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) – Desired cell occupancy. Defaults to halmd.mdsim.defaults.binning.occupancy() (GPU variant only).

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.

cell_occupancy

Current cell occupancy. Only available on GPU variant.

disconnect()

Disconnect binning module from profiler.