.
See http://pubs.rsc.org/en/Content/ArticleLanding/2012/CP/c1cp22446h#!divAbstract
I have discussed this in the sections 3.3 and 3.5 on probability flows and local density of states.
Best
Sridhar
If you know the geometry of the two isomers you can use a NEB (nudged elastic band) method to calculate the transition path. The NEB method is for example implemented in CP2K or Quantum Espresso.
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