In this exercise, we will find minimum-energy paths and transition states using the Nudged Elastic Band method. Another method for finding the transition state (i.e. the highest-energy state), the Dimer method, will also be explored.
Take a look at the Al(110) surface shown in the picture on the right. The red atom represents an Al adatom that can move around on the surface. The adatom can jump along the rows (into the picture) or across the rows (to the right in the picture).
The template script neb1.py will find the minimum-energy path for a jump along the rows. Read, understand, and run the script.
Hint
When opening a trajectory in ase-gui with calculated energies, the default plot window shows the energy versus frame number. To get a better feel of the energy barrier in an NEB calculation; choose Tools ‣ NEB. This will give a smooth curve of the energy as a function of the NEB path length, with the slope at each point estimated from the force.
In the NEB calculations above we knew the final states, so all we had to do was to calculate the path between the initial state and the final state. But in some cases we do not know the final state. Then the Dimer method can be used to find the transition state. The result of a Dimer calculation will hence not be the complete particle trajectory as in the NEB output, but rather the configuration of the transition-state image.
The template script dimer_along.py will find the transition-state image of the jump along the row. Again, read, understand and run the script.