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<div class="section" id="pair-style-snap-command">
<span id="index-0"></span><h1>pair_style snap command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">snap</span>
</pre></div>
</div>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">snap</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">snap</span> <span class="n">InP</span><span class="o">.</span><span class="n">snapcoeff</span> <span class="n">In</span> <span class="n">P</span> <span class="n">InP</span><span class="o">.</span><span class="n">snapparam</span> <span class="n">In</span> <span class="n">In</span> <span class="n">P</span> <span class="n">P</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
<p>Style <em>snap</em> computes interactions
using the spectral neighbor analysis potential (SNAP)
<a class="reference internal" href="#thompson2014"><span class="std std-ref">(Thompson)</span></a>. Like the GAP framework of Bartok et al.
<a class="reference internal" href="#bartok2010"><span class="std std-ref">(Bartok2010)</span></a>, <a class="reference internal" href="#bartok2013"><span class="std std-ref">(Bartok2013)</span></a>
it uses bispectrum components
to characterize the local neighborhood of each atom
in a very general way. The mathematical definition of the
bispectrum calculation used by SNAP is identical
to that used of <a class="reference internal" href="compute_sna_atom.html"><span class="doc">compute sna/atom</span></a>.
In SNAP, the total energy is decomposed into a sum over
atom energies. The energy of atom <em>i</em> is
expressed as a weighted sum over bispectrum components.</p>
<img alt="_images/pair_snap.jpg" class="align-center" src="_images/pair_snap.jpg" />
<p>where <em>B_k^i</em> is the <em>k</em>-th bispectrum component of atom <em>i</em>,
and <em>beta_k^alpha_i</em> is the corresponding linear coefficient
that depends on <em>alpha_i</em>, the SNAP element of atom <em>i</em>. The
number of bispectrum components used and their definitions
depend on the values of <em>twojmax</em> and <em>diagonalstyle</em>
defined in the SNAP parameter file described below.
The bispectrum calculation is described in more detail
in <a class="reference internal" href="compute_sna_atom.html"><span class="doc">compute sna/atom</span></a>.</p>
<p>Note that unlike for other potentials, cutoffs for SNAP potentials are
not set in the pair_style or pair_coeff command; they are specified in
the SNAP potential files themselves.</p>
<p>Only a single pair_coeff command is used with the <em>snap</em> style which
specifies two SNAP files and the list SNAP element(s) to be
extracted.
The SNAP elements are mapped to LAMMPS atom types by specifying
N additional arguments after the 2nd filename in the pair_coeff
command, where N is the number of LAMMPS atom types:</p>
<ul class="simple">
<li>SNAP element file</li>
<li>Elem1, Elem2, ...</li>
<li>SNAP parameter file</li>
<li>N element names = mapping of SNAP elements to atom types</li>
</ul>
<p>As an example, if a LAMMPS indium phosphide simulation has 4 atoms
types, with the first two being indium and the 3rd and 4th being
phophorous, the pair_coeff command would look like this:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">snap</span> <span class="n">InP</span><span class="o">.</span><span class="n">snapcoeff</span> <span class="n">In</span> <span class="n">P</span> <span class="n">InP</span><span class="o">.</span><span class="n">snapparam</span> <span class="n">In</span> <span class="n">In</span> <span class="n">P</span> <span class="n">P</span>
</pre></div>
</div>
<p>The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
The two filenames are for the element and parameter files, respectively.
The &#8216;In&#8217; and &#8216;P&#8217; arguments (between the file names) are the two elements
which will be extracted from the element file. The
two trailing &#8216;In&#8217; arguments map LAMMPS atom types 1 and 2 to the
SNAP &#8216;In&#8217; element. The two trailing &#8216;P&#8217; arguments map LAMMPS atom types
3 and 4 to the SNAP &#8216;P&#8217; element.</p>
<p>If a SNAP mapping value is
specified as NULL, the mapping is not performed.
This can be used when a <em>snap</em> potential is used as part of the
<em>hybrid</em> pair style. The NULL values are placeholders for atom types
that will be used with other potentials.</p>
<p>The name of the SNAP element file usually ends in the
&#8221;.snapcoeff&#8221; extension. It may contain coefficients
for many SNAP elements.
Only those elements listed in the pair_coeff command are extracted.
The name of the SNAP parameter file usually ends in the &#8221;.snapparam&#8221;
extension. It contains a small number
of parameters that define the overall form of the SNAP potential.
See the <a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a> doc page for alternate ways
to specify the path for these files.</p>
<p>Quite commonly,
SNAP potentials are combined with one or more other LAMMPS pair styles
using the <em>hybrid/overlay</em> pair style. As an example, the SNAP
tantalum potential provided in the LAMMPS potentials directory
combines the <em>snap</em> and <em>zbl</em> pair styles. It is invoked
by the following commands:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span>variable zblcutinner equal 4
variable zblcutouter equal 4.8
variable zblz equal 73
pair_style hybrid/overlay &amp;
zbl ${zblcutinner} ${zblcutouter} snap
pair_coeff * * zbl 0.0
pair_coeff 1 1 zbl ${zblz}
pair_coeff * * snap ../potentials/Ta06A.snapcoeff Ta &amp;
../potentials/Ta06A.snapparam Ta
</pre></div>
</div>
<p>It is convenient to keep these commands in a separate file that can
be inserted in any LAMMPS input script using the <a class="reference internal" href="include.html"><span class="doc">include</span></a>
command.</p>
<p>The top of the SNAP element file can contain any number of blank and comment
lines (start with #), but follows a strict
format after that. The first non-blank non-comment
line must contain two integers:</p>
<ul class="simple">
<li>nelem = Number of elements</li>
<li>ncoeff = Number of coefficients</li>
</ul>
<p>This is followed by one block for each of the <em>nelem</em> elements.
The first line of each block contains three entries:</p>
<ul class="simple">
<li>Element symbol (text string)</li>
<li>R = Element radius (distance units)</li>
<li>w = Element weight (dimensionless)</li>
</ul>
<p>This line is followed by <em>ncoeff</em> coefficients, one per line.</p>
<p>The SNAP parameter file can contain blank and comment lines (start
with #) anywhere. Each non-blank non-comment line must contain one
keyword/value pair. The required keywords are <em>rcutfac</em> and
<em>twojmax</em>. Optional keywords are <em>rfac0</em>, <em>rmin0</em>, <em>diagonalstyle</em>,
and <em>switchflag</em>.</p>
<p>The default values for these keywords are</p>
<ul class="simple">
<li><em>rfac0</em> = 0.99363</li>
<li><em>rmin0</em> = 0.0</li>
<li><em>diagonalstyle</em> = 3</li>
<li><em>switchflag</em> = 0</li>
</ul>
<p>Detailed definitions of these keywords are given on the <a class="reference internal" href="compute_sna_atom.html"><span class="doc">compute sna/atom</span></a> doc page.</p>
<hr class="docutils" />
<p><strong>Mixing, shift, table, tail correction, restart, rRESPA info</strong>:</p>
<p>For atom type pairs I,J and I != J, where types I and J correspond to
two different element types, mixing is performed by LAMMPS with
user-specifiable parameters as described above. You never need to
specify a pair_coeff command with I != J arguments for this style.</p>
<p>This pair style does not support the <a class="reference internal" href="pair_modify.html"><span class="doc">pair_modify</span></a>
shift, table, and tail options.</p>
<p>This pair style does not write its information to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>, since it is stored in potential files. Thus, you
need to re-specify the pair_style and pair_coeff commands in an input
script that reads a restart file.</p>
<p>This pair style can only be used via the <em>pair</em> keyword of the
<a class="reference internal" href="run_style.html"><span class="doc">run_style respa</span></a> command. It does not support the
<em>inner</em>, <em>middle</em>, <em>outer</em> keywords.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>This style is part of the SNAP package. It is only enabled if
LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p><a class="reference internal" href="compute_sna_atom.html"><span class="doc">compute sna/atom</span></a>,
<a class="reference internal" href="compute_sna_atom.html"><span class="doc">compute snad/atom</span></a>,
<a class="reference internal" href="compute_sna_atom.html"><span class="doc">compute snav/atom</span></a></p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<p id="thompson2014"><strong>(Thompson)</strong> Thompson, Swiler, Trott, Foiles, Tucker, under review, preprint
available at <a class="reference external" href="http://arxiv.org/abs/1409.3880">arXiv:1409.3880</a></p>
<p id="bartok2010"><strong>(Bartok2010)</strong> Bartok, Payne, Risi, Csanyi, Phys Rev Lett, 104, 136403 (2010).</p>
<p id="bartok2013"><strong>(Bartok2013)</strong> Bartok, Gillan, Manby, Csanyi, Phys Rev B 87, 184115 (2013).</p>
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