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<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
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<li>neighbor command</li>
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<div class="section" id="neighbor-command">
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<span id="index-0"></span><h1>neighbor command</h1>
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<div class="section" id="syntax">
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<h2>Syntax</h2>
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<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">neighbor</span> <span class="n">skin</span> <span class="n">style</span>
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</pre></div>
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</div>
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<ul class="simple">
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<li>skin = extra distance beyond force cutoff (distance units)</li>
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<li>style = <em>bin</em> or <em>nsq</em> or <em>multi</em></li>
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</ul>
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</div>
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<div class="section" id="examples">
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<h2>Examples</h2>
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<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">neighbor</span> <span class="mf">0.3</span> <span class="nb">bin</span>
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<span class="n">neighbor</span> <span class="mf">2.0</span> <span class="n">nsq</span>
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</pre></div>
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</div>
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</div>
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<div class="section" id="description">
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<h2>Description</h2>
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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 <em>skin</em> 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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<em>skin</em> depends on the choice of units for the simulation; see the
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default values below.</p>
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<p>The <em>skin</em> distance is also used to determine how often atoms migrate
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to new processors if the <em>check</em> option of the
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<a class="reference internal" href="neigh_modify.html"><span class="doc">neigh_modify</span></a> command is set to <em>yes</em>. 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.</p>
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<p>The <em>style</em> value selects what algorithm is used to build the list.
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The <em>bin</em> 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 <em>nsq</em> style which scales as (N/P)^2. For
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unsolvated small molecules in a non-periodic box, the <em>nsq</em> choice can
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sometimes be faster. Either style should give the same answers.</p>
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<p>The <em>multi</em> 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 <em>bin</em> 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 <em>multi</em> 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 class="reference internal" href="comm_modify.html"><span class="doc">comm_modify mode multi</span></a> command for a communication option option
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that may also be beneficial for simulations of this kind.</p>
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<p>The <a class="reference internal" href="neigh_modify.html"><span class="doc">neigh_modify</span></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.</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 class="reference internal" href="Section_start.html#start-8"><span class="std std-ref">this section</span></a> for details.</p>
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</div>
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<div class="section" id="restrictions">
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<h2>Restrictions</h2>
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<blockquote>
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<div>none</div></blockquote>
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</div>
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<div class="section" id="related-commands">
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<h2>Related commands</h2>
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<p><a class="reference internal" href="neigh_modify.html"><span class="doc">neigh_modify</span></a>, <a class="reference internal" href="units.html"><span class="doc">units</span></a>,
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<span class="xref doc">comm_modify</span></p>
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</div>
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<div class="section" id="default">
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<h2>Default</h2>
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<div class="line-block">
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<div class="line">0.3 bin for units = lj, skin = 0.3 sigma</div>
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<div class="line">2.0 bin for units = real or metal, skin = 2.0 Angstroms</div>
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<div class="line">0.001 bin for units = si, skin = 0.001 meters = 1.0 mm</div>
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<div class="line">0.1 bin for units = cgs, skin = 0.1 cm = 1.0 mm</div>
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<div class="line"><br /></div>
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