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neigh_modify command

Syntax:

neigh_modify keyword values ... 

Examples:

neigh_modify every 2 delay 5 check yes
neigh_modify exclude type 2 3
neigh_modify exclude group frozen frozen check no
neigh_modify exclude group residue1 chain3
neigh_modify exclude molecule rigid 

Description:

This command sets parameters that affect the pairwise neighbor list.

The every, delay, and check options affect how often the list is built as a simulation runs. The delay setting means never build a new list until at least N steps after the previous build. The every setting means build the list every N steps (after the delay has passed). If the check setting is no, the list is built on the 1st step that satisfies the delay and every settings. If the check setting is yes, then the list is only built on a particular step if some atom has moved more than half the skin distance (specified in the neighbor command) since the last build.

When the rRESPA integrator is used (see the run_style command), the every and delay parameters refer to the longest (outermost) timestep.

The exclude option turns off pairwise interactions between certain pairs of atoms, by not including them in the neighbor list. These are sample scenarios where this is useful:

The exclude type option turns off the pairwise interaction if one atom is of type M and the other of type N. M can equal N. The exclude group option turns off the interaction if one atom is in the first group and the other is the second. Group1-ID can equal group2-ID. The exclude molecule option turns off the interaction if both atoms are in the specified group and in the same molecule, as determined by their molecule ID.

Each of the exclude options can be specified multiple times. The exclude type option is the most efficient option to use; it requries only a single check, no matter how many times it has been specified. The other exclude options are more expensive if specified multiple times; they require one check for each time they have been specified.

Note that the exclude options only affect pairwise interactions; see the delete_bonds command for information on turning off bond interactions.

Restrictions:

The exclude molecule option can only be used with atom styles that define molecule IDs.

Related commands:

neighbor, delete_bonds

Default:

The option defaults are delay = 10, every = 1, check = yes, and exclude = none.