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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-l2"><a class="reference internal" href="Python_error.html">2.9. Handling LAMMPS errors</a></li>
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<li class="breadcrumb-item active"><span class="section-number">2.3.6. </span>System properties</li>
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<p><span class="math notranslate nohighlight">\(\renewcommand{\AA}{\text{Å}}\)</span></p>
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<section id="system-properties">
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<h1><span class="section-number">2.3.6. </span>System properties<a class="headerlink" href="#system-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_properties.html"><span class="doc">System 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 different kinds
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of information about the active LAMMPS instance and also to modify some of it. The
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main difference between the interfaces is how the information 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">natoms</span> <span class="o">=</span> <span class="n">lmp</span><span class="o">.</span><span class="n">get_natoms</span><span class="p">()</span>
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<span class="nb">print</span><span class="p">(</span><span class="sa">f</span><span class="s2">"running simulation with </span><span class="si">{</span><span class="n">natoms</span><span class="si">}</span><span class="s2"> atoms"</span><span class="p">)</span>
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<span class="n">lmp</span><span class="o">.</span><span class="n">command</span><span class="p">(</span><span class="s2">"run 1000 post no"</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="mi">10</span><span class="p">):</span>
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<span class="n">lmp</span><span class="o">.</span><span class="n">command</span><span class="p">(</span><span class="s2">"run 100 pre no post no"</span><span class="p">)</span>
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<span class="n">pe</span> <span class="o">=</span> <span class="n">lmp</span><span class="o">.</span><span class="n">get_thermo</span><span class="p">(</span><span class="s2">"pe"</span><span class="p">)</span>
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<span class="n">ke</span> <span class="o">=</span> <span class="n">lmp</span><span class="o">.</span><span class="n">get_thermo</span><span class="p">(</span><span class="s2">"ke"</span><span class="p">)</span>
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<span class="nb">print</span><span class="p">(</span><span class="sa">f</span><span class="s2">"PE = </span><span class="si">{</span><span class="n">pe</span><span class="si">}</span><span class="se">\n</span><span class="s2">KE = </span><span class="si">{</span><span class="n">ke</span><span class="si">}</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.version" title="lammps.lammps.version"><code class="xref py py-meth docutils literal notranslate"><span class="pre">version()</span></code></a>: return the numerical version id, e.g. LAMMPS 2 Sep 2015 -> 20150902</p></li>
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<li><p><a class="reference internal" href="Python_module.html#lammps.lammps.get_thermo" title="lammps.lammps.get_thermo"><code class="xref py py-meth docutils literal notranslate"><span class="pre">get_thermo()</span></code></a>: return current value of a thermo keyword</p></li>
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<li><p><a class="reference internal" href="Python_module.html#lammps.lammps.last_thermo" title="lammps.lammps.last_thermo"><code class="xref py py-meth docutils literal notranslate"><span class="pre">last_thermo()</span></code></a>: return a dictionary of the last thermodynamic output</p></li>
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<li><p><a class="reference internal" href="Python_module.html#lammps.lammps.get_natoms" title="lammps.lammps.get_natoms"><code class="xref py py-meth docutils literal notranslate"><span class="pre">get_natoms()</span></code></a>: total # of atoms as int</p></li>
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<li><p><a class="reference internal" href="Python_module.html#lammps.lammps.reset_box" title="lammps.lammps.reset_box"><code class="xref py py-meth docutils literal notranslate"><span class="pre">reset_box()</span></code></a>: reset the simulation box size</p></li>
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<li><p><a class="reference internal" href="Python_module.html#lammps.lammps.extract_setting" title="lammps.lammps.extract_setting"><code class="xref py py-meth docutils literal notranslate"><span class="pre">extract_setting()</span></code></a>: return a global setting</p></li>
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<li><p><a class="reference internal" href="Python_module.html#lammps.lammps.extract_global" title="lammps.lammps.extract_global"><code class="xref py py-meth docutils literal notranslate"><span class="pre">extract_global()</span></code></a>: extract a global quantity</p></li>
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<li><p><a class="reference internal" href="Python_module.html#lammps.lammps.extract_box" title="lammps.lammps.extract_box"><code class="xref py py-meth docutils literal notranslate"><span class="pre">extract_box()</span></code></a>: extract box info</p></li>
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<li><p><a class="reference internal" href="Python_module.html#lammps.lammps.create_atoms" title="lammps.lammps.create_atoms"><code class="xref py py-meth docutils literal notranslate"><span class="pre">create_atoms()</span></code></a>: create N atoms with IDs, types, x, v, and image flags</p></li>
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</ul>
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<p><strong>Properties</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.last_thermo_step" title="lammps.lammps.last_thermo_step"><code class="xref py py-attr docutils literal notranslate"><span class="pre">last_thermo_step</span></code></a>: the last timestep thermodynamic output was computed</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>In addition to the functions provided by <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> objects
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have several properties which allow you to query the system state:</p>
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<dl class="simple">
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<dt>L.system</dt><dd><p>Is a dictionary describing the system such as the bounding box or number of atoms</p>
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</dd>
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<dt>L.system.xlo, L.system.xhi</dt><dd><p>bounding box limits along x-axis</p>
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</dd>
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<dt>L.system.ylo, L.system.yhi</dt><dd><p>bounding box limits along y-axis</p>
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</dd>
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<dt>L.system.zlo, L.system.zhi</dt><dd><p>bounding box limits along z-axis</p>
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</dd>
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<dt>L.communication</dt><dd><p>configuration of communication subsystem, such as the number of threads or processors</p>
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</dd>
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<dt>L.communication.nthreads</dt><dd><p>number of threads used by each LAMMPS process</p>
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</dd>
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<dt>L.communication.nprocs</dt><dd><p>number of MPI processes used by LAMMPS</p>
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</dd>
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<dt>L.fixes</dt><dd><p>List of fixes in the current system</p>
|
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</dd>
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<dt>L.computes</dt><dd><p>List of active computes in the current system</p>
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</dd>
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<dt>L.dump</dt><dd><p>List of active dumps in the current system</p>
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</dd>
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<dt>L.groups</dt><dd><p>List of groups present in the current system</p>
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</dd>
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</dl>
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<p><strong>Retrieving the value of an arbitrary LAMMPS expressions</strong></p>
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<p>LAMMPS expressions can be immediately evaluated by using the <code class="docutils literal notranslate"><span class="pre">eval</span></code> method. The
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passed string parameter can be any expression containing global <a class="reference internal" href="thermo.html"><span class="doc">thermo command</span></a> values,
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variables, compute or fix data (see <a class="reference internal" href="Howto_output.html"><span class="doc">Output from LAMMPS (thermo, dumps, computes, fixes, variables)</span></a>):</p>
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<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="n">result</span> <span class="o">=</span> <span class="n">L</span><span class="o">.</span><span class="n">eval</span><span class="p">(</span><span class="s2">"ke"</span><span class="p">)</span> <span class="c1"># kinetic energy</span>
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<span class="n">result</span> <span class="o">=</span> <span class="n">L</span><span class="o">.</span><span class="n">eval</span><span class="p">(</span><span class="s2">"pe"</span><span class="p">)</span> <span class="c1"># potential energy</span>
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<span class="n">result</span> <span class="o">=</span> <span class="n">L</span><span class="o">.</span><span class="n">eval</span><span class="p">(</span><span class="s2">"v_t/2.0"</span><span class="p">)</span>
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</pre></div>
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</div>
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<p><strong>Example</strong></p>
|
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<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">PyLammps</span>
|
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|
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<span class="n">L</span> <span class="o">=</span> <span class="n">PyLammps</span><span class="p">()</span>
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<span class="n">L</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="nb">print</span><span class="p">(</span><span class="sa">f</span><span class="s2">"running simulation with </span><span class="si">{</span><span class="n">L</span><span class="o">.</span><span class="n">system</span><span class="o">.</span><span class="n">natoms</span><span class="si">}</span><span class="s2"> atoms"</span><span class="p">)</span>
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<span class="n">L</span><span class="o">.</span><span class="n">run</span><span class="p">(</span><span class="mi">1000</span><span class="p">,</span> <span class="s2">"post no"</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="mi">10</span><span class="p">):</span>
|
|
<span class="n">L</span><span class="o">.</span><span class="n">run</span><span class="p">(</span><span class="mi">100</span><span class="p">,</span> <span class="s2">"pre no post no"</span><span class="p">)</span>
|
|
<span class="n">pe</span> <span class="o">=</span> <span class="n">L</span><span class="o">.</span><span class="n">eval</span><span class="p">(</span><span class="s2">"pe"</span><span class="p">)</span>
|
|
<span class="n">ke</span> <span class="o">=</span> <span class="n">L</span><span class="o">.</span><span class="n">eval</span><span class="p">(</span><span class="s2">"ke"</span><span class="p">)</span>
|
|
<span class="nb">print</span><span class="p">(</span><span class="sa">f</span><span class="s2">"PE = </span><span class="si">{</span><span class="n">pe</span><span class="si">}</span><span class="se">\n</span><span class="s2">KE = </span><span class="si">{</span><span class="n">ke</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
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</pre></div>
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