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<title>pair_style comb command — LAMMPS 15 May 2015 version documentation</title>
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<div class="section" id="pair-style-comb-command">
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<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>
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</div>
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<div class="section" id="pair-style-comb-omp-command">
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<h1>pair_style comb/omp command<a class="headerlink" href="#pair-style-comb-omp-command" title="Permalink to this headline">¶</a></h1>
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</div>
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<div class="section" id="pair-style-comb3-command">
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<h1>pair_style comb3 command<a class="headerlink" href="#pair-style-comb3-command" title="Permalink to this headline">¶</a></h1>
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<div class="section" id="syntax">
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<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline">¶</a></h2>
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<div class="highlight-python"><div class="highlight"><pre>pair_style comb
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pair_style comb3 keyword
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</pre></div>
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</div>
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<pre class="literal-block">
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keyword = <em>polar</em>
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<em>polar</em> value = <em>polar_on</em> or <em>polar_off</em> = whether or not to include atomic polarization
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</pre>
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</div>
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<div class="section" id="examples">
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<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h2>
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<div class="highlight-python"><div class="highlight"><pre>pair_style comb
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pair_coeff * * ../potentials/ffield.comb Si
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pair_coeff * * ../potentials/ffield.comb Hf Si O
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</pre></div>
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</div>
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<div class="highlight-python"><div class="highlight"><pre>pair_style comb3 polar_off
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pair_coeff * * ../potentials/ffield.comb3 O Cu N C O
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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<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
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<p>Style <em>comb</em> computes the second-generation variable charge COMB
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(Charge-Optimized Many-Body) potential. Style <em>comb3</em> computes the
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third-generation COMB potential. These COMB potentials are described
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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
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<em>E<sub>T</sub></em> of a system of atoms is given by</p>
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<img alt="_images/pair_comb1.jpg" class="align-center" src="_images/pair_comb1.jpg" />
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<p>where <em>E<sub>i</sub><sup>self</sup></em> is the self-energy of atom <em>i</em>
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(including atomic ionization energies and electron affinities),
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<em>E<sub>ij</sub><sup>short</sup></em> is the bond-order potential between
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atoms <em>i</em> and <em>j</em>,
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<em>E<sub>ij</sub><sup>Coul</sup></em> is the Coulomb interactions,
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<em>E<sup>polar</sup></em> is the polarization term for organic systems
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(style <em>comb3</em> only),
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<em>E<sup>vdW</sup></em> is the van der Waals energy (style <em>comb3</em> only),
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<em>E<sup>barr</sup></em> is a charge barrier function, and
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<em>E<sup>corr</sup></em> are angular correction terms.</p>
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<p>The COMB potentials (styles <em>comb</em> and <em>comb3</em>) are variable charge
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potentials. The equilibrium charge on each atom is calculated by the
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electronegativity equalization (QEq) method. See <a class="reference internal" href="#rick"><span>Rick</span></a> for
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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
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specified in the input script when running a model with the COMB
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potential. The <a class="reference internal" href="fix_qeq_comb.html"><em>fix qeq/comb</em></a> command has options
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that determine how often charge equilibration is performed, its
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convergence criterion, and which atoms are included in the
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calculation.</p>
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<p>Only a single pair_coeff command is used with the <em>comb</em> and <em>comb3</em>
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styles which specifies the COMB potential file with parameters for all
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needed elements. These are mapped to LAMMPS atom types by specifying
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N additional arguments after the potential file in the pair_coeff
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command, where N is the number of LAMMPS atom types.</p>
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<p>For example, if your LAMMPS simulation of a Si/SiO<sub>2</sub>/
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HfO<sub>2</sub> interface has 4 atom types, and you want the 1st and
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last to be Si, the 2nd to be Hf, and the 3rd to be O, and you would
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use the following pair_coeff command:</p>
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<div class="highlight-python"><div class="highlight"><pre>pair_coeff * * ../potentials/ffield.comb Si Hf O Si
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</pre></div>
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</div>
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<p>The first two arguments must be * * so as to span all LAMMPS atom
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types. The first and last Si arguments map LAMMPS atom types 1 and 4
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to the Si element in the <em>ffield.comb</em> file. The second Hf argument
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maps LAMMPS atom type 2 to the Hf element, and the third O argument
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maps LAMMPS atom type 3 to the O element in the potential file. If a
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mapping value is specified as NULL, the mapping is not performed.
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This can be used when a <em>comb</em> potential is used as part of the
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<em>hybrid</em> pair style. The NULL values are placeholders for atom types
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that will be used with other potentials.</p>
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<p>For style <em>comb</em>, the provided potential file <em>ffield.comb</em> contains
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all currently-available 2nd generation COMB parameterizations: for Si,
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Cu, Hf, Ti, O, their oxides and Zr, Zn and U metals. For style
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<em>comb3</em>, the potential file <em>ffield.comb3</em> contains all
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currently-available 3rd generation COMB paramterizations: O, Cu, N, C,
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H, Ti, Zn and Zr. The status of the optimization of the compounds, for
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example Cu<sub>2</sub>O, TiN and hydrocarbons, are given in the
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following table:</p>
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<img alt="_images/pair_comb2.jpg" class="align-center" src="_images/pair_comb2.jpg" />
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<p>For style <em>comb3</em>, in addition to ffield.comb3, a special parameter
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file, <em>lib.comb3</em>, that is exclusively used for C/O/H systems, will be
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automatically loaded if carbon atom is detected in LAMMPS input
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structure. This file must be in your working directory or in the
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directory pointed to by the environment variable LAMMPS_POTENTIALS, as
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described on the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command doc page.</p>
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<p>Keyword <em>polar</em> indicates whether the force field includes
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the atomic polarization. Since the equilibration of the polarization
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has not yet been implemented, it can only set polar_off at present.</p>
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<div class="admonition warning">
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<p class="first admonition-title">Warning</p>
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<p class="last">You can not use potential file <em>ffield.comb</em> with
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style <em>comb3</em>, nor file <em>ffield.comb3</em> with style <em>comb</em>.</p>
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</div>
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<hr class="docutils" />
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<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
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functionally the same as the corresponding style without the suffix.
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They have been optimized to run faster, depending on your available
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hardware, as discussed in <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a>
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of the manual. The accelerated styles take the same arguments and
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should produce the same results, except for round-off and precision
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issues.</p>
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<p>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
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KOKKOS, USER-OMP and OPT packages, respectively. They are only
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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>
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<p>You can specify the accelerated styles explicitly in your input script
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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
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use the <a class="reference internal" href="suffix.html"><em>suffix</em></a> command in your input script.</p>
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<p>See <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a> of the manual for
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more instructions on how to use the accelerated styles effectively.</p>
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<hr class="docutils" />
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<p><strong>Mixing, shift, table, tail correction, restart, rRESPA info</strong>:</p>
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<p>For atom type pairs I,J and I != J, where types I and J correspond to
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two different element types, mixing is performed by LAMMPS as
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described above from values in the potential file.</p>
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<p>These pair styles does not support the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a>
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shift, table, and tail options.</p>
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<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
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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
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restart file.</p>
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<p>These pair styles can only be used via the <em>pair</em> keyword of the
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<a class="reference internal" href="run_style.html"><em>run_style respa</em></a> command. It does not support the
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<em>inner</em>, <em>middle</em>, <em>outer</em> keywords.</p>
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</div>
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<hr class="docutils" />
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<div class="section" id="restrictions">
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<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
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<p>These pair styles are part of the MANYBODY package. It is only enabled
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if LAMMPS was built with that package (which it is by default). See
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the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
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<p>These pair styles requires the <a class="reference internal" href="newton.html"><em>newton</em></a> setting to be “on”
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for pair interactions.</p>
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<p>The COMB potentials in the <em>ffield.comb</em> and <em>ffield.comb3</em> files provided
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with LAMMPS (see the potentials directory) are parameterized for metal
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<a class="reference internal" href="units.html"><em>units</em></a>. You can use the COMB potential with any LAMMPS
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units, but you would need to create your own COMB potential file with
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coefficients listed in the appropriate units if your simulation
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doesn’t use “metal” units.</p>
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</div>
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<div class="section" id="related-commands">
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<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline">¶</a></h2>
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<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>,
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<a class="reference internal" href="fix_qeq_comb.html"><em>fix_qeq/comb</em></a></p>
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<p><strong>Default:</strong> none</p>
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<hr class="docutils" />
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<p id="comb"><strong>(COMB)</strong> T.-R. Shan, B. D. Devine, T. W. Kemper, S. B. Sinnott, and
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S. R. Phillpot, Phys. Rev. B 81, 125328 (2010)</p>
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<p id="comb3"><strong>(COMB3)</strong> T. Liang, T.-R. Shan, Y.-T. Cheng, B. D. Devine, M. Noordhoek,
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Y. Li, Z. Lu, S. R. Phillpot, and S. B. Sinnott, Mat. Sci. & Eng: R 74,
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255-279 (2013).</p>
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<p id="rick"><strong>(Rick)</strong> S. W. Rick, S. J. Stuart, B. J. Berne, J Chem Phys 101, 6141
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(1994).</p>
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