KMC fiber attachment sites

[blackwer]

Time to consider motors/fixed binding sites

Sites should have a very small memory footprint, and most computation is extremely fast, so can easily be done on all ranks. The main consideration is that fibers are not distributed across all ranks. This requires some communication between ranks, though I think I've worked out something that should be fairly minimal. Basic algorithm is as follows:

• Activate/deactivate array of motors on all ranks (poisson statistics - use deterministic RNG so results are same)

• Calculate neighbors on all ranks (this will have different results on each rank, because different fibers)

  • Segment search? Not clear
  • OpenMP?

• All_Gather [motorid, rank, fiberid] tuples

• Select motor-fiber pairs (deterministic RNG)

• If same rank...

  • find fiber binding point
  • bind [how? what data structure is needed?]

• Input?

• Boundary condition swap?

  • BC logic needs a bit of an overhaul anyway...