atom_modify command — LIGGGHTS v3.X documentation

# atom_modify command

## Syntax

    atom_modify keyword values ...

- one or more keyword/value pairs may be appended
- keyword = map or first or sort

    map value = array or hash
    first value = group-ID = group whose atoms will appear first in internal atom lists
    sort values = Nfreq binsize
      Nfreq = sort atoms spatially every this many time steps
      binsize = bin size for spatial sorting (distance units)

## Examples

    atom_modify map hash
    atom_modify map array sort 10000 2.0
    atom_modify first colloid

## Description

Modify properties of the atom style selected within LIGGGHTS(R)-PUBLIC.

The map keyword determines how atom ID lookup is done for molecular problems. Lookups are performed by bond (angle, etc) routines in LIGGGHTS(R)-PUBLIC to find the local atom index associated with a global atom ID. When the array value is used, each processor stores a lookup table of length N, where N is the total # of atoms in the system. This is the fastest method for most simulations, but a processor can run out of memory to store the table for very large simulations. The hash value uses a hash table to perform the lookups. This method can be slightly slower than the array method, but its memory cost is proportional to N/P on each processor, where P is the total number of processors running the simulation.

The first keyword allows a group to be specified whose atoms will be maintained as the first atoms in each processor’s list of owned atoms. This in only useful when the specified group is a small fraction of all the atoms, and there are other operations LIGGGHTS(R)-PUBLIC is performing that will be sped-up significantly by being able to loop over the smaller set of atoms. Otherwise the reordering required by this option will be a net slow-down. The neigh_modify include and communicate group commands are two examples of commands that require this setting to work efficiently. Several fixes, most notably time integration fixes like fix nve, also take advantage of this setting if the group they operate on is the group specified by this command. Note that specifying “all” as the group-ID effectively turns off the first option.

It is OK to use the first keyword with a group that has not yet been defined, e.g. to use the atom_modify first command at the beginning of your input script. LIGGGHTS(R)-PUBLIC does not use the group until a simulation is run.

The sort keyword turns on a spatial sorting or reordering of atoms within each processor’s sub-domain every Nfreq timesteps. If Nfreq is set to 0, then sorting is turned off. Sorting can improve cache performance and thus speed-up a LIGGGHTS(R)-PUBLIC simulation, as discussed in a paper by (Meloni). Its efficiency depends on the problem size (atoms/processor), how quickly the system becomes disordered, and various other factors. As a general rule, sorting is typically more effective at speeding up simulations of liquids as opposed to solids. In tests we have done, the speed-up can range from zero to 3-4x.

Reordering is performed every Nfreq timesteps during a dynamics run or iterations during a minimization. More precisely, reordering occurs at the first reneighboring that occurs after the target timestep. The reordering is performed locally by each processor, using bins of the specified binsize. If binsize is set to 0.0, then a binsize equal to half the neighbor cutoff distance (force cutoff plus skin distance) is used, which is a reasonable value. After the atoms have been binned, they are reordered so that atoms in the same bin are adjacent to each other in the processor’s 1d list of atoms.

The goal of this procedure is for atoms to put atoms close to each other in the processor’s one-dimensional list of atoms that are also near to each other spatially. This can improve cache performance when pairwise interactions and neighbor lists are computed. Note that if bins are too small, there will be few atoms/bin. Likewise if bins are too large, there will be many atoms/bin. In both cases, the goal of cache locality will be undermined.

Warning

Running a simulation with sorting on versus off should not change the simulation results in a statistical sense. However, a different ordering will induce round-off differences, which will lead to diverging trajectories over time when comparing two simulations. Various commands, particularly those which use random numbers, may generate (statistically identical) results which depend on the order in which atoms are processed. The order of atoms in a dump file will also typically change if sorting is enabled.

## Restrictions

The map keyword can only be used before the simulation box is defined by a read_data or create_box command.

The first and sort options cannot be used together. Since sorting is on by default, it will be turned off if the first keyword is used with a group-ID that is not “all”.

Related commands: none

## Default

By default, non-molecular problems do not allocate maps. For molecular problems, the option default is map = array. By default, a “first” group is not defined. By default, sorting is enabled with a frequency of 1000 and a binsize of 0.0, which means the neighbor cutoff will be used to set the bin size.

(Meloni) Meloni, Rosati and Colombo, J Chem Phys, 126, 121102 (2007).