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<div class="section" id="pair-style-gauss-command">
<span id="index-0"></span><h1>pair_style gauss command<a class="headerlink" href="#pair-style-gauss-command" title="Permalink to this headline">¶</a></h1>
</div>
<div class="section" id="pair-style-gauss-gpu-command">
<h1>pair_style gauss/gpu command<a class="headerlink" href="#pair-style-gauss-gpu-command" title="Permalink to this headline">¶</a></h1>
</div>
<div class="section" id="pair-style-gauss-omp-command">
<h1>pair_style gauss/omp command<a class="headerlink" href="#pair-style-gauss-omp-command" title="Permalink to this headline">¶</a></h1>
</div>
<div class="section" id="pair-style-gauss-cut-command">
<h1>pair_style gauss/cut command<a class="headerlink" href="#pair-style-gauss-cut-command" title="Permalink to this headline">¶</a></h1>
</div>
<div class="section" id="pair-style-gauss-cut-omp-command">
<h1>pair_style gauss/cut/omp command<a class="headerlink" href="#pair-style-gauss-cut-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 gauss cutoff
pair_style gauss/cut cutoff
</pre></div>
</div>
<ul class="simple">
<li>cutoff = global cutoff for Gauss interactions (distance units)</li>
</ul>
</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 gauss 12.0
pair_coeff * * 1.0 0.9
pair_coeff 1 4 1.0 0.9 10.0
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>pair_style gauss/cut 3.5
pair_coeff 1 4 0.2805 1.45 0.112
</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>gauss</em> computes a tethering potential of the form</p>
<img alt="_images/pair_gauss.jpg" class="align-center" src="_images/pair_gauss.jpg" />
<p>between an atom and its corresponding tether site which will typically
be a frozen atom in the simulation. Rc is the cutoff.</p>
<p>The following coefficients must be defined for each pair of atom types
via the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command as in the examples above,
or in the data file or restart files read by the
<a class="reference internal" href="read_data.html"><em>read_data</em></a> or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a>
commands:</p>
<ul class="simple">
<li>A (energy units)</li>
<li>B (1/distance^2 units)</li>
<li>cutoff (distance units)</li>
</ul>
<p>The last coefficient is optional. If not specified, the global cutoff
is used.</p>
<p>Style <em>gauss/cut</em> computes a generalized Gaussian interaction potential
between pairs of particles:</p>
<img alt="_images/pair_gauss_cut.jpg" class="align-center" src="_images/pair_gauss_cut.jpg" />
<p>where H determines together with the standard deviation sigma_h the
peak height of the Gaussian function, and r_mh the peak position.
Examples of the use of the Gaussian potentials include implicit
solvent simulations of salt ions <a class="reference internal" href="#lenart"><span>(Lenart)</span></a> and of surfactants
<a class="reference internal" href="#jusufi"><span>(Jusufi)</span></a>. In these instances the Gaussian potential mimics
the hydration barrier between a pair of particles. The hydration
barrier is located at r_mh and has a width of sigma_h. The prefactor
determines the hight of the potential barrier.</p>
<p>The following coefficients must be defined for each pair of atom types
via the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command as in the example above,
or in the data file or restart files read by the
<a class="reference internal" href="read_data.html"><em>read_data</em></a> or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a>
commands:</p>
<ul class="simple">
<li>H (energy * distance units)</li>
<li>r_mh (distance units)</li>
<li>sigma_h (distance units)</li>
</ul>
<p>The global cutoff (r_c) specified in the pair_style command is used.</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 &#8220;-suffix command-line
switch7_Section_start.html#start_6 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>These pair styles do not support mixing. Thus, coefficients for all
I,J pairs must be specified explicitly.</p>
<p>The <em>gauss</em> style does not support the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a>
shift option. There is no effect due to the Gaussian well beyond the
cutoff; hence reasonable cutoffs need to be specified.</p>
<p>The <em>gauss/cut</em> style supports the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> shift
option for the energy of the Gauss-potential portion of the pair
interaction.</p>
<p>The <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> table and tail options are not
relevant for these pair styles.</p>
<p>These pair styles write their information to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>, so pair_style and pair_coeff commands do not need
to be specified 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. They do not support the
<em>inner</em>, <em>middle</em>, <em>outer</em> keywords.</p>
<p>The <em>gauss</em> pair style tallies an &#8220;occupancy&#8221; count of how many Gaussian-well
sites have an atom within the distance at which the force is a maximum
= sqrt(0.5/b). This quantity can be accessed via the <a class="reference internal" href="compute_pair.html"><em>compute pair</em></a> command as a vector of values of length 1.</p>
<p>To print this quantity to the log file (with a descriptive column
heading) the following commands could be included in an input script:</p>
<div class="highlight-python"><div class="highlight"><pre>compute gauss all pair gauss
variable occ equal c_gauss[1]
thermo_style custom step temp epair v_occ
</pre></div>
</div>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
<p>The <em>gauss/cut</em> style is part of the &#8220;user-misc&#8221; package. It is only
enabled if LAMMPS is build with that package. See the <span class="xref std std-ref">Making of LAMMPS</span> section for more info.</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>,
<a class="reference internal" href="pair_coul_diel.html"><em>pair_style coul/diel</em></a></p>
<p><strong>Default:</strong> none</p>
<p id="lenart"><strong>(Lenart)</strong> Lenart , Jusufi, and Panagiotopoulos, J Chem Phys, 126,
044509 (2007).</p>
<p id="jusufi"><strong>(Jusufi)</strong> Jusufi, Hynninen, and Panagiotopoulos, J Phys Chem B, 112,
13783 (2008).</p>
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