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<li>fix external command</li>
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<div class="section" id="fix-external-command">
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<span id="index-0"></span><h1>fix external command</h1>
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<div class="section" id="syntax">
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<h2>Syntax</h2>
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<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">external</span> <span class="n">mode</span> <span class="n">args</span>
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</pre></div>
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</div>
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<ul class="simple">
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<li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> command</li>
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<li>external = style name of this fix command</li>
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<li>mode = <em>pf/callback</em> or <em>pf/array</em></li>
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</ul>
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<pre class="literal-block">
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<em>pf/callback</em> args = Ncall Napply
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Ncall = make callback every Ncall steps
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Napply = apply callback forces every Napply steps
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<em>pf/array</em> args = Napply
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Napply = apply array forces every Napply steps
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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</h2>
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<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">external</span> <span class="n">pf</span><span class="o">/</span><span class="n">callback</span> <span class="mi">1</span> <span class="mi">1</span>
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<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">external</span> <span class="n">pf</span><span class="o">/</span><span class="n">callback</span> <span class="mi">100</span> <span class="mi">1</span>
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<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">external</span> <span class="n">pf</span><span class="o">/</span><span class="n">array</span> <span class="mi">10</span>
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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</h2>
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<p>This fix allows external programs that are running LAMMPS through its
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<a class="reference internal" href="Section_howto.html#howto-19"><span class="std std-ref">library interface</span></a> to modify certain
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LAMMPS properties on specific timesteps, similar to the way other
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fixes do. The external driver can be a <a class="reference internal" href="Section_howto.html#howto-19"><span class="std std-ref">C/C++ or Fortran program</span></a> or a <a class="reference internal" href="Section_python.html"><span class="doc">Python script</span></a>.</p>
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<hr class="docutils" />
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<p>If mode is <em>pf/callback</em> then the fix will make a callback every
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<em>Ncall</em> timesteps or minimization iterations to the external program.
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The external program computes forces on atoms by setting values in an
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array owned by the fix. The fix then adds these forces to each atom
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in the group, once every <em>Napply</em> steps, similar to the way the <a class="reference internal" href="fix_addforce.html"><span class="doc">fix addforce</span></a> command works. Note that if <em>Ncall</em> >
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<em>Napply</em>, the force values produced by one callback will persist, and
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be used multiple times to update atom forces.</p>
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<p>The callback function “foo” is invoked by the fix as:</p>
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<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">foo</span><span class="p">(</span><span class="n">void</span> <span class="o">*</span><span class="n">ptr</span><span class="p">,</span> <span class="n">bigint</span> <span class="n">timestep</span><span class="p">,</span> <span class="nb">int</span> <span class="n">nlocal</span><span class="p">,</span> <span class="nb">int</span> <span class="o">*</span><span class="n">ids</span><span class="p">,</span> <span class="n">double</span> <span class="o">**</span><span class="n">x</span><span class="p">,</span> <span class="n">double</span> <span class="o">**</span><span class="n">fexternal</span><span class="p">);</span>
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</pre></div>
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</div>
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<p>The arguments are as follows:</p>
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<ul class="simple">
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<li>ptr = pointer provided by and simply passed back to external driver</li>
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<li>timestep = current LAMMPS timestep</li>
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<li>nlocal = # of atoms on this processor</li>
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<li>ids = list of atom IDs on this processor</li>
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<li>x = coordinates of atoms on this processor</li>
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<li>fexternal = forces to add to atoms on this processor</li>
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</ul>
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<p>Note that timestep is a “bigint” which is defined in src/lmptype.h,
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typically as a 64-bit integer.</p>
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<p>Fexternal are the forces returned by the driver program.</p>
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<p>The fix has a set_callback() method which the external driver can call
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to pass a pointer to its foo() function. See the
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couple/lammps_quest/lmpqst.cpp file in the LAMMPS distribution for an
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example of how this is done. This sample application performs
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classical MD using quantum forces computed by a density functional
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code <a class="reference external" href="http://dft.sandia.gov/Quest">Quest</a>.</p>
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<hr class="docutils" />
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<p>If mode is <em>pf/array</em> then the fix simply stores force values in an
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array. The fix adds these forces to each atom in the group, once
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every <em>Napply</em> steps, similar to the way the <a class="reference internal" href="fix_addforce.html"><span class="doc">fix addforce</span></a> command works.</p>
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<p>The name of the public force array provided by the FixExternal
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class is</p>
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<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">double</span> <span class="o">**</span><span class="n">fexternal</span><span class="p">;</span>
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</pre></div>
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</div>
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<p>It is allocated by the FixExternal class as an (N,3) array where N is
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the number of atoms owned by a processor. The 3 corresponds to the
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fx, fy, fz components of force.</p>
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<p>It is up to the external program to set the values in this array to
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the desired quantities, as often as desired. For example, the driver
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program might perform an MD run in stages of 1000 timesteps each. In
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between calls to the LAMMPS <a class="reference internal" href="run.html"><span class="doc">run</span></a> command, it could retrieve
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atom coordinates from LAMMPS, compute forces, set values in fexternal,
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etc.</p>
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<hr class="docutils" />
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<p>To use this fix during energy minimization, the energy corresponding
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to the added forces must also be set so as to be consistent with the
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added forces. Otherwise the minimization will not converge correctly.</p>
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<p>This can be done from the external driver by calling this public
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method of the FixExternal class:</p>
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<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">void</span> <span class="n">set_energy</span><span class="p">(</span><span class="n">double</span> <span class="n">eng</span><span class="p">);</span>
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</pre></div>
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</div>
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<p>where eng is the potential energy. Eng is an extensive quantity,
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meaning it should be the sum over per-atom energies of all affected
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atoms. It should also be provided in <a class="reference internal" href="units.html"><span class="doc">energy units</span></a>
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consistent with the simulation. See the details below for how to
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insure this energy setting is used appropriately in a minimization.</p>
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</div>
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<hr class="docutils" />
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<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
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<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
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<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.</p>
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<p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>energy</em> option is supported by this
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fix to add the potential “energy” set by the external driver to the
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system’s potential energy as part of <a class="reference internal" href="thermo_style.html"><span class="doc">thermodynamic output</span></a>. This is a fictitious quantity but is
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needed so that the <a class="reference internal" href="minimize.html"><span class="doc">minimize</span></a> command can include the
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forces added by this fix in a consistent manner. I.e. there is a
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decrease in potential energy when atoms move in the direction of the
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added force.</p>
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<p>This fix computes a global scalar which can be accessed by various
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<a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>. The scalar is the
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potential energy discussed above. The scalar stored by this fix
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is “extensive”.</p>
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<p>No parameter of this fix can be used with the <em>start/stop</em> keywords of
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the <a class="reference internal" href="run.html"><span class="doc">run</span></a> command.</p>
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<p>The forces due to this fix are imposed during an energy minimization,
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invoked by the <a class="reference internal" href="minimize.html"><span class="doc">minimize</span></a> command.</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 you want the fictitious potential energy associated with the
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added forces to be included in the total potential energy of the
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system (the quantity being minimized), you MUST enable the
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<a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>energy</em> option for this fix.</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</h2>
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<blockquote>
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<div>none</div></blockquote>
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<p><strong>Related commands:</strong> none</p>
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<p><strong>Default:</strong> none</p>
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<p>
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