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neigh_modify.html
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<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>neigh_modify command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>neigh_modify keyword values ...
</PRE>
<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>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>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
</PRE>
<PRE> <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 pairwise neighbor list.
</P>
<P>The <I>every</I>, <I>delay</I>, and <I>check</I> options affect how often the list is
built as a simulation runs. The <I>delay</I> setting means never build a
new list until at least N steps after the previous build. The <I>every</I>
setting means build the list every M steps (after the delay has
passed). If the <I>check</I> setting is <I>no</I>, the list is built on the 1st
step that satisfies the <I>delay</I> and <I>every</I> settings. If the <I>check</I>
setting is <I>yes</I>, then the list is only built on a particular step if
some atom has moved more than half the skin distance (specified in the
<A HREF = "neighbor.html">neighbor</A> command) since the last build.
</P>
<P>When the rRESPA integrator is used (see the <A HREF = "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>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
"atom_modify first" command.
</P>
<P>The <I>exclude</I> 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:
</P>
<UL><LI>In crack simulations, pairwise interactions can be shut off between 2
slabs of atoms to effectively create a crack.
<LI>When a large collection of atoms is treated as frozen, interactions
between those atoms can be turned off to save needless
computation. E.g. Using the <A HREF = "fix_setforce.html">fix setforce</A> command
to freeze a wall or portion of a bio-molecule.
<LI>When one or more rigid bodies are specified, interactions within each
body can be turned off to save needless computation. See the <A HREF = "fix_rigid.html">fix
rigid</A> command for more details.
</UL>
<P>The <I>exclude type</I> option turns off the pairwise interaction if one
atom is of type M and the other of type N. M can equal N. The
<I>exclude group</I> 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 <I>exclude molecule</I> option turns off the interaction if
both atoms are in the specified group and in the same molecule, as
determined by their molecule ID.
</P>
<P>Each of the exclude options can be specified multiple times. The
<I>exclude type</I> option is the most efficient option to use; it requires
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.
</P>
<P>Note that the exclude options only affect pairwise interactions; see
the <A HREF = "delete_bonds.html">delete_bonds</A> command for information on
turning off bond interactions.
</P>
<P>The <I>page</I> and <I>one</I> 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
<I>page</I> value. A new page is allocated when the next atom's neighbors
could potentially overflow the list. This threshold is set by the
<I>one</I> value which tells LAMMPS the maximum number of neighbor's one
atom can have.
</P>
<P>The <I>binsize</I> option allows you to specify what size of bins will be
used in neighbor list construction to sort and find neighboring atoms.
By default, for <A HREF = "neighbor.html">neighbor style bin</A>, LAMMPS uses bins
that are 1/2 the size of the maximum pair cutoff. For <A HREF = "neighbor.html">neighbor style
multi</A>, the bins are 1/2 the size of the minimum pair
cutoff. Typically these are good values values for minimizing the
time for neighbor list construction. This setting overrides the
default. If you make it too big, there is little overhead due to
looping over bins, but more atoms are checked. If you make it too
small, the optimal number of atoms is checked, but bin overhead goes
up. If you set the binsize to 0.0, LAMMPS will use the default
binsize of 1/2 the cutoff.
</P>
<P><B>Restrictions:</B>
</P>
<P>If the "delay" setting is non-zero, then it must be a multiple of the
"every" setting.
</P>
<P>The exclude molecule option can only be used with atom styles that
define molecule IDs.
</P>
<P>The value of the <I>page</I> setting must be at least 10x larger than the
<I>one</I> setting. This insures neighbor pages are not mostly empty
space.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "neighbor.html">neighbor</A>, <A HREF = "delete_bonds.html">delete_bonds</A>
</P>
<P><B>Default:</B>
</P>
<P>The option defaults are delay = 10, every = 1, check = yes, include =
all, exclude = none, page = 100000, one = 2000, and binsize = 0.0.
</P>
</HTML>
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