<p>Note that even if your simulation starts with no bonds, you must
define a <aclass="reference internal"href="bond_style.html"><spanclass="doc">bond_style</span></a> and use the
<aclass="reference internal"href="bond_coeff.html"><spanclass="doc">bond_coeff</span></a> command to specify coefficients for the
<em>bondtype</em>. Similarly, if new atom types are specified by the
<em>iparam</em> or <em>jparam</em> keywords, they must be within the range of atom
types allowed by the simulation and pairwise coefficients must be
specified for the new types.</p>
<p>Computationally, each timestep this fix operates, it loops over
neighbor lists and computes distances between pairs of atoms in the
list. It also communicates between neighboring processors to
coordinate which bonds are created. Moreover, if any bonds are
created, neighbor lists must be immediately updated on the same
timestep. This is to insure that any pairwise interactions that
should be turned “off” due to a bond creation, because they are now
excluded by the presence of the bond and the settings of the
<aclass="reference internal"href="special_bonds.html"><spanclass="doc">special_bonds</span></a> command, will be immediately
recognized. All of these operations increase the cost of a timestep.
Thus you should be cautious about invoking this fix too frequently.</p>
<p>You can dump out snapshots of the current bond topology via the <aclass="reference internal"href="dump.html"><spanclass="doc">dump local</span></a> command.</p>
<divclass="admonition note">
<pclass="first admonition-title">Note</p>
<pclass="last">Creating a bond typically alters the energy of a system. You
should be careful not to choose bond creation criteria that induce a
dramatic change in energy. For example, if you define a very stiff
harmonic bond and create it when 2 atoms are separated by a distance
far from the equilibribum bond length, then the 2 atoms will oscillate
dramatically when the bond is formed. More generally, you may need to
thermostat your system to compensate for energy changes resulting from
created bonds (and angles, dihedrals, impropers).</p>
</div>
<hrclass="docutils"/>
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
<p>No information about this fix is written to <aclass="reference internal"href="restart.html"><spanclass="doc">binary restart files</span></a>. None of the <aclass="reference internal"href="fix_modify.html"><spanclass="doc">fix_modify</span></a> options
are relevant to this fix.</p>
<p>This fix computes two statistics which it stores in a global vector of
length 2, which can be accessed by various <aclass="reference internal"href="Section_howto.html#howto-15"><spanclass="std std-ref">output commands</span></a>. The vector values calculated
by this fix are “intensive”.</p>
<p>These are the 2 quantities:</p>
<ulclass="simple">
<li><olclass="first arabic">
<li># of bonds created on the most recent creation timestep</li>
</ol>
</li>
<li><olclass="first arabic"start="2">
<li>cummulative # of bonds created</li>
</ol>
</li>
</ul>
<p>No parameter of this fix can be used with the <em>start/stop</em> keywords of
the <aclass="reference internal"href="run.html"><spanclass="doc">run</span></a> command. This fix is not invoked during <aclass="reference internal"href="minimize.html"><spanclass="doc">energy minimization</span></a>.</p>
</div>
<divclass="section"id="restrictions">
<h2>Restrictions</h2>
<p>This fix is part of the MC package. It is only enabled if LAMMPS was
built with that package. See the <aclass="reference internal"href="Section_start.html#start-3"><spanclass="std std-ref">Making LAMMPS</span></a> section for more info.</p>
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