neighbor command

neighbor_skin command


neighbor skin style
neighbor_skin skin
  • skin = extra distance beyond force cutoff (distance units)
  • style = bin or nsq or multi


neighbor 0.3 bin
neighbor 2.0 nsq
neighbor_skin 0.3


These commands set parameters that affect the building of pairwise neighbor lists. All atom pairs within a neighbor cutoff distance equal to the their force cutoff plus the skin distance are stored in the list. Typically, the larger the skin distance, the less often neighbor lists need to be built, but more pairs must be checked for possible force interactions every timestep. The default value for skin depends on the choice of units for the simulation; see the default values below. The “neighbor_skin” command is a wrapper for “neighbor” that only takes the skin value as input and sets style to bin.

The skin distance is also used to determine how often atoms migrate to new processors if the check option of the neigh_modify command is set to yes. Atoms are migrated (communicated) to new processors on the same timestep that neighbor lists are re-built.

The style value selects what algorithm is used to build the list. The bin style creates the list by binning which is an operation that scales linearly with N/P, the number of atoms per processor where N = total number of atoms and P = number of processors. It is almost always faster than the nsq style which scales as (N/P)^2. For unsolvated small molecules in a non-periodic box, the nsq choice can sometimes be faster. Either style should give the same answers.

The multi style is a modified binning algorithm that is useful for systems with a wide range of cutoff distances, e.g. due to different size particles. For the bin style, the bin size is set to 1/2 of the largest cutoff distance between any pair of atom types and a single set of bins is defined to search over for all atom types. This can be inefficient if one pair of types has a very long cutoff, but other type pairs have a much shorter cutoff. For style multi the bin size is set to 1/2 of the shortest cutoff distance and multiple sets of bins are defined to search over for different atom types. This imposes some extra setup overhead, but the searches themselves may be much faster for the short-cutoff cases. See the communicate multi command for a communication option option that may also be beneficial for simulations of this kind.

The neigh_modify command has additional options that control how often neighbor lists are built and which pairs are stored in the list.

When a run is finished, counts of the number of neighbors stored in the pairwise list and the number of times neighbor lists were built are printed to the screen and log file. See this section for details.




0.3 bin for units = lj, skin = 0.3 sigma
2.0 bin for units = real or metal, skin = 2.0 Angstroms
0.001 bin for units = si, skin = 0.001 meters = 1.0 mm
0.1 bin for units = cgs, skin = 0.1 cm = 1.0 mm