or three bool Periodic boundary conditions flags. Examples: True, False, 0, 1, (1, 1, 0), (True,
False, False). Default value: False.
constraint: constraint object(s) Used for applying one or more constraints during structure optimization.
calculator: calculator object Used to attach a calculator for calculating energies and atomic forces.
info: dict of key-value pairs Dictionary of key-value pairs with additional information about the system.
The following keys may be used by ase:
• spacegroup: Spacegroup instance
58 Chapter 7. Documentation for modules in ASE