Binning

This module implements the method of cell lists. It splits up the simulation box into smaller boxes and assigns each particle into one sub-box. This enables faster look-up for particles that interact with a cut-off potential.

class halmd.mdsim.binning(args)

Construct binning module instance.

Parameters:
  • args (table) – keyword arguments
  • args.particle – instance of halmd.mdsim.particle
  • args.box – instance of halmd.mdsim.box
  • args.r_cut (table) – cutoff radius matrix for the potentials
  • args.skin (number) – neighbour list skin (default: 0.5)
  • args.occupancy (number) – initial cell occupancy (GPU variant only, default: 0.5)
r_cut

Cut-off radius matrix for the particle interactions.

r_skin

“Skin” of the particle. This is an additional distance ratio added to the cutoff radius for the minimal edge lengths of the cells.

particle

Instance of halmd.mdsim.particle.

disconnect()

Disconnect binning module from profiler.