started new branch for more efficient neighbors
added new neighbour code model. It is extremely beautiful compared to the previous shit.
rewrote reaction setup using the new neighbour framework. Things are lot faster. Fixed some bugs, cleaned up the code. Got rid of unnecessary functions and placed functions in the classes they should be (out of the solver). Made it so that when sites were updated, so were the reactions, and then also the neighboring (all specified levels of neighbors) reactions.
changed energy model to something more realistic, a power law as a function of distance. Works very well, energy minima (sphere) is now reached from any initial configuration rather rapidly. Need to find a good model for the saddle energy tho. Not satisfied with the current.
added a unit test for testing neighbors. Worked. Fixed a bug in the distance calculation where the peridicity was negleced.
Started work on adding parameters through config file
merged branch newNeigborModel
Merge branch 'master' of github.com:jorgehog/kMC