atom_modify command

Syntax

atom_modify keyword values ...

  • one or more keyword/value pairs may be appended

  • keyword = id or map or first or sort

    id value = yes or no
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 certain attributes of atoms defined and stored within LAMMPS, in addition to what is specified by the atom_style command. The id and map keywords must be specified before a simulation box is defined; other keywords can be specified any time.

The id keyword determines whether non-zero atom IDs can be assigned to each atom. If the value is yes, which is the default, IDs are assigned, whether you use the create atoms or read_data or read_restart commands to initialize atoms. If the value is no the IDs for all atoms are assumed to be 0.

If atom IDs are used, they must all be positive integers. They should also be unique, though LAMMPS does not check for this. Typically they should also be consecutively numbered (from 1 to Natoms), though this is not required. Molecular atom styles are those that store bond topology information (styles bond, angle, molecular, full). These styles require atom IDs since the IDs are used to encode the topology. Some other LAMMPS commands also require the use of atom IDs. E.g. some many-body pair styles use them to avoid double computation of the I-J interaction between two atoms.

The only reason not to use atom IDs is if you are running an atomic simulation so large that IDs cannot be uniquely assigned. For a default LAMMPS build this limit is 2^31 or about 2 billion atoms. However, even in this case, you can use 64-bit atom IDs, allowing 2^63 or about 9e18 atoms, if you build LAMMPS with the - DLAMMPS_BIGBIG switch. This is described in Section 2.2 of the manual. If atom IDs are not used, they must be specified as 0 for all atoms, e.g. in a data or restart file.

The map keyword determines how atom ID lookup is done for molecular atom styles. Lookups are performed by bond (angle, etc) routines in LAMMPS 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 largest atom ID in the system. This is a fast, simple method for many simulations, but requires too much memory for large simulations. The hash value uses a hash table to perform the lookups. This can be slightly slower than the array method, but its memory cost is proportional to the number of atoms owned by a processor, i.e. N/P when N is the total number of atoms in the system and P is the number of processors.

When this setting is not specified in your input script, LAMMPS creates a map, if one is needed, as an array or hash. See the discussion of default values below for how LAMMPS chooses which kind of map to build. Note that atomic systems do not normally need to create a map. However, even in this case some LAMMPS commands will create a map to find atoms (and then destroy it), or require a permanent map. An example of the former is the velocity loop all command, which uses a map when looping over all atoms and insuring the same velocity values are assigned to an atom ID, no matter which processor owns it.

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 LAMMPS 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 comm_modify 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. LAMMPS does not use the group until a simullation 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 LAMMPS simulation, as discussed in a paper by (Meloni). Its efficacy 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 peformed 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 intereractions 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.

Note

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 simluations. Various commands, particularly those which use random numbers (e.g. velocity create, and fix langevin), 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 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, id is yes. By default, atomic systems (no bond topology info) do not use a map. For molecular systems (with bond topology info), a map is used. The default map style is array if no atom ID is larger than 1 million, otherwise the default is hash. 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).