comm_modify command

Syntax

comm_modify keyword value ...
  • one or more keyword/value pairs may be appended

  • keyword = mode or cutoff or cutoff/multi or group or reduce/multi or vel

    mode value = single, multi, or multi/old = communicate atoms within a single or multiple distances
    cutoff value = Rcut (distance units) = communicate atoms from this far away
    cutoff/multi collection value
       collection = atom collection or collection range (supports asterisk notation)
       value = Rcut (distance units) = communicate atoms for selected types from this far away
    reduce/multi arg = none = reduce number of communicated ghost atoms for multi style
    cutoff/multi/old type value
       type = atom type or type range (supports asterisk notation)
       value = Rcut (distance units) = communicate atoms for selected types from this far away
    group value = group-ID = only communicate atoms in the group
    vel value = yes or no = do or do not communicate velocity info with ghost atoms

Examples

comm_modify mode multi reduce/multi
comm_modify mode multi group solvent
comm_modify mode multi cutoff/multi 1 10.0 cutoff/multi 2*4 15.0
comm_modify vel yes
comm_modify mode single cutoff 5.0 vel yes
comm_modify cutoff/multi * 0.0

Description

This command sets parameters that affect the inter-processor communication of atom information that occurs each timestep as coordinates and other properties are exchanged between neighboring processors and stored as properties of ghost atoms.

Note

These options apply to the currently defined comm style. When you specify a comm_style or read_restart command, all communication settings are restored to their default or stored values, including those previously reset by a comm_modify command. Thus if your input script specifies a comm_style or read_restart command, you should use the comm_modify command after it.

The mode keyword determines whether a single or multiple cutoff distances are used to determine which atoms to communicate.

The default mode is single which means each processor acquires information for ghost atoms that are within a single distance from its sub-domain. The distance is by default the maximum of the neighbor cutoff across all atom type pairs.

For many systems this is an efficient algorithm, but for systems with widely varying cutoffs for different type pairs, the multi or multi/old mode can be faster. In multi, each atom is assigned to a collection which should correspond to a set of atoms with similar interaction cutoffs. In this case, each atom collection is assigned its own distance cutoff for communication purposes, and fewer atoms will be communicated. in multi/old, a similar technique is used but atoms are grouped by atom type. See the neighbor multi and neighbor multi/old commands for neighbor list construction options that may also be beneficial for simulations of this kind. The multi communication mode is only compatible with the multi neighbor style. The multi/old communication mode is comparable with both the multi and multi/old neighbor styles.

The cutoff keyword allows you to extend the ghost cutoff distance for communication mode single, which is the distance from the borders of a processor’s sub-domain at which ghost atoms are acquired from other processors. By default the ghost cutoff = neighbor cutoff = pairwise force cutoff + neighbor skin. See the neighbor command for more information about the skin distance. If the specified Rcut is greater than the neighbor cutoff, then extra ghost atoms will be acquired. If the provided cutoff is smaller, the provided value will be ignored, the ghost cutoff is set to the neighbor cutoff and a warning will be printed. Specifying a cutoff value of 0.0 will reset any previous value to the default. If bonded interactions exist and equilibrium bond length information is available, then also a heuristic based on that bond length is computed. It is used as communication cutoff, if there is no pair style present and no comm_modify cutoff command used. Otherwise a warning is printed, if this bond based estimate is larger than the communication cutoff used.

The cutoff/multi option is equivalent to cutoff, but applies to communication mode multi instead. Since the communication cutoffs are determined per atom collections, a collection specifier is needed and cutoff for one or multiple collections can be extended. Also ranges of collections using the usual asterisk notation can be given. Collections are indexed from 1 to N where N is the total number of collections. Note that the arguments for cutoff/multi are parsed right before each simulation to account for potential changes in the number of collections. Custom cutoffs are preserved between runs but if collections are redefined, one may want to re-specify the communication cutoffs. For granular pair styles,the default cutoff is set to the sum of the current maximum atomic radii for each collection. The cutoff/multi/old option is similar to cutoff/multi except it operates on atom types as opposed to collections.

The reduce/multi option applies to multi and sets the communication cutoff for a particle equal to the maximum interaction distance between particles in the same collection. This reduces the number of ghost atoms that need to be communicated. This method is only compatible with the multi neighbor style and requires a half neighbor list and Newton on. See the neighbor multi command for more information.

These are simulation scenarios in which it may be useful or even necessary to set a ghost cutoff > neighbor cutoff:

  • a single polymer chain with bond interactions, but no pairwise interactions

  • bonded interactions (e.g. dihedrals) extend further than the pairwise cutoff

  • ghost atoms beyond the pairwise cutoff are needed for some computation

In the first scenario, a pairwise potential is not defined. Thus the pairwise neighbor cutoff will be 0.0. But ghost atoms are still needed for computing bond, angle, etc interactions between atoms on different processors, or when the interaction straddles a periodic boundary.

The appropriate ghost cutoff depends on the newton bond setting. For newton bond off, the distance needs to be the furthest distance between any two atoms in the bond, angle, etc. E.g. the distance between 1-4 atoms in a dihedral. For newton bond on, the distance between the central atom in the bond, angle, etc and any other atom is sufficient. E.g. the distance between 2-4 atoms in a dihedral.

In the second scenario, a pairwise potential is defined, but its neighbor cutoff is not sufficiently long enough to enable bond, angle, etc terms to be computed. As in the previous scenario, an appropriate ghost cutoff should be set.

In the last scenario, a fix or compute or pairwise potential needs to calculate with ghost atoms beyond the normal pairwise cutoff for some computation it performs (e.g. locate neighbors of ghost atoms in a manybody pair potential). Setting the ghost cutoff appropriately can insure it will find the needed atoms.

Note

In these scenarios, if you do not set the ghost cutoff long enough, and if there is only one processor in a periodic dimension (e.g. you are running in serial), then LAMMPS may “find” the atom it is looking for (e.g. the partner atom in a bond), that is on the far side of the simulation box, across a periodic boundary. This will typically lead to bad dynamics (i.e. the bond length is now the simulation box length). To detect if this is happening, see the neigh_modify cluster command.

The group keyword will limit communication to atoms in the specified group. This can be useful for models where no ghost atoms are needed for some kinds of particles. All atoms (not just those in the specified group) will still migrate to new processors as they move. The group specified with this option must also be specified via the atom_modify first command.

The vel keyword enables velocity information to be communicated with ghost particles. Depending on the atom_style, velocity info includes the translational velocity, angular velocity, and angular momentum of a particle. If the vel option is set to yes, then ghost atoms store these quantities; if no then they do not. The yes setting is needed by some pair styles which require the velocity state of both the I and J particles to compute a pairwise I,J interaction, as well as by some compute and fix commands.

Note that if the fix deform command is being used with its “remap v” option enabled, then the velocities for ghost atoms (in the fix deform group) mirrored across a periodic boundary will also include components due to any velocity shift that occurs across that boundary (e.g. due to dilation or shear).

Restrictions

Communication mode multi is currently only available for comm_style brick.

Default

The option defaults are mode = single, group = all, cutoff = 0.0, vel = no. The cutoff default of 0.0 means that ghost cutoff = neighbor cutoff = pairwise force cutoff + neighbor skin.