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<li class="toctree-l2"><a class="reference internal" href="Python_overview.html">2.1. Overview</a></li>
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<li class="toctree-l2 current"><a class="reference internal" href="Python_run.html">2.3. Run LAMMPS from Python</a><ul class="current">
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<li class="toctree-l3"><a class="reference internal" href="Python_launch.html">2.3.1. Running LAMMPS and Python in serial</a></li>
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<li class="toctree-l3"><a class="reference internal" href="Python_launch.html#running-lammps-and-python-in-parallel-with-mpi">2.3.2. Running LAMMPS and Python in parallel with MPI</a></li>
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<li class="toctree-l3"><a class="reference internal" href="Python_launch.html#running-python-scripts">2.3.3. Running Python scripts</a></li>
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<li class="toctree-l3"><a class="reference internal" href="Python_create.html">2.3.4. Creating or deleting a LAMMPS object</a></li>
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<li class="toctree-l3"><a class="reference internal" href="Python_execute.html">2.3.5. Executing commands</a></li>
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<li class="toctree-l3"><a class="reference internal" href="Python_properties.html">2.3.6. System properties</a></li>
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<li class="toctree-l3 current"><a class="current reference internal" href="#">2.3.7. Per-atom properties</a></li>
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<li class="toctree-l3"><a class="reference internal" href="Python_objects.html">2.3.8. Compute, fixes, variables</a></li>
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<li class="toctree-l3"><a class="reference internal" href="Python_scatter.html">2.3.9. Scatter/gather operations</a></li>
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<li class="toctree-l3"><a class="reference internal" href="Python_neighbor.html">2.3.10. Neighbor list access</a></li>
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<li class="toctree-l3"><a class="reference internal" href="Python_config.html">2.3.11. Configuration information</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Python_module.html">2.4. The <code class="docutils literal notranslate"><span class="pre">lammps</span></code> Python module</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Python_ext.html">2.5. Extending the Python interface</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Python_call.html">2.6. Calling Python from LAMMPS</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Python_formats.html">2.7. Output Readers</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Python_examples.html">2.8. Example Python scripts</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Python_error.html">2.9. Handling LAMMPS errors</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Python_trouble.html">2.10. Troubleshooting</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Modify.html">3. Modifying & extending LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
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<li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>
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<li class="breadcrumb-item active"><span class="section-number">2.3.7. </span>Per-atom properties</li>
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<a href="https://www.lammps.org"><img src="_static/lammps-logo.png" width="64" height="16" alt="LAMMPS Homepage"></a> | <a href="Commands_all.html">Commands</a>
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<p><span class="math notranslate nohighlight">\(\renewcommand{\AA}{\text{Å}}\)</span></p>
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<section id="per-atom-properties">
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<h1><span class="section-number">2.3.7. </span>Per-atom properties<a class="headerlink" href="#per-atom-properties" title="Link to this heading"></a></h1>
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<p>Similar to what is described in <a class="reference internal" href="Library_atoms.html"><span class="doc">Per-atom properties</span></a>, the instances of
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<a class="reference internal" href="Python_module.html#lammps.lammps" title="lammps.lammps"><code class="xref py py-class docutils literal notranslate"><span class="pre">lammps</span></code></a>, <a class="reference internal" href="Python_module.html#lammps.PyLammps" title="lammps.PyLammps"><code class="xref py py-class docutils literal notranslate"><span class="pre">PyLammps</span></code></a>, or
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<a class="reference internal" href="Python_module.html#lammps.IPyLammps" title="lammps.IPyLammps"><code class="xref py py-class docutils literal notranslate"><span class="pre">IPyLammps</span></code></a> can be used to extract atom quantities
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and modify some of them. The main difference between the interfaces is how the information
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is exposed.</p>
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<p>While the <a class="reference internal" href="Python_module.html#lammps.lammps" title="lammps.lammps"><code class="xref py py-class docutils literal notranslate"><span class="pre">lammps</span></code></a> is just a thin layer that wraps C API calls,
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<a class="reference internal" href="Python_module.html#lammps.PyLammps" title="lammps.PyLammps"><code class="xref py py-class docutils literal notranslate"><span class="pre">PyLammps</span></code></a> and <a class="reference internal" href="Python_module.html#lammps.IPyLammps" title="lammps.IPyLammps"><code class="xref py py-class docutils literal notranslate"><span class="pre">IPyLammps</span></code></a> expose
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information as objects and properties.</p>
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<p>In some cases the data returned is a direct reference to the original data
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inside LAMMPS cast to <code class="docutils literal notranslate"><span class="pre">ctypes</span></code> pointers. Where possible, the wrappers will
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determine the <code class="docutils literal notranslate"><span class="pre">ctypes</span></code> data type and cast pointers accordingly. If
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<code class="docutils literal notranslate"><span class="pre">numpy</span></code> is installed arrays can also be extracted as numpy arrays, which
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will access the C arrays directly and have the correct dimensions to protect
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against invalid accesses.</p>
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<div class="admonition warning">
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<p class="admonition-title">Warning</p>
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<p>When accessing per-atom data,
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please note that this data is the per-processor local data and indexed
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accordingly. These arrays can change sizes and order at every neighbor list
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rebuild and atom sort event as atoms are migrating between subdomains.</p>
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</div>
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<div class="sphinx-tabs docutils container">
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<div aria-label="Tabbed content" class="closeable" role="tablist"><button aria-controls="panel-0-0-0" aria-selected="true" class="sphinx-tabs-tab" id="tab-0-0-0" name="0-0" role="tab" tabindex="0">lammps API</button><button aria-controls="panel-0-0-1" aria-selected="false" class="sphinx-tabs-tab" id="tab-0-0-1" name="0-1" role="tab" tabindex="-1">PyLammps/IPyLammps API</button></div><div aria-labelledby="tab-0-0-0" class="sphinx-tabs-panel" id="panel-0-0-0" name="0-0" role="tabpanel" tabindex="0"><div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span><span class="w"> </span><span class="nn">lammps</span><span class="w"> </span><span class="kn">import</span> <span class="n">lammps</span>
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<span class="n">lmp</span> <span class="o">=</span> <span class="n">lammps</span><span class="p">()</span>
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<span class="n">lmp</span><span class="o">.</span><span class="n">file</span><span class="p">(</span><span class="s2">"in.sysinit"</span><span class="p">)</span>
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<span class="n">nlocal</span> <span class="o">=</span> <span class="n">lmp</span><span class="o">.</span><span class="n">extract_global</span><span class="p">(</span><span class="s2">"nlocal"</span><span class="p">)</span>
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<span class="n">x</span> <span class="o">=</span> <span class="n">lmp</span><span class="o">.</span><span class="n">extract_atom</span><span class="p">(</span><span class="s2">"x"</span><span class="p">)</span>
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<span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">nlocal</span><span class="p">):</span>
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<span class="nb">print</span><span class="p">(</span><span class="s2">"(x,y,z) = ("</span><span class="p">,</span> <span class="n">x</span><span class="p">[</span><span class="n">i</span><span class="p">][</span><span class="mi">0</span><span class="p">],</span> <span class="n">x</span><span class="p">[</span><span class="n">i</span><span class="p">][</span><span class="mi">1</span><span class="p">],</span> <span class="n">x</span><span class="p">[</span><span class="n">i</span><span class="p">][</span><span class="mi">2</span><span class="p">],</span> <span class="s2">")"</span><span class="p">)</span>
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<span class="n">lmp</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
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</pre></div>
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</div>
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<p><strong>Methods</strong>:</p>
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<ul class="simple">
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<li><p><a class="reference internal" href="Python_module.html#lammps.lammps.extract_atom" title="lammps.lammps.extract_atom"><code class="xref py py-meth docutils literal notranslate"><span class="pre">extract_atom()</span></code></a>: extract a per-atom quantity</p></li>
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</ul>
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<p><strong>Numpy Methods</strong>:</p>
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<ul class="simple">
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<li><p><a class="reference internal" href="Python_module.html#lammps.numpy_wrapper.numpy_wrapper.extract_atom" title="lammps.numpy_wrapper.numpy_wrapper.extract_atom"><code class="xref py py-meth docutils literal notranslate"><span class="pre">numpy.extract_atom()</span></code></a>: extract a per-atom quantity as numpy array</p></li>
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</ul>
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</div><div aria-labelledby="tab-0-0-1" class="sphinx-tabs-panel" hidden="true" id="panel-0-0-1" name="0-1" role="tabpanel" tabindex="0"><p>All atoms in the current simulation can be accessed by using the <a class="reference internal" href="Python_module.html#lammps.PyLammps.atoms" title="lammps.PyLammps.atoms"><code class="xref py py-attr docutils literal notranslate"><span class="pre">PyLammps.atoms</span></code></a> property.
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Each element of this list is a <a class="reference internal" href="Python_module.html#lammps.Atom" title="lammps.Atom"><code class="xref py py-class docutils literal notranslate"><span class="pre">Atom</span></code></a> or <a class="reference internal" href="Python_module.html#lammps.Atom2D" title="lammps.Atom2D"><code class="xref py py-class docutils literal notranslate"><span class="pre">Atom2D</span></code></a> object. The attributes of
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these objects provide access to their data (id, type, position, velocity, force, etc.):</p>
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<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="c1"># access first atom</span>
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<span class="n">L</span><span class="o">.</span><span class="n">atoms</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">id</span>
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<span class="n">L</span><span class="o">.</span><span class="n">atoms</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">type</span>
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<span class="c1"># access second atom</span>
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<span class="n">L</span><span class="o">.</span><span class="n">atoms</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">position</span>
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<span class="n">L</span><span class="o">.</span><span class="n">atoms</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">velocity</span>
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<span class="n">L</span><span class="o">.</span><span class="n">atoms</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">force</span>
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</pre></div>
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</div>
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<p>Some attributes can be changed:</p>
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<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="c1"># set position in 2D simulation</span>
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<span class="n">L</span><span class="o">.</span><span class="n">atoms</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">position</span> <span class="o">=</span> <span class="p">(</span><span class="mf">1.0</span><span class="p">,</span> <span class="mf">0.0</span><span class="p">)</span>
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<span class="c1"># set position in 3D simulation</span>
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<span class="n">L</span><span class="o">.</span><span class="n">atoms</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">position</span> <span class="o">=</span> <span class="p">(</span><span class="mf">1.0</span><span class="p">,</span> <span class="mf">0.0</span><span class="p">,</span> <span class="mf">1.0</span><span class="p">)</span>
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</pre></div>
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</div>
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</div></div>
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</section>
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