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<li>pair_style list command</li>
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<div class="section" id="pair-style-list-command">
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<span id="index-0"></span><h1>pair_style list command<a class="headerlink" href="#pair-style-list-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 list listfile cutoff keyword
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</pre></div>
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</div>
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<ul class="simple">
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<li>listfile = name of file with list of pairwise interactions</li>
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<li>cutoff = global cutoff (distance units)</li>
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<li>keyword = optional flag <em>nocheck</em> or <em>check</em> (default is <em>check</em>)</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<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 list restraints.txt 200.0
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pair_coeff * *
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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 hybrid/overlay lj/cut 1.1225 list pair_list.txt 300.0
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pair_coeff * * lj/cut 1.0 1.0
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pair_coeff 3* 3* list
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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>list</em> computes interactions between explicitly listed pairs of
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atoms with the option to select functional form and parameters for
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each individual pair. Because the parameters are set in the list
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file, the pair_coeff command has no parameters (but still needs to be
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provided). The <em>check</em> and <em>nocheck</em> keywords enable/disable a test
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that checks whether all listed bonds were present and computed.</p>
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<p>This pair style can be thought of as a hybrid between bonded,
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non-bonded, and restraint interactions. It will typically be used as
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an additional interaction within the <em>hybrid/overlay</em> pair style. It
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currently supports three interaction styles: a 12-6 Lennard-Jones, a
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Morse and a harmonic potential.</p>
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<p>The format of the list file is as follows:</p>
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<ul class="simple">
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<li>one line per pair of atoms</li>
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<li>empty lines will be ignored</li>
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<li>comment text starts with a ‘#’ character</li>
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<li>line syntax: <em>ID1 ID2 style coeffs cutoff</em></li>
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</ul>
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<div class="highlight-python"><div class="highlight"><pre>ID1 = atom ID of first atom
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ID2 = atom ID of second atom
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style = style of interaction
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coeffs = list of coeffs
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cutoff = cutoff for interaction (optional)
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</pre></div>
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</div>
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<p>The cutoff parameter is optional. If not specified, the global cutoff
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is used.</p>
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<p>Here is an example file:</p>
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<div class="highlight-python"><div class="highlight"><pre><span class="c"># this is a comment</span>
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</pre></div>
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</div>
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<div class="highlight-python"><div class="highlight"><pre>15 259 lj126 1.0 1.0 50.0
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15 603 morse 10.0 1.2 2.0 10.0 # and another comment
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18 470 harmonic 50.0 1.2 5.0
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</pre></div>
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</div>
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<p>The style <em>lj126</em> computes pairwise interactions with the formula</p>
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<img alt="_images/pair_lj.jpg" class="align-center" src="_images/pair_lj.jpg" />
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<p>and the coefficients:</p>
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<ul class="simple">
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<li>epsilon (energy units)</li>
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<li>sigma (distance units)</li>
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</ul>
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<p>The style <em>morse</em> computes pairwise interactions with the formula</p>
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<img alt="_images/pair_morse.jpg" class="align-center" src="_images/pair_morse.jpg" />
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<p>and the coefficients:</p>
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<ul class="simple">
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<li>D0 (energy units)</li>
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<li>alpha (1/distance units)</li>
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<li>r0 (distance units)</li>
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</ul>
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<p>The style <em>harmonic</em> computes pairwise interactions with the formula</p>
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<img alt="_images/bond_harmonic.jpg" class="align-center" src="_images/bond_harmonic.jpg" />
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<p>and the coefficients:</p>
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<ul class="simple">
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<li>K (energy units)</li>
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<li>r0 (distance units)</li>
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</ul>
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<p>Note that the usual 1/2 factor is included in K.</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>This pair style does not support mixing since all parameters are
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explicit for each pair.</p>
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<p>The <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> shift option is supported by this
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pair style.</p>
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<p>The <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> table and tail options are not
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relevant for this pair style.</p>
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<p>This pair style does not write its information to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>, so pair_style and pair_coeff commands 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"><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>This pair style does not use a neighbor list and instead identifies
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atoms by their IDs. This has two consequences: 1) The cutoff has to be
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chosen sufficiently large, so that the second atom of a pair has to be
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a ghost atom on the same node on which the first atom is local;
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otherwise the interaction will be skipped. You can use the <em>check</em>
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option to detect, if interactions are missing. 2) Unlike other pair
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styles in LAMMPS, an atom I will not interact with multiple images of
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atom J (assuming the images are within the cutoff distance), but only
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with the nearest image.</p>
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<p>This style is part of the USER-MISC package. It is only enabled if
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LAMMPS is build with that package. See the <span class="xref std std-ref">Making of LAMMPS</span> 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>,
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<a class="reference internal" href="pair_hybrid.html"><em>pair_style hybrid/overlay</em></a>,
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<a class="reference internal" href="pair_lj.html"><em>pair_style lj/cut</em></a>,
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<a class="reference internal" href="pair_morse.html"><em>pair_style morse</em></a>,
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<a class="reference internal" href="bond_harmonic.html"><em>bond_style harmonic</em></a></p>
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<p><strong>Default:</strong> none</p>
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