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<title>pair_style lj/sdk command — LAMMPS 15 May 2015 version documentation</title>
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<div class="section" id="pair-style-lj-sdk-command">
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<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>
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</div>
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<div class="section" id="pair-style-lj-sdk-gpu-command">
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<h1>pair_style lj/sdk/gpu command<a class="headerlink" href="#pair-style-lj-sdk-gpu-command" title="Permalink to this headline">¶</a></h1>
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</div>
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<div class="section" id="pair-style-lj-sdk-kk-command">
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<h1>pair_style lj/sdk/kk command<a class="headerlink" href="#pair-style-lj-sdk-kk-command" title="Permalink to this headline">¶</a></h1>
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</div>
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<div class="section" id="pair-style-lj-sdk-omp-command">
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<h1>pair_style lj/sdk/omp command<a class="headerlink" href="#pair-style-lj-sdk-omp-command" title="Permalink to this headline">¶</a></h1>
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</div>
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<div class="section" id="pair-style-lj-sdk-coul-long-command">
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<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>
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</div>
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<div class="section" id="pair-style-lj-sdk-coul-long-gpu-command">
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<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>
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</div>
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<div class="section" id="pair-style-lj-sdk-coul-long-omp-command">
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<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>
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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 style args
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</pre></div>
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</div>
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<ul class="simple">
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<li>style = <em>lj/sdk</em> or <em>lj/sdk/coul/long</em></li>
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<li>args = list of arguments for a particular style</li>
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</ul>
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<pre class="literal-block">
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<em>lj/sdk</em> args = cutoff
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cutoff = global cutoff for Lennard Jones interactions (distance units)
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<em>lj/sdk/coul/long</em> args = cutoff (cutoff2)
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cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
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cutoff2 = global cutoff for Coulombic (optional) (distance units)
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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 lj/sdk 2.5
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pair_coeff 1 1 lj12_6 1 1.1 2.8
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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 lj/sdk/coul/long 10.0
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pair_style lj/sdk/coul/long 10.0 12.0
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pair_coeff 1 1 lj9_6 100.0 3.5 12.0
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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>The <em>lj/sdk</em> styles compute a 9/6, 12/4, or 12/6 Lennard-Jones potential,
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given by</p>
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<img alt="_images/pair_cmm.jpg" class="align-center" src="_images/pair_cmm.jpg" />
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<p>as required for the SDK Coarse-grained MD parametrization discussed in
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<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>
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<p>Style <em>lj/sdk/coul/long</em> computes the adds Coulombic interactions
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with an additional damping factor applied so it can be used in
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conjunction with the <a class="reference internal" href="kspace_style.html"><em>kspace_style</em></a> command and
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its <em>ewald</em> or <em>pppm</em> or <em>pppm/cg</em> option. The Coulombic cutoff
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specified for this style means that pairwise interactions within
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this distance are computed directly; interactions outside that
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distance are computed in reciprocal space.</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"><em>pair_coeff</em></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"><em>read_data</em></a> or <a class="reference internal" href="read_restart.html"><em>read_restart</em></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>cg_type (lj9_6, lj12_4, or lj12_6)</li>
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<li>epsilon (energy units)</li>
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<li>sigma (distance units)</li>
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<li>cutoff1 (distance units)</li>
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</ul>
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<p>Note that sigma is defined in the LJ formula as the zero-crossing
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distance for the potential, not as the energy minimum. The prefactors
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are chosen so that the potential minimum is at -epsilon.</p>
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<p>The latter 2 coefficients are optional. If not specified, the global
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LJ and Coulombic cutoffs specified in the pair_style command are used.
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If only one cutoff is specified, it is used as the cutoff for both LJ
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and Coulombic interactions for this type pair. If both coefficients
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are specified, they are used as the LJ and Coulombic cutoffs for this
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type pair.</p>
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<p>For <em>lj/sdk/coul/long</em> only the LJ cutoff can be specified since a
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Coulombic cutoff cannot be specified for an individual I,J type pair.
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All type pairs use the same global Coulombic cutoff specified in the
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pair_style command.</p>
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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, and 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 all of the lj/sdk pair styles <em>cannot</em> be mixed,
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since different pairs may have different exponents. So all parameters
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for all pairs have to be specified explicitly through the “pair_coeff”
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command. Defining then in a data file is also not supported, due to
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limitations of that file format.</p>
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<p>All of the lj/sdk pair styles support the
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<a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> shift option for the energy of the
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Lennard-Jones portion of the pair interaction.</p>
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<p>The <em>lj/sdk/coul/long</em> pair styles support the
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<a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> table option since they can tabulate
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the short-range portion of the long-range Coulombic interaction.</p>
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<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
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not need to be specified in an input script that reads a restart file.</p>
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<p>The lj/sdk and lj/cut/coul/long pair styles do not support
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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>
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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>All of the lj/sdk pair styles are part of the USER-CG-CMM package.
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The <em>lj/sdk/coul/long</em> style also requires the KSPACE package to be
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built (which is enabled by default). They are only enabled if LAMMPS
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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>
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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_coeff.html"><em>pair_coeff</em></a>, <a class="reference internal" href="angle_sdk.html"><em>angle_style sdk</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="shinoda"><strong>(Shinoda)</strong> Shinoda, DeVane, Klein, Mol Sim, 33, 27 (2007).</p>
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<p id="devane"><strong>(DeVane)</strong> Shinoda, DeVane, Klein, Soft Matter, 4, 2453-2462 (2008).</p>
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