comm_modify command

Syntax

comm_modify keyword value ...

• zero or more keyword/value pairs may be appended

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

  mode value = single or multi = communicate atoms within a single or multiple distances
  cutoff value = Rcut (distance units) = communicate atoms from this far away
  cutoff/multi 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
comm_modify mode multi group solvent
comm_modift 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 command, all communication settings are restored to their default values, including those previously reset by a comm_modify command. Thus if your input script specifies a comm_style 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 mode can be faster. In this case, each atom type is assigned its own distance cutoff for communication purposes, and fewer atoms will be communicated. See the neighbor multi command for a neighbor list construction option that may also be beneficial for simulations of this kind.

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 and the ghost cutoff is set to the neighbor cutoff. Specifying a cutoff value of 0.0 will reset any previous value to the default.

The cutoff/multi option is equivalent to cutoff, but applies to communication mode multi instead. Since in this case the communication cutoffs are determined per atom type, a type specifier is needed and cutoff for one or multiple types can be extended. Also ranges of types using the usual asterisk notation can be given.

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 multibody 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.

Related commands

comm_style, neighbor

Default

The option defauls 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.