forked from lijiext/lammps
89 lines
3.6 KiB
HTML
89 lines
3.6 KiB
HTML
<HTML>
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<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>
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<H3>neighbor command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>neighbor skin style
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</PRE>
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<UL><LI>skin = extra distance beyond force cutoff (distance units)
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<LI>style = <I>bin</I> or <I>nsq</I> or <I>multi</I>
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</UL>
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<P><B>Examples:</B>
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</P>
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<PRE>neighbor 0.3 bin
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neighbor 2.0 nsq
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>This command sets parameters that affect the building of pairwise
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neighbor lists. All atom pairs within a neighbor cutoff distance
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equal to the their force cutoff plus the <I>skin</I> distance are stored in
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the list. Typically, the larger the skin distance, the less often
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neighbor lists need to be built, but more pairs must be checked for
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possible force interactions every timestep. The default value for
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<I>skin</I> depends on the choice of units for the simulation; see the
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default values below.
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</P>
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<P>The <I>skin</I> distance is also used to determine how often atoms migrate
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to new processors if the <I>check</I> option of the
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<A HREF = "neigh_modify.html">neigh_modify</A> command is set to <I>yes</I>. Atoms are
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migrated (communicated) to new processors on the same timestep that
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neighbor lists are re-built.
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</P>
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<P>The <I>style</I> value selects what algorithm is used to build the list.
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The <I>bin</I> style creates the list by binning which is an operation that
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scales linearly with N/P, the number of atoms per processor where N =
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total number of atoms and P = number of processors. It is almost
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always faster than the <I>nsq</I> style which scales as (N/P)^2. For
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unsolvated small molecules in a non-periodic box, the <I>nsq</I> choice can
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sometimes be faster. Either style should give the same answers.
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</P>
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<P>The <I>multi</I> style is a modified binning algorithm that is useful for
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systems with a wide range of cutoff distances, e.g. due to different
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size particles. For the <I>bin</I> style, the bin size is set to 1/2 of
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the largest cutoff distance between any pair of atom types and a
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single set of bins is defined to search over for all atom types. This
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can be inefficient if one pair of types has a very long cutoff, but
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other type pairs have a much shorter cutoff. For style <I>multi</I> the
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bin size is set to 1/2 of the shortest cutoff distance and multiple
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sets of bins are defined to search over for different atom types.
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This imposes some extra setup overhead, but the searches themselves
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may be much faster for the short-cutoff cases. See the <A HREF = "communicate.html">communicate
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multi</A> command for a communication option option that
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may also be beneficial for simulations of this kind.
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</P>
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<P>The <A HREF = "neigh_modify.html">neigh_modify</A> command has additional options
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that control how often neighbor lists are built and which pairs are
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stored in the list.
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</P>
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<P>When a run is finished, counts of the number of neighbors stored in
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the pairwise list and the number of times neighbor lists were built
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are printed to the screen and log file. See <A HREF = "Section_start.html#2_7">this
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section</A> for details.
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</P>
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<P><B>Restrictions:</B> none
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</P>
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<P><B>Related commands:</B>
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</P>
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<P><A HREF = "neigh_modify.html">neigh_modify</A>, <A HREF = "units.html">units</A>,
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<A HREF = "communicate.html">communicate</A>
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</P>
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<P><B>Default:</B>
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</P>
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0.3 bin for units = lj, skin = 0.3 sigma<BR>
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2.0 bin for units = real or metal, skin = 2.0 Angstroms<BR>
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0.001 bin for units = si, skin = 0.001 meters = 1.0 mm<BR>
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0.1 bin for units = cgs, skin = 0.1 cm = 1.0 mm <BR>
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</HTML>
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