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<li>pair_style gayberne command</li>
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<div class="section" id="pair-style-gayberne-command">
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<span id="index-0"></span><h1>pair_style gayberne command</h1>
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</div>
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<div class="section" id="pair-style-gayberne-gpu-command">
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<h1>pair_style gayberne/gpu command</h1>
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</div>
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<div class="section" id="pair-style-gayberne-intel-command">
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<h1>pair_style gayberne/intel command</h1>
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</div>
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<div class="section" id="pair-style-gayberne-omp-command">
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<h1>pair_style gayberne/omp 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">pair_style</span> <span class="n">gayberne</span> <span class="n">gamma</span> <span class="n">upsilon</span> <span class="n">mu</span> <span class="n">cutoff</span>
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</pre></div>
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</div>
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<ul class="simple">
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<li>gamma = shift for potential minimum (typically 1)</li>
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<li>upsilon = exponent for eta orientation-dependent energy function</li>
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<li>mu = exponent for chi orientation-dependent energy function</li>
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<li>cutoff = global cutoff for interactions (distance units)</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">pair_style</span> <span class="n">gayberne</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">10.0</span>
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<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">1.0</span> <span class="mf">1.7</span> <span class="mf">1.7</span> <span class="mf">3.4</span> <span class="mf">3.4</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">1.0</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>The <em>gayberne</em> styles compute a Gay-Berne anisotropic LJ interaction
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<a class="reference internal" href="#berardi"><span class="std std-ref">(Berardi)</span></a> between pairs of ellipsoidal particles or an
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ellipsoidal and spherical particle via the formulas</p>
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<img alt="_images/pair_gayberne.jpg" class="align-center" src="_images/pair_gayberne.jpg" />
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<p>where A1 and A2 are the transformation matrices from the simulation
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box frame to the body frame and r12 is the center to center vector
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between the particles. Ur controls the shifted distance dependent
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interaction based on the distance of closest approach of the two
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particles (h12) and the user-specified shift parameter gamma. When
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both particles are spherical, the formula reduces to the usual
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Lennard-Jones interaction (see details below for when Gay-Berne treats
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a particle as “spherical”).</p>
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<p>For large uniform molecules it has been shown that the energy
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parameters are approximately representable in terms of local contact
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curvatures <a class="reference internal" href="pair_resquared.html#everaers"><span class="std std-ref">(Everaers)</span></a>:</p>
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<img alt="_images/pair_gayberne2.jpg" class="align-center" src="_images/pair_gayberne2.jpg" />
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<p>The variable names utilized as potential parameters are for the most
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part taken from <a class="reference internal" href="pair_resquared.html#everaers"><span class="std std-ref">(Everaers)</span></a> in order to be consistent with
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the <a class="reference internal" href="pair_resquared.html"><span class="doc">RE-squared pair potential</span></a>. Details on the
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upsilon and mu parameters are given
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<a class="reference external" href="PDF/pair_resquared_extra.pdf">here</a>.</p>
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<p>More details of the Gay-Berne formulation are given in the references
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listed below and in <a class="reference external" href="PDF/pair_gayberne_extra.pdf">this supplementary document</a>.</p>
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<p>Use of this pair style requires the NVE, NVT, or NPT fixes with the
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<em>asphere</em> extension (e.g. <a class="reference internal" href="fix_nve_asphere.html"><span class="doc">fix nve/asphere</span></a>) in
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order to integrate particle rotation. Additionally, <a class="reference internal" href="atom_style.html"><span class="doc">atom_style ellipsoid</span></a> should be used since it defines the
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rotational state and the size and shape of each ellipsoidal particle.</p>
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<p>The following coefficients must be defined for each pair of atoms
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types via the <a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a> command as in the examples
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above, or in the data file or restart files read by the
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<a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> or <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a>
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commands, or by mixing as described below:</p>
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<ul class="simple">
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<li>epsilon = well depth (energy units)</li>
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<li>sigma = minimum effective particle radii (distance units)</li>
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<li>epsilon_i_a = relative well depth of type I for side-to-side interactions</li>
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<li>epsilon_i_b = relative well depth of type I for face-to-face interactions</li>
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<li>epsilon_i_c = relative well depth of type I for end-to-end interactions</li>
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<li>epsilon_j_a = relative well depth of type J for side-to-side interactions</li>
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<li>epsilon_j_b = relative well depth of type J for face-to-face interactions</li>
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<li>epsilon_j_c = relative well depth of type J for end-to-end interactions</li>
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<li>cutoff (distance units)</li>
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</ul>
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<p>The last coefficient is optional. If not specified, the global
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cutoff specified in the pair_style command is used.</p>
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<p>It is typical with the Gay-Berne potential to define <em>sigma</em> as the
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minimum of the 3 shape diameters of the particles involved in an I,I
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interaction, though this is not required. Note that this is a
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different meaning for <em>sigma</em> than the <a class="reference internal" href="pair_resquared.html"><span class="doc">pair_style resquared</span></a> potential uses.</p>
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<p>The epsilon_i and epsilon_j coefficients are actually defined for atom
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types, not for pairs of atom types. Thus, in a series of pair_coeff
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commands, they only need to be specified once for each atom type.</p>
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<p>Specifically, if any of epsilon_i_a, epsilon_i_b, epsilon_i_c are
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non-zero, the three values are assigned to atom type I. If all the
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epsilon_i values are zero, they are ignored. If any of epsilon_j_a,
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epsilon_j_b, epsilon_j_c are non-zero, the three values are assigned
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to atom type J. If all three epsilon_j values are zero, they are
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ignored. Thus the typical way to define the epsilon_i and epsilon_j
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coefficients is to list their values in “pair_coeff I J” commands when
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I = J, but set them to 0.0 when I != J. If you do list them when I !=
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J, you should insure they are consistent with their values in other
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pair_coeff commands, since only the last setting will be in effect.</p>
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<p>Note that if this potential is being used as a sub-style of
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<a class="reference internal" href="pair_hybrid.html"><span class="doc">pair_style hybrid</span></a>, and there is no “pair_coeff I I”
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setting made for Gay-Berne for a particular type I (because I-I
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interactions are computed by another hybrid pair potential), then you
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still need to insure the epsilon a,b,c coefficients are assigned to
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that type. e.g. in a “pair_coeff I J” command.</p>
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<div class="admonition note">
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<p class="first admonition-title">Note</p>
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<p class="last">If the epsilon a = b = c for an atom type, and if the shape of
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the particle itself is spherical, meaning its 3 shape parameters are
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all the same, then the particle is treated as an LJ sphere by the
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Gay-Berne potential. This is significant because if two LJ spheres
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interact, then the simple Lennard-Jones formula is used to compute
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their interaction energy/force using the specified epsilon and sigma
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as the standard LJ parameters. This is much cheaper to compute than
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the full Gay-Berne formula. To treat the particle as a LJ sphere with
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sigma = D, you should normally set epsilon a = b = c = 1.0, set the
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pair_coeff sigma = D, and also set the 3 shape parameters for the
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particle to D. The one exception is that if the 3 shape parameters
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are set to 0.0, which is a valid way in LAMMPS to specify a point
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particle, then the Gay-Berne potential will treat that as shape
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parameters of 1.0 (i.e. a LJ particle with sigma = 1), since it
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requires finite-size particles. In this case you should still set the
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pair_coeff sigma to 1.0 as well.</p>
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</div>
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<hr class="docutils" />
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<p>Styles with a <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"><span class="doc">Section_accelerate</span></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 GPU, USER-INTEL, KOKKOS,
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USER-OMP and OPT packages, respectively. They are only enabled if
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LAMMPS was built with those packages. 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>
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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 class="std std-ref">-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"><span class="doc">suffix</span></a> command in your input script.</p>
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<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></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, the epsilon and sigma coefficients
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and cutoff distance for this pair style can be mixed. The default mix
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value is <em>geometric</em>. See the “pair_modify” command for details.</p>
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<p>This pair styles supports the <a class="reference internal" href="pair_modify.html"><span class="doc">pair_modify</span></a> shift
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option for the energy of the Lennard-Jones portion of the pair
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interaction, but only for sphere-sphere interactions. There is no
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shifting performed for ellipsoidal interactions due to the anisotropic
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dependence of the interaction.</p>
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<p>The <a class="reference internal" href="pair_modify.html"><span class="doc">pair_modify</span></a> table option is not relevant
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for this pair style.</p>
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<p>This pair style does not support the <a class="reference internal" href="pair_modify.html"><span class="doc">pair_modify</span></a>
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tail option for adding long-range tail corrections to energy and
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pressure.</p>
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<p>This pair style writes its information to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>, so pair_style and pair_coeff commands do not need
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to be specified in an input script that reads a restart file.</p>
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<p>This pair style can only be used via the <em>pair</em> keyword of the
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<a class="reference internal" href="run_style.html"><span class="doc">run_style respa</span></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</h2>
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<p>The <em>gayberne</em> style is part of the ASPHERE package. It is only
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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>
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<p>These pair style require that atoms store torque and a quaternion to
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represent their orientation, as defined by the
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<a class="reference internal" href="atom_style.html"><span class="doc">atom_style</span></a>. It also require they store a per-type
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<span class="xref doc">shape</span>. The particles cannot store a per-particle
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diameter.</p>
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<p>This pair style requires that atoms be ellipsoids as defined by the
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<a class="reference internal" href="atom_style.html"><span class="doc">atom_style ellipsoid</span></a> command.</p>
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<p>Particles acted on by the potential can be finite-size aspherical or
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spherical particles, or point particles. Spherical particles have all
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3 of their shape parameters equal to each other. Point particles have
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all 3 of their shape parameters equal to 0.0.</p>
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<p>The Gay-Berne potential does not become isotropic as r increases
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<a class="reference internal" href="pair_resquared.html#everaers"><span class="std std-ref">(Everaers)</span></a>. The distance-of-closest-approach
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approximation used by LAMMPS becomes less accurate when high-aspect
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ratio ellipsoids are used.</p>
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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="pair_coeff.html"><span class="doc">pair_coeff</span></a>, <a class="reference internal" href="fix_nve_asphere.html"><span class="doc">fix nve/asphere</span></a>,
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<a class="reference internal" href="compute_temp_asphere.html"><span class="doc">compute temp/asphere</span></a>, <a class="reference internal" href="pair_resquared.html"><span class="doc">pair_style resquared</span></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="everaers"><strong>(Everaers)</strong> Everaers and Ejtehadi, Phys Rev E, 67, 041710 (2003).</p>
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<p id="berardi"><strong>(Berardi)</strong> Berardi, Fava, Zannoni, Chem Phys Lett, 297, 8-14 (1998).
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Berardi, Muccioli, Zannoni, J Chem Phys, 128, 024905 (2008).</p>
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<p id="perram"><strong>(Perram)</strong> Perram and Rasmussen, Phys Rev E, 54, 6565-6572 (1996).</p>
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<p id="allen"><strong>(Allen)</strong> Allen and Germano, Mol Phys 104, 3225-3235 (2006).</p>
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