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<p><span class="math notranslate nohighlight">\(\renewcommand{\AA}{\text{Å}}\)</span></p>
<section id="compute-fixes-variables">
<h1><span class="section-number">2.3.8. </span>Compute, fixes, variables<a class="headerlink" href="#compute-fixes-variables" title="Link to this heading"></a></h1>
<p>This section documents accessing or modifying data from objects like
computes, fixes, or variables in LAMMPS using the <a class="reference internal" href="Python_module.html#module-lammps" title="lammps"><code class="xref py py-mod docutils literal notranslate"><span class="pre">lammps</span></code></a> module.</p>
<div class="sphinx-tabs docutils container">
<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"><p>For <a class="reference internal" href="Python_module.html#lammps.lammps.extract_compute" title="lammps.lammps.extract_compute"><code class="xref py py-meth docutils literal notranslate"><span class="pre">lammps.extract_compute()</span></code></a> and
<a class="reference internal" href="Python_module.html#lammps.lammps.extract_fix" title="lammps.lammps.extract_fix"><code class="xref py py-meth docutils literal notranslate"><span class="pre">lammps.extract_fix()</span></code></a>, the global, per-atom,
or local data calculated by the compute or fix can be accessed. What is returned
depends on whether the compute or fix calculates a scalar or vector or array.
For a scalar, a single double value is returned. If the compute or fix calculates
a vector or array, a pointer to the internal LAMMPS data is returned, which you can
use via normal Python subscripting.</p>
<p>The one exception is that for a fix that calculates a
global vector or array, a single double value from the vector or array
is returned, indexed by I (vector) or I and J (array). I,J are
zero-based indices.
See the <a class="reference internal" href="Howto_output.html"><span class="doc">Howto output</span></a> page for a discussion of
global, per-atom, and local data, and of scalar, vector, and array
data types. See the doc pages for individual <a class="reference internal" href="compute.html"><span class="doc">computes</span></a>
and <a class="reference internal" href="fix.html"><span class="doc">fixes</span></a> for a description of what they calculate and
store.</p>
<p>For <a class="reference internal" href="Python_module.html#lammps.lammps.extract_variable" title="lammps.lammps.extract_variable"><code class="xref py py-meth docutils literal notranslate"><span class="pre">lammps.extract_variable()</span></code></a>,
an <a class="reference internal" href="variable.html"><span class="doc">equal-style or atom-style variable</span></a> is evaluated and
its result returned.</p>
<p>For equal-style variables a single <code class="docutils literal notranslate"><span class="pre">c_double</span></code> value is returned and the
group argument is ignored. For atom-style variables, a vector of
<code class="docutils literal notranslate"><span class="pre">c_double</span></code> is returned, one value per atom, which you can use via normal
Python subscripting. The values will be zero for atoms not in the
specified group.</p>
<p><a class="reference internal" href="Python_module.html#lammps.numpy_wrapper.numpy_wrapper.extract_compute" title="lammps.numpy_wrapper.numpy_wrapper.extract_compute"><code class="xref py py-meth docutils literal notranslate"><span class="pre">lammps.numpy.extract_compute()</span></code></a>,
<a class="reference internal" href="Python_module.html#lammps.numpy_wrapper.numpy_wrapper.extract_fix" title="lammps.numpy_wrapper.numpy_wrapper.extract_fix"><code class="xref py py-meth docutils literal notranslate"><span class="pre">lammps.numpy.extract_fix()</span></code></a>, and
<a class="reference internal" href="Python_module.html#lammps.numpy_wrapper.numpy_wrapper.extract_variable" title="lammps.numpy_wrapper.numpy_wrapper.extract_variable"><code class="xref py py-meth docutils literal notranslate"><span class="pre">lammps.numpy.extract_variable()</span></code></a> are
equivalent NumPy implementations that return NumPy arrays instead of <code class="docutils literal notranslate"><span class="pre">ctypes</span></code> pointers.</p>
<p>The <a class="reference internal" href="Python_module.html#lammps.lammps.set_variable" title="lammps.lammps.set_variable"><code class="xref py py-meth docutils literal notranslate"><span class="pre">lammps.set_variable()</span></code></a> method sets an
existing string-style variable to a new string value, so that subsequent LAMMPS
commands can access the variable.</p>
<p><strong>Methods</strong>:</p>
<ul class="simple">
<li><p><a class="reference internal" href="Python_module.html#lammps.lammps.extract_compute" title="lammps.lammps.extract_compute"><code class="xref py py-meth docutils literal notranslate"><span class="pre">lammps.extract_compute()</span></code></a>: extract value(s) from a compute</p></li>
<li><p><a class="reference internal" href="Python_module.html#lammps.lammps.extract_fix" title="lammps.lammps.extract_fix"><code class="xref py py-meth docutils literal notranslate"><span class="pre">lammps.extract_fix()</span></code></a>: extract value(s) from a fix</p></li>
<li><p><a class="reference internal" href="Python_module.html#lammps.lammps.extract_variable" title="lammps.lammps.extract_variable"><code class="xref py py-meth docutils literal notranslate"><span class="pre">lammps.extract_variable()</span></code></a>: extract value(s) from a variable</p></li>
<li><p><a class="reference internal" href="Python_module.html#lammps.lammps.set_variable" title="lammps.lammps.set_variable"><code class="xref py py-meth docutils literal notranslate"><span class="pre">lammps.set_variable()</span></code></a>: set existing named string-style variable to value</p></li>
</ul>
<p><strong>NumPy Methods</strong>:</p>
<ul class="simple">
<li><p><a class="reference internal" href="Python_module.html#lammps.numpy_wrapper.numpy_wrapper.extract_compute" title="lammps.numpy_wrapper.numpy_wrapper.extract_compute"><code class="xref py py-meth docutils literal notranslate"><span class="pre">lammps.numpy.extract_compute()</span></code></a>: extract value(s) from a compute, return arrays as numpy arrays</p></li>
<li><p><a class="reference internal" href="Python_module.html#lammps.numpy_wrapper.numpy_wrapper.extract_fix" title="lammps.numpy_wrapper.numpy_wrapper.extract_fix"><code class="xref py py-meth docutils literal notranslate"><span class="pre">lammps.numpy.extract_fix()</span></code></a>: extract value(s) from a fix, return arrays as numpy arrays</p></li>
<li><p><a class="reference internal" href="Python_module.html#lammps.numpy_wrapper.numpy_wrapper.extract_variable" title="lammps.numpy_wrapper.numpy_wrapper.extract_variable"><code class="xref py py-meth docutils literal notranslate"><span class="pre">lammps.numpy.extract_variable()</span></code></a>: extract value(s) from a variable, return arrays as numpy arrays</p></li>
</ul>
</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>PyLammps and IPyLammps classes currently do not add any additional ways of
retrieving information out of computes and fixes. This information can still be accessed by using the lammps API:</p>
<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="n">L</span><span class="o">.</span><span class="n">lmp</span><span class="o">.</span><span class="n">extract_compute</span><span class="p">(</span><span class="o">...</span><span class="p">)</span>
<span class="n">L</span><span class="o">.</span><span class="n">lmp</span><span class="o">.</span><span class="n">extract_fix</span><span class="p">(</span><span class="o">...</span><span class="p">)</span>
<span class="c1"># OR</span>
<span class="n">L</span><span class="o">.</span><span class="n">lmp</span><span class="o">.</span><span class="n">numpy</span><span class="o">.</span><span class="n">extract_compute</span><span class="p">(</span><span class="o">...</span><span class="p">)</span>
<span class="n">L</span><span class="o">.</span><span class="n">lmp</span><span class="o">.</span><span class="n">numpy</span><span class="o">.</span><span class="n">extract_fix</span><span class="p">(</span><span class="o">...</span><span class="p">)</span>
</pre></div>
</div>
<p>LAMMPS variables can be both defined and accessed via the <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> interface.</p>
<p>To define a variable you can use the <a class="reference internal" href="variable.html"><span class="doc">variable</span></a> command:</p>
<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="n">L</span><span class="o">.</span><span class="n">variable</span><span class="p">(</span><span class="s2">&quot;a index 2&quot;</span><span class="p">)</span>
</pre></div>
</div>
<p>A dictionary of all variables is returned by the <a class="reference internal" href="Python_module.html#lammps.PyLammps.variables" title="lammps.PyLammps.variables"><code class="xref py py-attr docutils literal notranslate"><span class="pre">PyLammps.variables</span></code></a> property:</p>
<p>you can access an individual variable by retrieving a variable object from the
<code class="docutils literal notranslate"><span class="pre">L.variables</span></code> dictionary by name</p>
<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="n">a</span> <span class="o">=</span> <span class="n">L</span><span class="o">.</span><span class="n">variables</span><span class="p">[</span><span class="s1">&#39;a&#39;</span><span class="p">]</span>
</pre></div>
</div>
<p>The variable value can then be easily read and written by accessing the value
property of this object.</p>
<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="nb">print</span><span class="p">(</span><span class="n">a</span><span class="o">.</span><span class="n">value</span><span class="p">)</span>
<span class="n">a</span><span class="o">.</span><span class="n">value</span> <span class="o">=</span> <span class="mi">4</span>
</pre></div>
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