atom_modify command — LAMMPS documentation

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# 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 = yes or 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 yes
    atom_modify map hash 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 on the Build_settings doc page. If atom IDs are not used, they must be specified as 0 for all atoms, e.g. in a data or restart file.

Note

If a triclinic simulation box is used, atom IDs are required, due to how neighbor lists are built.

The map keyword determines how atoms with specific IDs are found when required. For example, the bond (angle, etc) methods need to find the local index of an atom with a specific global ID which is a bond (angle, etc) partner. LAMMPS performs this operation efficiently by creating a “map”, which is either an array or hash table, as described below.

When the map keyword is not specified in your input script, LAMMPS only creates a map for atom_styles for molecular systems which have permanent bonds (angles, etc). No map is created for atomic systems, since it is normally not needed. However some LAMMPS commands require a map, even for atomic systems, and will generate an error if one does not exist. The map keyword thus allows you to force the creation of a map.

Specifying a value of yes will create either an array-style or hash-style map, depending on the size of the system. If no atom ID is larger than 1 million, then an array-style map is used, otherwise a hash-style map is used. Specifying a value of array or hash creates an array-style or hash-style map respectively, regardless of the size of the system.

For an array-style map, 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. For a hash-style map, a hash table is created on each processor, which finds an atom ID in constant time (independent of the global number of atom IDs). It can be slightly slower than the array map, 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.

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 simulation is run.

The sort keyword turns on a spatial sorting or reordering of atoms within each processor’s subdomain 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 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.

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 simulations. 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.

Note

When running simple pair-wise potentials like Lennard Jones on GPUs with the KOKKOS package, using a larger binsize (e.g. 2x larger than default) and a more frequent reordering than default (e.g. every 100 time steps) may improve performance.

## 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), the default is to use a map of either array or hash style depending on the size of the system, as explained above for the map yes keyword/value option. 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. If no neighbor cutoff is defined, sorting will be turned off.

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