initial rewrite done. Made away with separation parameter and introduced
new class for particles. Diffusionreactions are now relative. Can these
be made static? testbed is now fucked up and needs rewriting.
started rewriting some tests. cant make diff reacs static
started adding neighbors to solutionparticles. moved energies and
neighbor counts to particles. before I calculated energies for all sites
even if inactive. Want to reduce memory of sites substancially. Todo:
make updating of neighbors and energies robust and finish cleaning
tests.
continued working on adding memory efficient neighbors
neighbor updating added. Cleanups. Todo: update particle states
efficiently and for neighbors. Cap at range 1. No recursiveness.
particletypes should now be updated as well. Moved an associated
particle into sites and replaced def as active to associated particle
not being null.
code compiles. Tests _not_ checked for inconsistencies.

TODO:

shape up tests.
removed alot of the eventloop specific parameters such as ncycles etc
and switched to use ignis'. Cleanups.
fixed a bug in the site info dump
bugfixes to asserts and some neighbor stuff. Asserts still break for
neighbors.
Fixed some debug stuff and fixed the site info.. again..
continued debugging. It is a dodgy one!
updated ignis
fixed a bug causing neighbors to be removed incorrectly.
fixed a bug where the x value was return for all dimensions.
removed some debug statements
started working on fixing tests.
made xyz available in solver. fixed bug in initializecrystal
fixed a bug in concentration calculation
test for particlestates implemented and passed.