Syntax:
neigh_modify keyword values ...
keyword = delay or every or check or exclude or page or one delay value = N N = delay building until this many steps since last build every value = N N = build neighbor list every this many steps check value = yes or no yes = only build if some atom has moved half the skin distance or more no = always build on 1st step that every and delay are satisfied exclude values: type M N M,N = exclude if one atom in pair is type M, other is type N group group1-ID group2-ID group1-ID,group2-ID = exclude if one atom is in 1st group, other in 2nd molecule group-ID groupname = exclude if both atoms are in the same molecule and in the same group none delete all exclude settings page value = N N = number of pairs stored in a single neighbor page one value = N N = max number of neighbors of one atom
Examples:
neigh_modify every 2 delay 5 check yes page 100000 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.
The page and one options affect how memory is allocated for the neighbor lists. For most simulations the default settings for these options are fine, but if a very large problem is being run or a very long cutoff is being used, these parameters can be tuned. The indices of neighboring atoms are stored in "pages", which are allocated one after another as they fill up. The size of each page is set by the page value. A new page is allocated when the next atom's neighbors could potentially overflow the list. This threshhold is set by the one value which tells LAMMPS the maximum number of neighbor's one atom can have.
Restrictions:
The exclude molecule option can only be used with atom styles that define molecule IDs.
Related commands:
Default:
The option defaults are delay = 10, every = 1, check = yes, exclude = none, page = 10000, and one = 2000.