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<li class="toctree-l3"><a class="reference internal" href="Howto_mdi.html">8.1.7. Using LAMMPS with the MDI library for code coupling</a></li>
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<li class="breadcrumb-item active"><span class="section-number">8.1.8. </span>Broken Bonds</li>
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<p><span class="math notranslate nohighlight">\(\renewcommand{\AA}{\text{Å}}\)</span></p>
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<section id="broken-bonds">
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<h1><span class="section-number">8.1.8. </span>Broken Bonds<a class="headerlink" href="#broken-bonds" title="Link to this heading"></a></h1>
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<p>Typically, molecular bond interactions persist for the duration of a
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simulation in LAMMPS. However, some commands break bonds dynamically,
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including the following:</p>
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<ul class="simple">
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<li><p><a class="reference internal" href="bond_quartic.html"><span class="doc">bond_style quartic</span></a></p></li>
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<li><p><a class="reference internal" href="fix_bond_break.html"><span class="doc">fix bond/break</span></a></p></li>
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<li><p><a class="reference internal" href="fix_bond_react.html"><span class="doc">fix bond/react</span></a></p></li>
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<li><p><a class="reference internal" href="Howto_bpm.html"><span class="doc">BPM package</span></a> bond styles</p></li>
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</ul>
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<p>A bond can break if it is stretched beyond a user-defined threshold or
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more generally if other criteria are met.</p>
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<p>For the quartic bond style, when a bond is broken its bond type is set
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to 0 to effectively break it and pairwise forces between the two atoms
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in the broken bond are “turned on”. Angles, dihedrals, etc cannot be
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defined for a system when <a class="reference internal" href="bond_quartic.html"><span class="doc">bond_style quartic</span></a> is
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used.</p>
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<p>Similarly, bond styles in the BPM package are also incompatible with
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angles, dihedrals, etc. and when a bond breaks its type is set to zero.
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However, in the BPM package one can either turn off all pair interactions
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between bonded particles or leave them on, overlaying pair forces on
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top of bond forces. To remove pair forces, the special bond list is
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dynamically updated. More details can be found on the <a class="reference internal" href="Howto_bpm.html"><span class="doc">Howto BPM</span></a> page.</p>
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<p>The <a class="reference internal" href="fix_bond_break.html"><span class="doc">fix bond/break</span></a> and <a class="reference internal" href="fix_bond_react.html"><span class="doc">fix bond/react</span></a> commands allow breaking of bonds within a molecular
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topology with may also define angles, dihedrals, etc. These commands
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update internal topology data structures to remove broken bonds, as
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well as the appropriate angle, dihedral, etc interactions which
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include the bond. They also trigger a rebuild of the neighbor list
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when this occurs, to turn on the appropriate pairwise forces.</p>
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<p>Note that when bonds are dumped to a file via the <a class="reference internal" href="dump.html"><span class="doc">dump local</span></a> command, bonds with type 0 are not included.</p>
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<p>The <a class="reference internal" href="delete_bonds.html"><span class="doc">delete_bonds</span></a> command can be used to query
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the status of broken bonds with type = 0 or permanently delete them,
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e.g.:</p>
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<div class="highlight-LAMMPS notranslate"><div class="highlight"><pre><span></span><span class="k">delete_bonds </span><span class="nv nv-Identifier">all</span><span class="w"> </span><span class="n">stats</span>
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<span class="k">delete_bonds </span><span class="nv nv-Identifier">all</span><span class="w"> </span><span class="n">bond</span><span class="w"> </span><span class="m">0</span><span class="w"> </span><span class="n">remove</span>
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</pre></div>
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</div>
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<p>The compute <a class="reference internal" href="compute_count_type.html"><span class="doc">count/type</span></a> command tallies the
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current number of bonds (or angles, etc) for each bond (angle, etc)
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type. It also tallies broken bonds with type = 0.</p>
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<p>The compute <a class="reference internal" href="compute_nbond_atom.html"><span class="doc">nbond/atom</span></a> command tallies the
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current number of bonds each atom is part of, excluding broken bonds
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with type = 0.</p>
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