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<title>pair_style lj/sdk command &mdash; LAMMPS 17 Dec 2015 documentation</title>
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<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
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<div class="section" id="pair-style-lj-sdk-command">
<span id="index-0"></span><h1>pair_style lj/sdk command<a class="headerlink" href="#pair-style-lj-sdk-command" title="Permalink to this headline">¶</a></h1>
</div>
<div class="section" id="pair-style-lj-sdk-gpu-command">
<h1>pair_style lj/sdk/gpu command<a class="headerlink" href="#pair-style-lj-sdk-gpu-command" title="Permalink to this headline">¶</a></h1>
</div>
<div class="section" id="pair-style-lj-sdk-kk-command">
<h1>pair_style lj/sdk/kk command<a class="headerlink" href="#pair-style-lj-sdk-kk-command" title="Permalink to this headline">¶</a></h1>
</div>
<div class="section" id="pair-style-lj-sdk-omp-command">
<h1>pair_style lj/sdk/omp command<a class="headerlink" href="#pair-style-lj-sdk-omp-command" title="Permalink to this headline">¶</a></h1>
</div>
<div class="section" id="pair-style-lj-sdk-coul-long-command">
<h1>pair_style lj/sdk/coul/long command<a class="headerlink" href="#pair-style-lj-sdk-coul-long-command" title="Permalink to this headline">¶</a></h1>
</div>
<div class="section" id="pair-style-lj-sdk-coul-long-gpu-command">
<h1>pair_style lj/sdk/coul/long/gpu command<a class="headerlink" href="#pair-style-lj-sdk-coul-long-gpu-command" title="Permalink to this headline">¶</a></h1>
</div>
<div class="section" id="pair-style-lj-sdk-coul-long-omp-command">
<h1>pair_style lj/sdk/coul/long/omp command<a class="headerlink" href="#pair-style-lj-sdk-coul-long-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 style args
</pre></div>
</div>
<ul class="simple">
<li>style = <em>lj/sdk</em> or <em>lj/sdk/coul/long</em></li>
<li>args = list of arguments for a particular style</li>
</ul>
<pre class="literal-block">
<em>lj/sdk</em> args = cutoff
cutoff = global cutoff for Lennard Jones interactions (distance units)
<em>lj/sdk/coul/long</em> args = cutoff (cutoff2)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
</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 lj/sdk 2.5
pair_coeff 1 1 lj12_6 1 1.1 2.8
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>pair_style lj/sdk/coul/long 10.0
pair_style lj/sdk/coul/long 10.0 12.0
pair_coeff 1 1 lj9_6 100.0 3.5 12.0
</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>lj/sdk</em> styles compute a 9/6, 12/4, or 12/6 Lennard-Jones potential,
given by</p>
<img alt="_images/pair_cmm.jpg" class="align-center" src="_images/pair_cmm.jpg" />
<p>as required for the SDK Coarse-grained MD parametrization discussed in
<a class="reference internal" href="#shinoda"><span>(Shinoda)</span></a> and <a class="reference internal" href="#devane"><span>(DeVane)</span></a>. Rc is the cutoff.</p>
<p>Style <em>lj/sdk/coul/long</em> computes the adds Coulombic interactions
with an additional damping factor applied so it can be used in
conjunction with the <a class="reference internal" href="kspace_style.html"><em>kspace_style</em></a> command and
its <em>ewald</em> or <em>pppm</em> or <em>pppm/cg</em> option. The Coulombic cutoff
specified for this style means that pairwise interactions within
this distance are computed directly; interactions outside that
distance are computed in reciprocal space.</p>
<p>The following coefficients must be defined for each pair of atoms
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, or by mixing as described below:</p>
<ul class="simple">
<li>cg_type (lj9_6, lj12_4, or lj12_6)</li>
<li>epsilon (energy units)</li>
<li>sigma (distance units)</li>
<li>cutoff1 (distance units)</li>
</ul>
<p>Note that sigma is defined in the LJ formula as the zero-crossing
distance for the potential, not as the energy minimum. The prefactors
are chosen so that the potential minimum is at -epsilon.</p>
<p>The latter 2 coefficients are optional. If not specified, the global
LJ and Coulombic cutoffs specified in the pair_style command are used.
If only one cutoff is specified, it is used as the cutoff for both LJ
and Coulombic interactions for this type pair. If both coefficients
are specified, they are used as the LJ and Coulombic cutoffs for this
type pair.</p>
<p>For <em>lj/sdk/coul/long</em> only the LJ cutoff can be specified since a
Coulombic cutoff cannot be specified for an individual I,J type pair.
All type pairs use the same global Coulombic cutoff specified in the
pair_style command.</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, and rRESPA info</strong>:</p>
<p>For atom type pairs I,J and I != J, the epsilon and sigma coefficients
and cutoff distance for all of the lj/sdk pair styles <em>cannot</em> be mixed,
since different pairs may have different exponents. So all parameters
for all pairs have to be specified explicitly through the &#8220;pair_coeff&#8221;
command. Defining then in a data file is also not supported, due to
limitations of that file format.</p>
<p>All of the lj/sdk pair styles support the
<a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> shift option for the energy of the
Lennard-Jones portion of the pair interaction.</p>
<p>The <em>lj/sdk/coul/long</em> pair styles support the
<a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> table option since they can tabulate
the short-range portion of the long-range Coulombic interaction.</p>
<p>All of the lj/sdk 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>The lj/sdk and lj/cut/coul/long pair styles do not support
the use of the <em>inner</em>, <em>middle</em>, and <em>outer</em> keywords of the <a class="reference internal" href="run_style.html"><em>run_style respa</em></a> command.</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>All of the lj/sdk pair styles are part of the USER-CG-CMM package.
The <em>lj/sdk/coul/long</em> style also requires the KSPACE package to be
built (which is enabled by default). They are only enabled if LAMMPS
was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> 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="angle_sdk.html"><em>angle_style sdk</em></a></p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<p id="shinoda"><strong>(Shinoda)</strong> Shinoda, DeVane, Klein, Mol Sim, 33, 27 (2007).</p>
<p id="devane"><strong>(DeVane)</strong> Shinoda, DeVane, Klein, Soft Matter, 4, 2453-2462 (2008).</p>
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