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--- abinitio:ase_atom [2022/08/23 16:58] – kimi
+++ abinitio:ase_atom [2022/08/24 11:03] (現在) – kimi
@@ 行 1: / 行 1: @@
-<html>
+====== ase.atom ======
-<h1>The Atom object<a class="headerlink" href="#the-atom-object" title="Permalink to this headline">¶</a></h1>
+<html><head><title>Python: module ase.atom</title></head><body bgcolor="#f0f0f8"><br>
-<p>ASE defines a python class called <a class="reference internal" href="#ase.atom.Atom" title="ase.atom.Atom"><code class="xref py py-class docutils literal notranslate"><span class="pre">Atom</span></code></a> to setup and handle atoms
+<p>
-in electronic structure and molecular simulations. From a python
-script, atoms can be created like this:</p>
-<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">ase</span> <span class="kn">import</span> <span class="n">Atom</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">a1</span> <span class="o">=</span> <span class="n">Atom</span><span class="p">(</span><span class="s1">&#39;Si&#39;</span><span class="p">,</span> <span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">))</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">a2</span> <span class="o">=</span> <span class="n">Atom</span><span class="p">(</span><span class="s1">&#39;H&#39;</span><span class="p">,</span> <span class="p">(</span><span class="mf">1.3</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">),</span> <span class="n">mass</span><span class="o">=</span><span class="mi">2</span><span class="p">)</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">a3</span> <span class="o">=</span> <span class="n">Atom</span><span class="p">(</span><span class="mi">14</span><span class="p">,</span> <span class="n">position</span><span class="o">=</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">))</span>  <span class="c1"># same as a1</span>
-</pre></div>
-</div>
-<dl class="py class">
-<dt class="sig sig-object py" id="ase.atom.Atom">
-<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">ase.atom.</span></span><span class="sig-name descname"><span class="pre">Atom</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">symbol</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'X'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">position</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">(0,</span> <span class="pre">0,</span> <span class="pre">0)</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">tag</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">momentum</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mass</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">magmom</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">charge</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">atoms</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">index</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/ase/atom.html#Atom"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#ase.atom.Atom" title="Permalink to this definition">¶</a></dt>
-<dd><p>Class for representing a single atom.</p>
-<p>Parameters:</p>
-<dl class="simple">
-<dt>symbol: str or int</dt><dd><p>Can be a chemical symbol (str) or an atomic number (int).</p>
-</dd>
-<dt>position: sequence of 3 floats</dt><dd><p>Atomic position.</p>
-</dd>
-<dt>tag: int</dt><dd><p>Special purpose tag.</p>
-</dd>
-<dt>momentum: sequence of 3 floats</dt><dd><p>Momentum for atom.</p>
-</dd>
-<dt>mass: float</dt><dd><p>Atomic mass in atomic units.</p>
-</dd>
-<dt>magmom: float or 3 floats</dt><dd><p>Magnetic moment.</p>
-</dd>
-<dt>charge: float</dt><dd><p>Atomic charge.</p>
-</dd>
-</dl>
-</dd></dl>
-<p>The first argument to the constructor of an <a class="reference internal" href="#ase.atom.Atom" title="ase.atom.Atom"><code class="xref py py-class docutils literal notranslate"><span class="pre">Atom</span></code></a> object is
+<table summary="section" border="0" cellpadding="2" cellspacing="0" width="100%">
-the chemical symbol, and the second argument is the position in Å
+<tbody>
-units (see <a class="reference internal" href="units.html#module-ase.units" title="ase.units"><code class="xref py py-mod docutils literal notranslate"><span class="pre">ase.units</span></code></a>).  The position can be any numerical sequence
-of length three.  The properties of an atom can also be set using
+<tr>
-keywords like it is done in the <em>a2</em> and <em>a3</em> examples above.</p>
+<td width="100%"><dl></dl>
-<p>More examples:</p>
+ <p>
-<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">a</span> <span class="o">=</span> <span class="n">Atom</span><span class="p">(</span><span class="s1">&#39;O&#39;</span><span class="p">,</span> <span class="n">charge</span><span class="o">=-</span><span class="mi">2</span><span class="p">)</span>
+<table summary="section" border="0" cellpadding="2" cellspacing="0" width="100%">
-<span class="gp">&gt;&gt;&gt; </span><span class="n">b</span> <span class="o">=</span> <span class="n">Atom</span><span class="p">(</span><span class="mi">8</span><span class="p">,</span> <span class="n">charge</span><span class="o">=-</span><span class="mi">2</span><span class="p">)</span>
+<tbody><tr bgcolor="#ffc8d8">
-<span class="gp">&gt;&gt;&gt; </span><span class="n">c</span> <span class="o">=</span> <span class="n">Atom</span><span class="p">(</span><span class="s1">&#39;H&#39;</span><span class="p">,</span> <span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">,</span> <span class="mi">3</span><span class="p">),</span> <span class="n">magmom</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
+<td colspan="3" valign="bottom">&nbsp;<br>
-<span class="gp">&gt;&gt;&gt; </span><span class="nb">print</span><span class="p">(</span><span class="n">a</span><span class="o">.</span><span class="n">charge</span><span class="p">,</span> <span class="n">a</span><span class="o">.</span><span class="n">position</span><span class="p">)</span>
+<font color="#000000" face="helvetica, arial"><a name="Atom">class <strong>Atom</strong></a>(<a href="__builtin__.html#object">__builtin__.object</a>)</font></td></tr>
-<span class="go">-2 [ 0.  0.  0.]</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">c</span><span class="o">.</span><span class="n">x</span> <span class="o">=</span> <span class="mf">0.0</span>
+<tr bgcolor="#ffc8d8"><td rowspan="2"><tt>&nbsp;&nbsp;&nbsp;</tt></td>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">c</span><span class="o">.</span><span class="n">position</span>
+<td colspan="2"><tt>Class&nbsp;for&nbsp;representing&nbsp;a&nbsp;single&nbsp;atom.<br>
-<span class="go">array([ 0.,  2.,  3.])</span>
+&nbsp;<br>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">b</span><span class="o">.</span><span class="n">symbol</span>
+Parameters:<br>
-<span class="go">&#39;O&#39;</span>
+&nbsp;<br>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">c</span><span class="o">.</span><span class="n">tag</span> <span class="o">=</span> <span class="mi">42</span>
+symbol:&nbsp;str&nbsp;or&nbsp;int<br>&nbsp;&nbsp;&nbsp;&nbsp;Can&nbsp;be&nbsp;a&nbsp;chemical&nbsp;symbol&nbsp;(str)&nbsp;or&nbsp;an&nbsp;atomic&nbsp;number&nbsp;(int).<br>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">c</span><span class="o">.</span><span class="n">number</span>
+position:&nbsp;sequence&nbsp;of&nbsp;3&nbsp;floats<br>
-<span class="go">1</span>
+&nbsp;&nbsp;&nbsp;&nbsp;Atomi&nbsp;position.<br>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">c</span><span class="o">.</span><span class="n">symbol</span> <span class="o">=</span> <span class="s1">&#39;Li&#39;</span>
+tag:&nbsp;int<br>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">c</span><span class="o">.</span><span class="n">number</span>
+&nbsp;&nbsp;&nbsp;&nbsp;Special&nbsp;purpose&nbsp;tag.<br>
-<span class="go">3</span>
+momentum:&nbsp;sequence&nbsp;of&nbsp;3&nbsp;floats<br>
-</pre></div>
+&nbsp;&nbsp;&nbsp;&nbsp;Momentum&nbsp;for&nbsp;atom.<br>
-</div>
+mass:&nbsp;float<br>
-<p>If the atom object belongs to an Atoms object, then assigning
+&nbsp;&nbsp;&nbsp;&nbsp;Atomic&nbsp;mass&nbsp;in&nbsp;atomic&nbsp;units.<br>
-values to the atom attributes will change the corresponding
+magmom:&nbsp;float&nbsp;or&nbsp;3&nbsp;floats<br>
-arrays of the atoms object:</p>
+&nbsp;&nbsp;&nbsp;&nbsp;Magnetic&nbsp;moment.<br>
-<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">ase</span> <span class="kn">import</span> <span class="n">Atoms</span>
+charge:&nbsp;float<br>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">OH</span> <span class="o">=</span> <span class="n">Atoms</span><span class="p">(</span><span class="s1">&#39;OH&#39;</span><span class="p">)</span>
+&nbsp;&nbsp;&nbsp;&nbsp;Atomic&nbsp;charge.<br>&nbsp;</tt></td></tr>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">OH</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">charge</span> <span class="o">=</span> <span class="o">-</span><span class="mi">1</span>
+<tr><td>&nbsp;</td>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">OH</span><span class="o">.</span><span class="n">get_initial_charges</span><span class="p">()</span>
+<td width="100%">Methods defined here:<br>
-<span class="go">array([-1.,  0.])</span>
-</pre></div>
-</div>
-<p>Another example:</p>
-<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="k">for</span> <span class="n">atom</span> <span class="ow">in</span> <span class="n">bulk</span><span class="p">:</span>
-<span class="gp">... </span>    <span class="k">if</span> <span class="n">atom</span><span class="o">.</span><span class="n">symbol</span> <span class="o">==</span> <span class="s1">&#39;Ni&#39;</span><span class="p">:</span>
-<span class="gp">... </span>        <span class="n">atom</span><span class="o">.</span><span class="n">magmom</span> <span class="o">=</span> <span class="mf">0.7</span>  <span class="c1"># set initial magnetic moment</span>
-</pre></div>
-</div>
-<p>The different properties of an atom can be obtained and changed via
-attributes (<code class="docutils literal notranslate"><span class="pre">position</span></code>, <code class="docutils literal notranslate"><span class="pre">number</span></code>, <code class="docutils literal notranslate"><span class="pre">tag</span></code>, <code class="docutils literal notranslate"><span class="pre">momentum</span></code>, <code class="docutils literal notranslate"><span class="pre">mass</span></code>,
-<code class="docutils literal notranslate"><span class="pre">magmom</span></code>, <code class="docutils literal notranslate"><span class="pre">charge</span></code>, <code class="docutils literal notranslate"><span class="pre">x</span></code>, <code class="docutils literal notranslate"><span class="pre">y</span></code>, <code class="docutils literal notranslate"><span class="pre">z</span></code>):</p>
-<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">a1</span><span class="o">.</span><span class="n">position</span> <span class="o">=</span> <span class="p">[</span><span class="mi">1</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">]</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">a1</span><span class="o">.</span><span class="n">position</span>
-<span class="go">[1, 0, 0]</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">a1</span><span class="o">.</span><span class="n">z</span> <span class="o">=</span> <span class="mf">2.5</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">a1</span><span class="o">.</span><span class="n">position</span>
-<span class="go">[1, 0, 2.5]</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">a2</span><span class="o">.</span><span class="n">magmom</span> <span class="o">=</span> <span class="mf">1.0</span>
-</pre></div>
-</div>
-<p>That last line will set the initial magnetic moment that some
-calculators use (similar to the
-<a class="reference internal" href="atoms.html#ase.Atoms.set_initial_magnetic_moments" title="ase.Atoms.set_initial_magnetic_moments"><code class="xref py py-meth docutils literal notranslate"><span class="pre">set_initial_magnetic_moments()</span></code></a> method).</p>
-<div class="admonition note">
-<p class="admonition-title">Note</p>
-<p>The <code class="docutils literal notranslate"><span class="pre">position</span></code> and <code class="docutils literal notranslate"><span class="pre">momentum</span></code> attributes refer to mutable
-objects, so in some cases, you may want to use
-<code class="docutils literal notranslate"><span class="pre">a1.position.copy()</span></code> in order to avoid changing the position of
-<code class="docutils literal notranslate"><span class="pre">a1</span></code> by accident.</p>
-</div>
-<section id="getting-an-atom-from-an-atoms-object">
-<h2>Getting an Atom from an Atoms object<a class="headerlink" href="#getting-an-atom-from-an-atoms-object" title="Permalink to this headline">¶</a></h2>
-<p>Indexing an <a class="reference internal" href="atoms.html#ase.Atoms" title="ase.Atoms"><code class="xref py py-class docutils literal notranslate"><span class="pre">Atoms</span></code></a> object returns an <a class="reference internal" href="#ase.atom.Atom" title="ase.atom.Atom"><code class="xref py py-class docutils literal notranslate"><span class="pre">Atom</span></code></a> object
-still remembering that it belongs to the collective <a class="reference internal" href="atoms.html#ase.Atoms" title="ase.Atoms"><code class="xref py py-class docutils literal notranslate"><span class="pre">Atoms</span></code></a>:
-Modifying it will also change the atoms object:</p>
-<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">ase.build</span> <span class="kn">import</span> <span class="n">molecule</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">atoms</span> <span class="o">=</span> <span class="n">molecule</span><span class="p">(</span><span class="s1">&#39;CH4&#39;</span><span class="p">)</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">atoms</span><span class="o">.</span><span class="n">get_positions</span><span class="p">()</span>
-<span class="go">array([[ 0.      ,  0.      ,  0.      ],</span>
-<span class="go">       [ 0.629118,  0.629118,  0.629118],</span>
-<span class="go">       [-0.629118, -0.629118,  0.629118],</span>
-<span class="go">       [ 0.629118, -0.629118, -0.629118],</span>
-<span class="go">       [-0.629118,  0.629118, -0.629118]])</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">a</span> <span class="o">=</span> <span class="n">atoms</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">a</span>
-<span class="go">Atom(&#39;H&#39;, [-0.62911799999999996, -0.62911799999999996, 0.62911799999999996], index=2)</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">a</span><span class="o">.</span><span class="n">x</span> <span class="o">=</span> <span class="mi">0</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">atoms</span><span class="o">.</span><span class="n">get_positions</span><span class="p">()</span>
-<span class="go">array([[ 0.      ,  0.      ,  0.      ],</span>
-<span class="go">       [ 0.629118,  0.629118,  0.629118],</span>
-<span class="go">       [ 0.      , -0.629118,  0.629118],</span>
-<span class="go">       [ 0.629118, -0.629118, -0.629118],</span>
-<span class="go">       [-0.629118,  0.629118, -0.629118]])</span>
-</pre></div>
-</div>
-<div class="admonition seealso">
-<p class="admonition-title">See also</p>
-<dl class="simple">
-<dt><a class="reference internal" href="atoms.html#module-ase" title="ase"><code class="xref py py-mod docutils literal notranslate"><span class="pre">ase</span></code></a>:</dt><dd><p>More information about how to use collections of atoms.</p>
-</dd>
-<dt><a class="reference internal" href="calculators/calculators.html#module-ase.calculators" title="ase.calculators: Energy, force and stress calculators."><code class="xref py py-mod docutils literal notranslate"><span class="pre">ase.calculators</span></code></a>:</dt><dd><p>Information about how to calculate forces and energies of atoms.</p>
-</dd>
-</dl>
-</div>
-</section>
-</section>
-           </div>
+<dl><dt><a name="Atom-__init__"><strong>__init__</strong></a>(self, symbol<font color="#909090">='X'</font>, position<font color="#909090">=(0, 0, 0)</font>, tag<font color="#909090">=None</font>, momentum<font color="#909090">=None</font>, mass<font color="#909090">=None</font>, magmom<font color="#909090">=None</font>, charge<font color="#909090">=None</font>, atoms<font color="#909090">=None</font>, index<font color="#909090">=None</font>)</dt></dl><dl><dt><a name="Atom-__repr__"><strong>__repr__</strong></a>(self)</dt></dl>
-          </div>
-          <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
-        <a href="dimer.html" class="btn btn-neutral float-left" title="Dimer method" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
-        <a href="transport/transport.html" class="btn btn-neutral float-right" title="Electron transport" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
-    </div>
-  <hr/>
+<dl><dt><a name="Atom-cut_reference_to_atoms"><strong>cut_reference_to_atoms</strong></a>(self)</dt><dd><tt>Cut&nbsp;reference&nbsp;to&nbsp;atoms&nbsp;<a href="__builtin__.html#object">object</a>.</tt></dd></dl>
-  <div role="contentinfo">
+<dl><dt><a name="Atom-delete"><strong>delete</strong></a>(self, name)</dt><dd><tt>Delete&nbsp;attribute.</tt></dd></dl>
-    <p>&#169; Copyright 2022, ASE-developers.
-      <span class="lastupdated">Last updated on Tue, 23 Aug 2022 07:38:04.
-      </span></p>
-  </div>
-  Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a
+<dl><dt><a name="Atom-get"><strong>get</strong></a>(self, name)</dt><dd><tt>Get&nbsp;attribute,&nbsp;return&nbsp;default&nbsp;if&nbsp;not&nbsp;explicitely&nbsp;set.</tt></dd></dl>
-    <a href="https://github.com/readthedocs/sphinx_rtd_theme">theme</a>
-    provided by <a href="https://readthedocs.org">Read the Docs</a>.
-</html>
+<dl><dt><a name="Atom-get_atomic_number"><strong>get_atomic_number</strong></a>(self)</dt></dl>
+<dl><dt><a name="Atom-get_charge"><strong>get_charge</strong></a>(self)</dt></dl>
+<dl><dt><a name="Atom-get_initial_magnetic_moment"><strong>get_initial_magnetic_moment</strong></a>(self)</dt></dl>
+<dl><dt><a name="Atom-get_mass"><strong>get_mass</strong></a>(self)</dt></dl>
+<dl><dt><a name="Atom-get_momentum"><strong>get_momentum</strong></a>(self)</dt></dl>
+<dl><dt><a name="Atom-get_position"><strong>get_position</strong></a>(self)</dt></dl>
+<dl><dt><a name="Atom-get_raw"><strong>get_raw</strong></a>(self, name)</dt><dd><tt>Get&nbsp;attribute,&nbsp;return&nbsp;None&nbsp;if&nbsp;not&nbsp;explicitely&nbsp;set.</tt></dd></dl>
+<dl><dt><a name="Atom-get_symbol"><strong>get_symbol</strong></a>(self)</dt></dl>
+<dl><dt><a name="Atom-get_tag"><strong>get_tag</strong></a>(self)</dt></dl>
+<dl><dt><a name="Atom-set"><strong>set</strong></a>(self, name, value)</dt><dd><tt>Set&nbsp;attribute.</tt></dd></dl>
+<dl><dt><a name="Atom-set_atomic_number"><strong>set_atomic_number</strong></a>(self, value)</dt></dl>
+<dl><dt><a name="Atom-set_charge"><strong>set_charge</strong></a>(self, value)</dt></dl>
+<dl><dt><a name="Atom-set_initial_magnetic_moment"><strong>set_initial_magnetic_moment</strong></a>(self, value)</dt></dl>
+<dl><dt><a name="Atom-set_mass"><strong>set_mass</strong></a>(self, value)</dt></dl>
+<dl><dt><a name="Atom-set_momentum"><strong>set_momentum</strong></a>(self, value)</dt></dl>
+<dl><dt><a name="Atom-set_position"><strong>set_position</strong></a>(self, value)</dt></dl>
+<dl><dt><a name="Atom-set_symbol"><strong>set_symbol</strong></a>(self, value)</dt></dl>
+<dl><dt><a name="Atom-set_tag"><strong>set_tag</strong></a>(self, value)</dt></dl>
+<hr>
+Data descriptors defined here:<br>
+<dl><dt><strong>atoms</strong></dt>
+</dl>
+<dl><dt><strong>charge</strong></dt>
+<dd><tt>Atomic&nbsp;charge</tt></dd>
+</dl>
+<dl><dt><strong>data</strong></dt>
+</dl>
+<dl><dt><strong>index</strong></dt>
+</dl>
+<dl><dt><strong>magmom</strong></dt>
+<dd><tt>Initial&nbsp;magnetic&nbsp;moment</tt></dd>
+</dl>
+<dl><dt><strong>mass</strong></dt>
+<dd><tt>Atomic&nbsp;mass</tt></dd>
+</dl>
+<dl><dt><strong>momentum</strong></dt>
+<dd><tt>XYZ-momentum</tt></dd>
+</dl>
+<dl><dt><strong>number</strong></dt>
+<dd><tt>Atomic&nbsp;number</tt></dd>
+</dl>
+<dl><dt><strong>position</strong></dt>
+<dd><tt>XYZ-coordinates</tt></dd>
+</dl>
+<dl><dt><strong>symbol</strong></dt>
+<dd><tt>Chemical&nbsp;symbol</tt></dd>
+</dl>
+<dl><dt><strong>tag</strong></dt>
+<dd><tt>Integer&nbsp;tag</tt></dd>
+</dl>
+<dl><dt><strong>x</strong></dt>
+<dd><tt>X-coordinate</tt></dd>
+</dl>
+<dl><dt><strong>y</strong></dt>
+<dd><tt>Y-coordinate</tt></dd>
+</dl>
+<dl><dt><strong>z</strong></dt>
+<dd><tt>Z-coordinat</tt></dd>
+</dl>
+</td></tr></tbody></table></p></td></tr></tbody></table></p><p><br>
+</p></body></html>