#!/usr/bin/env python3

from ase.build import fcc111, add_adsorbate
from ase.calculators.emt import EMT

from sella import Sella

# Set up your system as an ASE atoms object
slab = fcc111('Cu', (5, 5, 6), vacuum=7.5)
add_adsorbate(slab, 'Cu', 2.0, 'bridge')

# Define any constraints. Here we fix all atoms in the bottom half
# of the slab.
cart = [atom.index for atom in slab if atom.position[2] < slab.cell[2, 2] / 2.]

# Set up your calculator
slab.calc = EMT()

# Set up a Sella Dynamics object
dyn = Sella(slab,
            constraints=dict(cart=cart),
            trajectory='test_emt.traj')

dyn.run(1e-3, 1000)