started optimizing saddle point calculations.
started working on optimizations. added a testcase for reference
stash
fixed a bug with the potential which made it behave strange at times.
used sets to avoid updating same neighbor twice. test fails.
optimized neighbor updating by removing duplicate calls to the same site updating function by using a std set of sites in need of the update
much needed cleanups in the site header
a much needed syntax and function cleanup
something is very very weird... sequential test fails. No idea why.
fixed up the destructors and continued debugging for the fishy differences. Got something good going on noow tho. Added pointercounter to the solver class to catch misuse of object destruction.
fixed a bug with my usage of std set intersection. It is UNSAFE to use on pointer values and will fail in combination with periodic boundary conditions due to non sequential neighbors
Fixed an issue where spawned crystals which later became disconnected from the mother crystal upon deactivation remained as surfaces.
investigated renormalization of rates. Went nowhere. Need some basic rules.
added diffusionreactions as a neighbormatrix as well. Trying to rid recalculations of saddle energies.
diffusionreaction nighborlist added and tested.
working on crazy weird updating of reactions...
continued tweaking. Goal is to never update every rate
finally got the reaction dependencies right. Got a good feeling.
realized that you actually need to update the rates of every reaction once the energy changes, which it does for all neighbors anyway... waste of time.
about to insert optimized rate calculations by not recalculating saddle energies