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<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
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<li>create_bonds command</li>
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<div class="section" id="create-bonds-command">
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<span id="index-0"></span><h1>create_bonds command<a class="headerlink" href="#create-bonds-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>create_bonds group-ID group2-ID btype rmin rmax
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</pre></div>
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</div>
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<ul class="simple">
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<li>group-ID = ID of first group</li>
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<li>group2-ID = ID of second group, bonds will be between atoms in the 2 groups</li>
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<li>btype = bond type of created bonds</li>
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<li>rmin = minimum distance between pair of atoms to bond together</li>
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<li>rmax = minimum distance between pair of atoms to bond together</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>create_bonds all all 1 1.0 1.2
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create_bonds surf solvent 3 2.0 2.4
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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>Create bonds between pairs of atoms that meet specified distance
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criteria. The bond interactions can then be computed during a
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simulation by the bond potential defined by the
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<a class="reference internal" href="bond_style.html"><em>bond_style</em></a> and <a class="reference internal" href="bond_coeff.html"><em>bond_coeff</em></a>
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commands. This command is useful for adding bonds to a system,
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e.g. between nearest neighbors in a lattice of atoms, without having
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to enumerate all the bonds in the data file read by the
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<a class="reference internal" href="read_data.html"><em>read_data</em></a> command.</p>
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<p>Note that the flexibility of this command is limited. It can be used
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several times to create different types of bond at different
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distances. But it cannot typically create all the bonds that would
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normally be defined in a complex system of molecules. Also note that
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this command does not add any 3-body or 4-body interactions which,
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depending on your model, may be induced by added bonds,
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e.g. <a class="reference internal" href="angle_style.html"><em>angle</em></a>, <a class="reference internal" href="dihedral_style.html"><em>dihedral</em></a>, or
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<a class="reference internal" href="improper_style.html"><em>improper</em></a> interactions.</p>
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<p>All created bonds will be between pairs of atoms I,J where I is in one
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of the two specified groups, and J is in the other. The two groups
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can be the same, e.g. group “all”. The created bonds will be of bond
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type <em>btype</em>, where <em>btype</em> must be a value between 1 and the number
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of bond types defined. This maximum value is set by the “bond types”
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field in the header of the data file read by the
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<a class="reference internal" href="read_data.html"><em>read_data</em></a> command, or via the optional “bond/types”
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argument of the <a class="reference internal" href="create_box.html"><em>create_box</em></a> command.</p>
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<p>For a bond to be created, an I,J pair of atoms must be a distance D
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apart such that <em>rmin</em> <= D <= <em>rmax</em>.</p>
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<p>The following settings must have been made in an input
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script before this command is used:</p>
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<ul class="simple">
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<li>special_bonds weight for 1-2 interactions must be 0.0</li>
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<li>a <a class="reference internal" href="pair_style.html"><em>pair_style</em></a> must be defined</li>
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<li>no <a class="reference internal" href="kspace_style.html"><em>kspace_style</em></a> defined</li>
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<li>minimum <a class="reference internal" href="pair_style.html"><em>pair_style</em></a> cutoff + <a class="reference internal" href="neighbor.html"><em>neighbor</em></a> skin >= <em>rmax</em></li>
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</ul>
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<p>These settings are required so that a neighbor list can be created to
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search for nearby atoms. Pairs of atoms that are already bonded
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cannot appear in the neighbor list, to avoid creation of duplicate
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bonds. The neighbor list for all atom type pairs must also extend to
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a distance that encompasses the <em>rmax</em> for new bonds to create.</p>
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<p>An additional requirement is that your system must be ready to perform
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a simulation. This means, for example, that all
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<a class="reference internal" href="pair_style.html"><em>pair_style</em></a> coefficients be set via the
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<a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command. A <a class="reference internal" href="bond_style.html"><em>bond_style</em></a>
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command and all bond coefficients must also be set, even if no bonds
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exist before this command is invoked. This is because the building of
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neighbor list requires initialization and setup of a simulation,
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similar to what a <a class="reference internal" href="run.html"><em>run</em></a> command would require.</p>
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<p>Note that you can change any of these settings after this command
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executes, e.g. if you wish to use long-range Coulombic interactions
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via the <a class="reference internal" href="kspace_style.html"><em>kspace_style</em></a> command for your subsequent
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simulation.</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 system has no bonds to begin with, or if more bonds per
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atom are being added than currently exist, then you must insure that
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the number of bond types and the maximum number of bonds per atom are
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set to large enough values. Otherwise an error may occur when too
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many bonds are added to an atom. If the <a class="reference internal" href="read_data.html"><em>read_data</em></a>
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command is used to define the system, these 2 parameters can be set
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via the “bond types” and “extra bond per atom” fields in the header
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section of the data file. If the <a class="reference internal" href="create_box.html"><em>create_box</em></a> command
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is used to define the system, these 2 parameters can be set via its
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optional “bond/types” and “extra/bond/per/atom” arguments. See the
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doc pages for the 2 commands for details.</p>
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</div>
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</div>
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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 command cannot be used with molecular systems defined using
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molecule template files via the <a class="reference internal" href="molecule.html"><em>molecule</em></a> and
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<a class="reference internal" href="atom_style.html"><em>atom_style template</em></a> commands.</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="create_atoms.html"><em>create_atoms</em></a>, <a class="reference internal" href="delete_bonds.html"><em>delete_bonds</em></a></p>
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<p><strong>Default:</strong> none</p>
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