<UL><LI>one or more keyword/value pairs may be listed
<PRE>keyword = <I>delay</I> or <I>every</I> or <I>check</I> or <I>once</I> or <I>cluster</I> or <I>include</I> or <I>exclude</I> or <I>page</I> or <I>one</I> or <I>binsize</I>
<I>delay</I> value = N
N = delay building until this many steps since last build
<I>every</I> value = M
M = build neighbor list every this many steps
<I>check</I> value = <I>yes</I> or <I>no</I>
<I>yes</I> = only build if some atom has moved half the skin distance or more
<I>no</I> = always build on 1st step that <I>every</I> and <I>delay</I> are satisfied
<I>once</I>
<I>yes</I> = only build neighbor list once at start of run and never rebuild
<I>no</I> = rebuild neighbor list according to other settings
<I>cluster</I>
<I>yes</I> = check bond,angle,etc neighbor list for nearby clusters
<I>no</I> = do not check bond,angle,etc neighbor list for nearby clusters
<I>include</I> value = group-ID
group-ID = only build pair neighbor lists for atoms in this group
<I>exclude</I> 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
<I>page</I> value = N
N = number of pairs stored in a single neighbor page
<I>one</I> value = N
N = max number of neighbors of one atom
<I>binsize</I> value = size
size = bin size for neighbor list construction (distance units)
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>neigh_modify every 2 delay 10 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
</PRE>
<P><B>Description:</B>
</P>
<P>This command sets parameters that affect the building and use of
pairwise neighbor lists. Depending on what pair interactions and
other commands are defined, a simulation may require one or more
neighbor lists.
</P>
<P>The <I>every</I>, <I>delay</I>, <I>check</I>, and <I>once</I> options affect how often
lists are built as a simulation runs. The <I>delay</I> setting means never
build new lists until at least N steps after the previous build. The
<I>every</I> setting means build lists every M steps (after the delay has
passed). If the <I>check</I> setting is <I>no</I>, the lists are built on the
first step that satisfies the <I>delay</I> and <I>every</I> settings. If the
<I>check</I> setting is <I>yes</I>, then the <I>every</I> and <I>delay</I> settings
determine when a build may possibly be performed, but an actual build
only occurs if some atom has moved more than half the skin distance
(specified in the <AHREF ="neighbor.html">neighbor</A> command) since the last
build.
</P>
<P>If the <I>once</I> setting is yes, then the neighbor list is only built
once at the beginning of each run, and never rebuilt, except on steps
when a restart file is written, or steps when a fix forces a rebuild
to occur (e.g. fixes that create or delete atoms, such as <AHREF ="fix_deposit.html">fix
deposit</A> or <AHREF ="fix_evaporate.html">fix evaporate</A>).
This setting should only be made if you are certain atoms will not
move far enough that the neighbor list should be rebuilt, e.g. running
a simulation of a cold crystal. Note that it is not that expensive to
check if neighbor lists should be rebuilt.
</P>
<P>When the rRESPA integrator is used (see the <AHREF ="run_style.html">run_style</A>
command), the <I>every</I> and <I>delay</I> parameters refer to the longest
(outermost) timestep.
</P>
<P>The <I>cluster</I> option does a sanity test every time neighbor lists are
built for bond, angle, dihedral, and improper interactions, to check
that each set of 2, 3, or 4 atoms is a cluster of nearby atoms. It
does this by computing the distance between pairs of atoms in the
interaction and insuring they are not further apart than half the
periodic box length. If they are, an error is generated, since the
interaction would be computed between far-away atoms instead of their
nearby periodic images. The only way this should happen is if the
pairwise cutoff is so short that atoms that are part of the same
interaction are not communicated as ghost atoms. This is an unusual
model (e.g. no pair interactions at all) and the problem can be fixed
by use of the <AHREF ="comm_modify.html">comm_modify cutoff</A> command. Note
that to save time, the default <I>cluster</I> setting is <I>no</I>, so that this
check is not performed.
</P>
<P>The <I>include</I> option limits the building of pairwise neighbor lists to
atoms in the specified group. This can be useful for models where a
large portion of the simulation is particles that do not interact with
other particles or with each other via pairwise interactions. The
group specified with this option must also be specified via the