neighbor command

Syntax

neighbor skin style
  • skin = extra distance beyond force cutoff (distance units)

  • style = bin or nsq or multi or multi/old

Examples

neighbor 0.3 bin
neighbor 2.0 nsq

Description

This command sets 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 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 granular pair styles, cutoffs are set to the sum of the maximum atomic radii for each atom type. 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. The multi style uses different sized bins for collections of different sized particles, where “size” may mean the physical size of the particle or its cutoff distance for interacting with other particles. Different sets of bins are then used to construct the neighbor lists as as further described by Shire, Hanley, and Stratford (Shire). This imposes some extra setup overhead, but the searches themselves may be much faster. By default, each atom type defines a separate collection of particles. For systems where two or more atom types have the same size (either physical size or cutoff distance), the definition of collections can be customized, which can result in less overhead and faster performance. See the neigh_modify command for how to define custom collections. Whether the collection definition is customized or not, also see the comm_modify mode multi command for communication options that further improve performance in a manner consistent with neighbor style multi.

An alternate style, multi/old, sets the bin size to 1/2 of the shortest cutoff distance and multiple sets of bins are defined to search over for different atom types. This algorithm used to be the default multi algorithm in LAMMPS but was found to be significantly slower than the new approach. For now we are keeping the old option in case there are use cases where multi/old outperforms the new multi style.

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 the Run output doc page for details.

Restrictions

none

Default

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


(Shire) Shire, Hanley and Stratford, Comp Part Mech, (2020).