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<title>pair_style comb command &mdash; LAMMPS 15 Dec 2015 documentation</title>
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<div class="section" id="pair-style-comb-command">
<span id="index-0"></span><h1>pair_style comb command<a class="headerlink" href="#pair-style-comb-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-comb-omp-command">
<h1>pair_style comb/omp command<a class="headerlink" href="#pair-style-comb-omp-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-comb3-command">
<h1>pair_style comb3 command<a class="headerlink" href="#pair-style-comb3-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 comb
pair_style comb3 keyword
</pre></div>
</div>
<pre class="literal-block">
keyword = <em>polar</em>
<em>polar</em> value = <em>polar_on</em> or <em>polar_off</em> = whether or not to include atomic polarization
</pre>
</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 comb
pair_coeff * * ../potentials/ffield.comb Si
pair_coeff * * ../potentials/ffield.comb Hf Si O
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>pair_style comb3 polar_off
pair_coeff * * ../potentials/ffield.comb3 O Cu N C O
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Style <em>comb</em> computes the second-generation variable charge COMB
(Charge-Optimized Many-Body) potential. Style <em>comb3</em> computes the
third-generation COMB potential. These COMB potentials are described
in <a class="reference internal" href="#comb"><span>(COMB)</span></a> and <a class="reference internal" href="#comb3"><span>(COMB3)</span></a>. Briefly, the total energy
<em>E&lt;sub&gt;T&lt;/sub&gt;</em> of a system of atoms is given by</p>
<img alt="_images/pair_comb1.jpg" class="align-center" src="_images/pair_comb1.jpg" />
<p>where <em>E&lt;sub&gt;i&lt;/sub&gt;&lt;sup&gt;self&lt;/sup&gt;</em> is the self-energy of atom <em>i</em>
(including atomic ionization energies and electron affinities),
<em>E&lt;sub&gt;ij&lt;/sub&gt;&lt;sup&gt;short&lt;/sup&gt;</em> is the bond-order potential between
atoms <em>i</em> and <em>j</em>,
<em>E&lt;sub&gt;ij&lt;/sub&gt;&lt;sup&gt;Coul&lt;/sup&gt;</em> is the Coulomb interactions,
<em>E&lt;sup&gt;polar&lt;/sup&gt;</em> is the polarization term for organic systems
(style <em>comb3</em> only),
<em>E&lt;sup&gt;vdW&lt;/sup&gt;</em> is the van der Waals energy (style <em>comb3</em> only),
<em>E&lt;sup&gt;barr&lt;/sup&gt;</em> is a charge barrier function, and
<em>E&lt;sup&gt;corr&lt;/sup&gt;</em> are angular correction terms.</p>
<p>The COMB potentials (styles <em>comb</em> and <em>comb3</em>) are variable charge
potentials. The equilibrium charge on each atom is calculated by the
electronegativity equalization (QEq) method. See <a class="reference internal" href="pair_smtbq.html#rick"><span>Rick</span></a> for
further details. This is implemented by the <a class="reference internal" href="fix_qeq_comb.html"><em>fix qeq/comb</em></a> command, which should normally be
specified in the input script when running a model with the COMB
potential. The <a class="reference internal" href="fix_qeq_comb.html"><em>fix qeq/comb</em></a> command has options
that determine how often charge equilibration is performed, its
convergence criterion, and which atoms are included in the
calculation.</p>
<p>Only a single pair_coeff command is used with the <em>comb</em> and <em>comb3</em>
styles which specifies the COMB potential file with parameters for all
needed elements. These are mapped to LAMMPS atom types by specifying
N additional arguments after the potential file in the pair_coeff
command, where N is the number of LAMMPS atom types.</p>
<p>For example, if your LAMMPS simulation of a Si/SiO&lt;sub&gt;2&lt;/sub&gt;/
HfO&lt;sub&gt;2&lt;/sub&gt; interface has 4 atom types, and you want the 1st and
last to be Si, the 2nd to be Hf, and the 3rd to be O, and you would
use the following pair_coeff command:</p>
<div class="highlight-python"><div class="highlight"><pre>pair_coeff * * ../potentials/ffield.comb Si Hf O Si
</pre></div>
</div>
<p>The first two arguments must be * * so as to span all LAMMPS atom
types. The first and last Si arguments map LAMMPS atom types 1 and 4
to the Si element in the <em>ffield.comb</em> file. The second Hf argument
maps LAMMPS atom type 2 to the Hf element, and the third O argument
maps LAMMPS atom type 3 to the O element in the potential file. If a
mapping value is specified as NULL, the mapping is not performed.
This can be used when a <em>comb</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>For style <em>comb</em>, the provided potential file <em>ffield.comb</em> contains
all currently-available 2nd generation COMB parameterizations: for Si,
Cu, Hf, Ti, O, their oxides and Zr, Zn and U metals. For style
<em>comb3</em>, the potential file <em>ffield.comb3</em> contains all
currently-available 3rd generation COMB paramterizations: O, Cu, N, C,
H, Ti, Zn and Zr. The status of the optimization of the compounds, for
example Cu&lt;sub&gt;2&lt;/sub&gt;O, TiN and hydrocarbons, are given in the
following table:</p>
<img alt="_images/pair_comb2.jpg" class="align-center" src="_images/pair_comb2.jpg" />
<p>For style <em>comb3</em>, in addition to ffield.comb3, a special parameter
file, <em>lib.comb3</em>, that is exclusively used for C/O/H systems, will be
automatically loaded if carbon atom is detected in LAMMPS input
structure. This file must be in your working directory or in the
directory pointed to by the environment variable LAMMPS_POTENTIALS, as
described on the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command doc page.</p>
<p>Keyword <em>polar</em> indicates whether the force field includes
the atomic polarization. Since the equilibration of the polarization
has not yet been implemented, it can only set polar_off at present.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">You can not use potential file <em>ffield.comb</em> with style <em>comb3</em>,
nor file <em>ffield.comb3</em> with style <em>comb</em>.</p>
</div>
<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>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 as
described above from values in the potential file.</p>
<p>These pair styles does not support the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a>
shift, table, and tail options.</p>
<p>These pair styles do 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, pair_coeff, and <a class="reference internal" href="fix_qeq_comb.html"><em>fix qeq/comb</em></a> commands in an input script that reads a
restart file.</p>
<p>These pair styles 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>These pair styles are 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>These pair styles 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 COMB potentials in the <em>ffield.comb</em> and <em>ffield.comb3</em> 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 COMB potential with any LAMMPS
units, but you would need to create your own COMB 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_style.html"><em>pair_style</em></a>, <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a>,
<a class="reference internal" href="fix_qeq_comb.html"><em>fix_qeq/comb</em></a></p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<p id="comb"><strong>(COMB)</strong> T.-R. Shan, B. D. Devine, T. W. Kemper, S. B. Sinnott, and
S. R. Phillpot, Phys. Rev. B 81, 125328 (2010)</p>
<p id="comb3"><strong>(COMB3)</strong> T. Liang, T.-R. Shan, Y.-T. Cheng, B. D. Devine, M. Noordhoek,
Y. Li, Z. Lu, S. R. Phillpot, and S. B. Sinnott, Mat. Sci. &amp; Eng: R 74,
255-279 (2013).</p>
<p id="rick"><strong>(Rick)</strong> S. W. Rick, S. J. Stuart, B. J. Berne, J Chem Phys 101, 6141
(1994).</p>
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