ASE Manual Release 3.6.1.2825 CAMd - CampOS Wiki

view(slab, viewer=’VMD’, data=array)
Molecular dynamics
ASE Manual, Release 3.6.1.2828
Let us look at the nitrogen molecule as an example of molecular dynamics with the VelocityVerlet algorithm.
We first create the VelocityVerlet object giving it the molecule and the time step for the integration
of Newton’s law. We then perform the dynamics by calling its run() method and giving it the number of steps
to take:
from ase.md.verlet import VelocityVerlet
from ase import units
dyn = VelocityVerlet(molecule, dt=1.0 * units.fs)
for i in range(10):
pot = molecule.get_potential_energy()
kin = molecule.get_kinetic_energy()
print ’%2d: %.5f eV, %.5f eV, %.5f eV’ % (i, pot + kin, pot, kin)
dyn.run(steps=20)
6.2.2 Manipulating atoms
XXX rewrite this: use fcc111() function and do some relaxation ...
We will set up a one layer slab of Ni atoms with one Ag adatom.
Define the slab atoms:
>>> from ase import Atoms
>>> atoms = Atoms(’Ni4’, [(0, 0, 0),
... (0.45, 0, 0),
... (0, 0.5, 0),
... (0.5, 0.5, 0)])
Have a look at the individual atoms:
>>> atoms[0]
Atom(’Ni’, [0.0, 0.0, 0.0], atoms=..., index=0)
>>> atoms[1]
Atom(’Ni’, [0.45, 0.0, 0.0], atoms=..., index=1)
>>> atoms[2]
Atom(’Ni’, [0.0, 0.5, 0.0], atoms=..., index=2)
>>> atoms[3]
Atom(’Ni’, [0.5, 0.5, 0.0], atoms=..., index=3)
Let us assume we forgot how many atoms we set up:
>>> atoms[4]
Traceback (most recent call last):
File "", line 1, in ?
IndexError: list index out of range
Wrong because we only have four atoms
>>> len(atoms)
4
Change the position of the 2nd atom in the list
>>> atoms[1].x = 0.5
>>> atoms.get_positions()
array([[ 0. , 0. , 0. ],
[ 0.5, 0. , 0. ],
6.2. ASE 21