Initial Commit in variable timestep branch
Added code to make timesteps. Particles pos saved in large np array
Added Particles Class, Simulation now static
Particles abstracts a list of particles.
Sigma for step pdf depends on particle position.
Computed

TODO
  relationship between sigma and timestep
  maximize sigma subject to testable constraints
  analyze and document total # steps for all particles
    for the duration of the simulation of models
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