ASE Manual Release 3.6.1.2825 CAMd - CampOS Wiki

ASE Manual, Release 3.6.1.2828
NEB.interpolate()
Interpolate path linearly from initial to final state.
Only the internal images (not the endpoints) need have calculators attached.
See Also:
optimize: Information about energy minimization (optimization).
calculators: How to use calculators.
Tutorials:
• Diffusion of gold atom on Al(100) surface (NEB)
• Dissociation
• Dissociation
Note: If there are M images and each image has N atoms, then the NEB object behaves like one big Atoms
object with MN atoms, so its get_positions() method will return a MN × 3 array.
7.16.2 Trajectories
The code:
from ase.optimize import QuasiNewton
optimizer = QuasiNewton(neb, trajectory=’A2B.traj’)
will write all images to one file. The Trajectory object knows about NEB calculations, so it will write M images
with N atoms at every iteration and not one big configuration containing MN atoms.
The result of the latest iteration can now be analysed with this command: ag A2B.traj@-5:.
For the example above, you can write the images to individual trajectory files like this:
for i in range(1, 4):
qn.attach(io.PickleTrajectory(’A2B-%d.traj’ % i, ’w’, images[i]))
The result of the latest iteration can be analysed like this:
$ ag A.traj A2B-?.traj B.traj -n -1
7.16.3 Restarting
Restart the calculation like this:
images = io.read(’A2B.traj@-5:’)
7.16.4 Climbing image
The “climbing image” variation involves designating a specific image to behave differently to the rest of the chain:
it feels no spring forces, and the component of the potential force parallel to the chain is reversed, such that it
moves towards the saddle point. This depends on the adjacent images providing a reasonably good approximation
of the correct tangent at the location of the climbing image; thus in general the climbing image is not turned on
until some iterations have been run without it (generally 20% to 50% of the total number of iterations).
To use the climbing image NEB method, instantiate the NEB object like this:
neb = NEB(images, climb=True)
144 Chapter 7. Documentation for modules in ASE