ASE Manual Release 3.6.1.2825 CAMd - CampOS Wiki

ASE Manual, Release 3.6.1.2828
#from ASE.Dynamics.MDMin import MDMin
#from ASE.Trajectories.NetCDFTrajectory import NetCDFTrajectory
#from ASE.IO.NetCDF import ReadNetCDF
slab = read(’2N.traj’)
slab.set_calculator(EMT())
constraint = FixBondLength(-2, -1)
#mask=[atom.symbol != ’N’ for atom in slab])
#molecule = Subset(slab, indices=[-2, -1])
# Create a trajectory for the dissociation path:
path = PickleTrajectory(’association.traj’, slab)
# Put the initial state in the trajectory:
path.write()
# From now on, we relax the molecule under the constraint of fixed
# bond length:
#fixed = FixBondLength(molecule, 0, 1)
#relax = MDMin(fixed, dt=0.08, fmax=0.05)
relax = QuasiNewton(slab)
d = linalg.norm(slab[-2].position - slab[-1].position)
#d = fixed.GetBondLength()
delta = 0.1
e0 = slab.get_potential_energy()
print d, 0.0
while d > 1.10:
d -= delta
fixed.SetBondLength(d, fix=’first’)
# XXX
raise NotImplementedError
relax.run(fmax=.05)
path.write()
print d, slab.GetPotentialEnergy() - e0
6.2.10 Diffusion of gold atom on Al(100) surface (NEB)
First, set up the initial and final states:
34 Chapter 6. Tutorials