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<title>pair_style tersoff/mod command &mdash; LAMMPS 15 Dec 2015 documentation</title>
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<div class="section" id="pair-style-tersoff-mod-command">
<span id="index-0"></span><h1>pair_style tersoff/mod command<a class="headerlink" href="#pair-style-tersoff-mod-command" title="Permalink to this headline">¶</a></h1>
</div>
<div class="section" id="pair-style-tersoff-mod-kk-command">
<h1>pair_style tersoff/mod/kk command<a class="headerlink" href="#pair-style-tersoff-mod-kk-command" title="Permalink to this headline">¶</a></h1>
</div>
<div class="section" id="pair-style-tersoff-mod-omp-command">
<h1>pair_style tersoff/mod/omp command<a class="headerlink" href="#pair-style-tersoff-mod-omp-command" title="Permalink to this headline">¶</a></h1>
<div class="section" id="syntax">
<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline">¶</a></h2>
<div class="highlight-python"><div class="highlight"><pre>pair_style tersoff/mod
</pre></div>
</div>
</div>
<div class="section" id="examples">
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h2>
<div class="highlight-python"><div class="highlight"><pre>pair_style tersoff/mod
pair_coeff * * Si.tersoff.mod Si Si
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
<p>The <em>tersoff/mod</em> style computes a bond-order type interatomic
potential <a class="reference internal" href="#kumagai"><span>(Kumagai)</span></a> based on a 3-body Tersoff potential
<a class="reference internal" href="pair_tersoff_zbl.html#tersoff-1"><span>(Tersoff_1)</span></a>, <a class="reference internal" href="pair_tersoff_zbl.html#tersoff-2"><span>(Tersoff_2)</span></a> with modified
cutoff function and angular-dependent term, giving the energy E of a
system of atoms as</p>
<img alt="_images/pair_tersoff_mod.jpg" class="align-center" src="_images/pair_tersoff_mod.jpg" />
<p>where f_R is a two-body term and f_A includes three-body interactions.
The summations in the formula are over all neighbors J and K of atom I
within a cutoff distance = R + D.</p>
<p>The modified cutoff function f_C proposed by <a class="reference internal" href="#murty"><span>(Murty)</span></a> and
having a continuous second-order differential is employed. The
angular-dependent term g(theta) was modified to increase the
flexibility of the potential.</p>
<p>The <em>tersoff/mod</em> potential is fitted to both the elastic constants
and melting point by employing the modified Tersoff potential function
form in which the angular-dependent term is improved. The model
performs extremely well in describing the crystalline, liquid, and
amorphous phases <a class="reference internal" href="#schelling"><span>(Schelling)</span></a>.</p>
<p>Only a single pair_coeff command is used with the <em>tersoff/mod</em> style
which specifies a Tersoff/MOD potential file with parameters for all
needed elements. These are mapped to LAMMPS atom types by specifying
N additional arguments after the filename in the pair_coeff command,
where N is the number of LAMMPS atom types:</p>
<ul class="simple">
<li>filename</li>
<li>N element names = mapping of Tersoff/MOD elements to atom types</li>
</ul>
<p>As an example, imagine the Si.tersoff_mod file has Tersoff values for Si.
If your LAMMPS simulation has 3 Si atoms types, you would use the following
pair_coeff command:</p>
<div class="highlight-python"><div class="highlight"><pre>pair_coeff * * Si.tersoff_mod Si Si Si
</pre></div>
</div>
<p>The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
The three Si arguments map LAMMPS atom types 1,2,3 to the Si element
in the Tersoff/MOD file. If a mapping value is specified as NULL, the
mapping is not performed. This can be used when a <em>tersoff/mod</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>Tersoff/MOD file in the <em>potentials</em> directory of the LAMMPS
distribution have a &#8221;.tersoff.mod&#8221; suffix. Lines that are not blank
or comments (starting with #) define parameters for a triplet of
elements. The parameters in a single entry correspond to coefficients
in the formula above:</p>
<ul class="simple">
<li>element 1 (the center atom in a 3-body interaction)</li>
<li>element 2 (the atom bonded to the center atom)</li>
<li>element 3 (the atom influencing the 1-2 bond in a bond-order sense)</li>
<li>beta</li>
<li>alpha</li>
<li>h</li>
<li>eta</li>
<li>beta_ters = 1 (dummy parameter)</li>
<li>lambda2 (1/distance units)</li>
<li>B (energy units)</li>
<li>R (distance units)</li>
<li>D (distance units)</li>
<li>lambda1 (1/distance units)</li>
<li>A (energy units)</li>
<li>n</li>
<li>c1</li>
<li>c2</li>
<li>c3</li>
<li>c4</li>
<li>c5</li>
</ul>
<p>The n, eta, lambda2, B, lambda1, and A parameters are only used for
two-body interactions. The beta, alpha, c1, c2, c3, c4, c5, h
parameters are only used for three-body interactions. The R and D
parameters are used for both two-body and three-body interactions. The
non-annotated parameters are unitless.</p>
<p>The Tersoff/MOD potential file must contain entries for all the elements
listed in the pair_coeff command. It can also contain entries for
additional elements not being used in a particular simulation; LAMMPS
ignores those entries.</p>
<p>For a single-element simulation, only a single entry is required
(e.g. SiSiSi). As annotated above, the first element in the entry is
the center atom in a three-body interaction and it is bonded to the
2nd atom and the bond is influenced by the 3rd atom. Thus an entry
for SiSiSi means Si bonded to a Si with another Si atom influencing the bond.</p>
<hr class="docutils" />
<p>Styles with a <em>cuda</em>, <em>gpu</em>, <em>intel</em>, <em>kk</em>, <em>omp</em>, or <em>opt</em> suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed in <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a>
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.</p>
<p>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
KOKKOS, USER-OMP and OPT packages, respectively. They are only
enabled if LAMMPS was built with those packages. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
<p>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <a class="reference internal" href="Section_start.html#start-7"><span>-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
use the <a class="reference internal" href="suffix.html"><em>suffix</em></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
<hr class="docutils" />
<p><strong>Mixing, shift, table, tail correction, restart, rRESPA info</strong>:</p>
<p>This pair style does not support the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a>
shift, table, and tail options.</p>
<p>This pair style does not write its information to <a class="reference internal" href="restart.html"><em>binary restart files</em></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"><em>run_style respa</em></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<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
<p>This pair style is part of the MANYBODY package. It is only enabled
if LAMMPS was built with that package (which it is by default). See
the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
<p>This pair style requires the <a class="reference internal" href="newton.html"><em>newton</em></a> setting to be &#8220;on&#8221;
for pair interactions.</p>
<p>The Tersoff/MOD potential files provided with LAMMPS (see the potentials
directory) are parameterized for metal <a class="reference internal" href="units.html"><em>units</em></a>. You can
use the Tersoff/MOD potential with any LAMMPS units, but you would need to
create your own Tersoff/MOD potential file with coefficients listed in the
appropriate units if your simulation doesn&#8217;t use &#8220;metal&#8221; units.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline">¶</a></h2>
<p><a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a></p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<p id="kumagai"><strong>(Kumagai)</strong> T. Kumagai, S. Izumi, S. Hara, S. Sakai,
Comp. Mat. Science, 39, 457 (2007).</p>
<p id="tersoff-1"><strong>(Tersoff_1)</strong> J. Tersoff, Phys Rev B, 37, 6991 (1988).</p>
<p id="tersoff-2"><strong>(Tersoff_2)</strong> J. Tersoff, Phys Rev B, 38, 9902 (1988).</p>
<p id="murty"><strong>(Murty)</strong> M.V.R. Murty, H.A. Atwater, Phys Rev B, 51, 4889 (1995).</p>
<p id="schelling"><strong>(Schelling)</strong> Patrick K. Schelling, Comp. Mat. Science, 44, 274 (2008).</p>
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