Completed parts of the simulation.

Compute sigma from distance to beam. Compute dt from sigma.
stepParticle moves particle and adjusts intensity list.
limit at 1 billion particles to prevent swap crawl.

TODO:
  prof says min dt should be ~10 MICRO.
    timeStep(minsigma)~=10**-29. Either my minsigma is way
    too small or D is wrong or I am calculating dt wrong
  my code is really ugly and undocumented.
  try to change simulation.particles.intensity(i) to
    simulation.particle[i].intensity
  move dt utility functions out of particles
  add more classes