ASE Manual Release 3.6.1.2825 CAMd - CampOS Wiki

ASE Manual, Release 3.6.1.2828
>>> OH = Atoms(’OH’)
>>> OH[0].charge = -1
>>> OH.get_charges()
array([-1., 0.])
Another example:
>>> for atom in bulk:
... if atom.symbol = ’Ni’:
... atom.magmom = 0.7 # set initial magnetic moment
The different properties of an atom can be obtained and changed via attributes (position, number, tag,
momentum, mass, magmom, charge, x, y, z):
>>> a1.position = [1, 0, 0]
>>> a1.position
array([ 1., 0., 0.])
>>> a1.z = 2.5
>>> a1.position
array([ 1. , 0. , 2.5])
>>> a2.magmom = 1.0
That last line will set the initial magnetic moment that some calulators use (similar to the
set_initial_magnetic_moments() method).
Note: The position and momentum attributes refer to mutable objects, so in some cases, you may want to
use a1.position.copy() in order to avoid changing the position of a1 by accident.
7.2.1 Getting an Atom from an Atoms object
Indexing an Atoms object returns an Atom object still remembering that it belongs to the collective Atoms:
Modifying it will also change the atoms object:
>>> atoms = ase.data.molecules.molecule(’CH4’)
>>> atoms.get_positions()
array([[ 0. , 0. , 0. ],
[ 0.629118, 0.629118, 0.629118],
[-0.629118, -0.629118, 0.629118],
[ 0.629118, -0.629118, -0.629118],
[-0.629118, 0.629118, -0.629118]])
>>> a = atoms[2]
>>> a
Atom(’H’, [-0.62911799999999996, -0.62911799999999996, 0.62911799999999996], index=2)
>>> a.x = 0
>>> atoms.get_positions()
array([[ 0. , 0. , 0. ],
[ 0.629118, 0.629118, 0.629118],
[ 0. , -0.629118, 0.629118],
[ 0.629118, -0.629118, -0.629118],
[-0.629118, 0.629118, -0.629118]])
See Also:
Atom: All the details!
atoms: More information about how to use collections of atoms.
calculators: Information about how to calculate forces and energies of atoms.
66 Chapter 7. Documentation for modules in ASE