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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 class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
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<li>compute pe/atom command</li>
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<div class="section" id="compute-pe-atom-command">
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<span id="index-0"></span><h1>compute pe/atom 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">compute</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">pe</span><span class="o">/</span><span class="n">atom</span> <span class="n">keyword</span> <span class="o">...</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="compute.html"><span class="doc">compute</span></a> command</li>
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<li>pe/atom = style name of this compute command</li>
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<li>zero or more keywords may be appended</li>
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<li>keyword = <em>pair</em> or <em>bond</em> or <em>angle</em> or <em>dihedral</em> or <em>improper</em> or <em>kspace</em> or <em>fix</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</h2>
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<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">pe</span><span class="o">/</span><span class="n">atom</span>
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<span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">pe</span><span class="o">/</span><span class="n">atom</span> <span class="n">pair</span>
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<span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">pe</span><span class="o">/</span><span class="n">atom</span> <span class="n">pair</span> <span class="n">bond</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>Define a computation that computes the per-atom potential energy for
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each atom in a group. See the <a class="reference internal" href="compute_pe.html"><span class="doc">compute pe</span></a> command if
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you want the potential energy of the entire system.</p>
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<p>The per-atom energy is calculated by the various pair, bond, etc
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potentials defined for the simulation. If no extra keywords are
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listed, then the potential energy is the sum of pair, bond, angle,
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dihedral,improper, kspace (long-range), and fix energy. I.e. it is as
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if all the keywords were listed. If any extra keywords are listed,
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then only those components are summed to compute the potential energy.</p>
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<p>Note that the energy of each atom is due to its interaction with all
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other atoms in the simulation, not just with other atoms in the group.</p>
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<p>For an energy contribution produced by a small set of atoms (e.g. 4
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atoms in a dihedral or 3 atoms in a Tersoff 3-body interaction), that
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energy is assigned in equal portions to each atom in the set.
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E.g. 1/4 of the dihedral energy to each of the 4 atoms.</p>
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<p>The <a class="reference internal" href="dihedral_charmm.html"><span class="doc">dihedral_style charmm</span></a> style calculates
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pairwise interactions between 1-4 atoms. The energy contribution of
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these terms is included in the pair energy, not the dihedral energy.</p>
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<p>The KSpace contribution is calculated using the method in
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<a class="reference internal" href="compute_stress_atom.html#heyes"><span class="std std-ref">(Heyes)</span></a> for the Ewald method and a related method for PPPM,
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as specified by the <a class="reference internal" href="kspace_style.html"><span class="doc">kspace_style pppm</span></a> command.
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For PPPM, the calcluation requires 1 extra FFT each timestep that
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per-atom energy is calculated. Thie <a class="reference external" href="PDF/kspace.pdf">document</a>
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describes how the long-range per-atom energy calculation is performed.</p>
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<p>Various fixes can contribute to the per-atom potential energy of the
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system if the <em>fix</em> contribution is included. See the doc pages for
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<a class="reference internal" href="fix.html"><span class="doc">individual fixes</span></a> for details of which ones compute a
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per-atom potential energy.</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">The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify energy yes</span></a> command must also be
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specified if a fix is to contribute per-atom potential energy to this
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command.</p>
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</div>
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<p>As an example of per-atom potential energy compared to total potential
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energy, these lines in an input script should yield the same result
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in the last 2 columns of thermo output:</p>
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<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">peratom</span> <span class="nb">all</span> <span class="n">pe</span><span class="o">/</span><span class="n">atom</span>
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<span class="n">compute</span> <span class="n">pe</span> <span class="nb">all</span> <span class="n">reduce</span> <span class="nb">sum</span> <span class="n">c_peratom</span>
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<span class="n">thermo_style</span> <span class="n">custom</span> <span class="n">step</span> <span class="n">temp</span> <span class="n">etotal</span> <span class="n">press</span> <span class="n">pe</span> <span class="n">c_pe</span>
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</pre></div>
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</div>
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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">The per-atom energy does not any Lennard-Jones tail corrections
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invoked by the <a class="reference internal" href="pair_modify.html"><span class="doc">pair_modify tail yes</span></a> command, since
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those are global contributions to the system energy.</p>
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</div>
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<p><strong>Output info:</strong></p>
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<p>This compute calculates a per-atom vector, which can be accessed by
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any command that uses per-atom values from a compute as input. See
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<a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">Section_howto 15</span></a> for an overview of
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LAMMPS output options.</p>
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<p>The per-atom vector values will be in energy <a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
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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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</div>
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<div class="section" id="related-commands">
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<h2>Related commands</h2>
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<p><a class="reference internal" href="compute_pe.html"><span class="doc">compute pe</span></a>, <a class="reference internal" href="compute_stress_atom.html"><span class="doc">compute stress/atom</span></a></p>
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<p><strong>Default:</strong> none</p>
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<hr class="docutils" />
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<p id="heyes"><strong>(Heyes)</strong> Heyes, Phys Rev B 49, 755 (1994),</p>
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