this is a lost cause
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Barak Hirshberg
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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 current"><a class="current reference internal" href="#">2.3.5. Executing commands</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-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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<p><span class="math notranslate nohighlight">\(\renewcommand{\AA}{\text{Å}}\)</span></p>
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<section id="executing-commands">
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<h1><span class="section-number">2.3.5. </span>Executing commands<a class="headerlink" href="#executing-commands" title="Link to this heading"></a></h1>
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<p>Once an instance of 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>,
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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>, 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> class is created, there are
|
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multiple ways to “feed” it commands. In a way that is not very different from
|
||||
running a LAMMPS input script, except that Python has many more facilities
|
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for structured programming than the LAMMPS input script syntax. Furthermore
|
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it is possible to “compute” what the next LAMMPS command should be.</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>Same as in the equivalent
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||||
<a class="reference internal" href="Library_execute.html"><span class="doc">C library functions</span></a>, commands can be read from a file, a
|
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single string, a list of strings and a block of commands in a single
|
||||
multi-line string. They are processed under the same boundary conditions
|
||||
as the C library counterparts. The example below demonstrates the use
|
||||
of <code class="xref py py-func docutils literal notranslate"><span class="pre">lammps.file()</span></code>, <code class="xref py py-func docutils literal notranslate"><span class="pre">lammps.command()</span></code>,
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||||
<code class="xref py py-func docutils literal notranslate"><span class="pre">lammps.commands_list()</span></code>, and <code class="xref py py-func docutils literal notranslate"><span class="pre">lammps.commands_string()</span></code>:</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">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="c1"># read commands from file 'in.melt'</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="s1">'in.melt'</span><span class="p">)</span>
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<span class="c1"># issue a single command</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="s1">'variable zpos index 1.0'</span><span class="p">)</span>
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||||
<span class="c1"># create 10 groups with 10 atoms each</span>
|
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<span class="n">cmds</span> <span class="o">=</span> <span class="p">[</span><span class="s2">"group g</span><span class="si">{}</span><span class="s2"> id </span><span class="si">{}</span><span class="s2">:</span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">i</span><span class="p">,</span><span class="mi">10</span><span class="o">*</span><span class="n">i</span><span class="o">+</span><span class="mi">1</span><span class="p">,</span><span class="mi">10</span><span class="o">*</span><span class="p">(</span><span class="n">i</span><span class="o">+</span><span class="mi">1</span><span class="p">))</span> <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">lmp</span><span class="o">.</span><span class="n">commands_list</span><span class="p">(</span><span class="n">cmds</span><span class="p">)</span>
|
||||
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||||
<span class="c1"># run commands from a multi-line string</span>
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||||
<span class="n">block</span> <span class="o">=</span> <span class="s2">"""</span>
|
||||
<span class="s2">clear</span>
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||||
<span class="s2">region box block 0 2 0 2 0 2</span>
|
||||
<span class="s2">create_box 1 box</span>
|
||||
<span class="s2">create_atoms 1 single 1.0 1.0 $</span><span class="si">{zpos}</span>
|
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<span class="s2">"""</span>
|
||||
<span class="n">lmp</span><span class="o">.</span><span class="n">commands_string</span><span class="p">(</span><span class="n">block</span><span class="p">)</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</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>Unlike the lammps API, the PyLammps/IPyLammps APIs allow running LAMMPS
|
||||
commands by calling equivalent member functions of <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> instances.</p>
|
||||
<p>For instance, the following LAMMPS command</p>
|
||||
<div class="highlight-LAMMPS notranslate"><div class="highlight"><pre><span></span><span class="k">region </span><span class="nv nv-Identifier">box</span><span class="w"> </span><span class="n">block</span><span class="w"> </span><span class="m">0</span><span class="w"> </span><span class="m">10</span><span class="w"> </span><span class="m">0</span><span class="w"> </span><span class="m">5</span><span class="w"> </span><span class="o">-</span><span class="m">0.5</span><span class="w"> </span><span class="m">0.5</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>can be executed using with the lammps API with the following Python code if <code class="docutils literal notranslate"><span class="pre">lmp</span></code> is an
|
||||
instance of <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>:</p>
|
||||
<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>
|
||||
|
||||
<span class="n">lmp</span> <span class="o">=</span> <span class="n">lammps</span><span class="p">()</span>
|
||||
<span class="n">lmp</span><span class="o">.</span><span class="n">command</span><span class="p">(</span><span class="s2">"region box block 0 10 0 5 -0.5 0.5"</span><span class="p">)</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>With the PyLammps interface, any LAMMPS command can be split up into arbitrary parts.
|
||||
These parts are then passed to a member function with the name of the <a class="reference internal" href="Commands_all.html"><span class="doc">command</span></a>.
|
||||
For the <a class="reference internal" href="region.html"><span class="doc">region</span></a> command that means the <code class="code docutils literal notranslate"><span class="pre">region()</span></code> method can be called.
|
||||
The arguments of the command can be passed as one string, or
|
||||
individually.</p>
|
||||
<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>
|
||||
|
||||
<span class="n">L</span> <span class="o">=</span> <span class="n">PyLammps</span><span class="p">()</span>
|
||||
|
||||
<span class="c1"># pass command parameters as one string</span>
|
||||
<span class="n">L</span><span class="o">.</span><span class="n">region</span><span class="p">(</span><span class="s2">"box block 0 10 0 5 -0.5 0.5"</span><span class="p">)</span>
|
||||
|
||||
<span class="c1"># OR pass them individually</span>
|
||||
<span class="n">L</span><span class="o">.</span><span class="n">region</span><span class="p">(</span><span class="s2">"box block"</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">10</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">5</span><span class="p">,</span> <span class="o">-</span><span class="mf">0.5</span><span class="p">,</span> <span class="mf">0.5</span><span class="p">)</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>In the latter example, all parameters except the first are Python floating-point literals. The
|
||||
member function takes the entire parameter list and transparently merges it to a single command
|
||||
string.</p>
|
||||
<p>The benefit of this approach is avoiding redundant command calls and easier
|
||||
parameterization. In the lammps API parameterization needed to be done
|
||||
manually by creating formatted command strings.</p>
|
||||
<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="n">lmp</span><span class="o">.</span><span class="n">command</span><span class="p">(</span><span class="s2">"region box block </span><span class="si">%f</span><span class="s2"> </span><span class="si">%f</span><span class="s2"> </span><span class="si">%f</span><span class="s2"> </span><span class="si">%f</span><span class="s2"> </span><span class="si">%f</span><span class="s2"> </span><span class="si">%f</span><span class="s2">"</span> <span class="o">%</span> <span class="p">(</span><span class="n">xlo</span><span class="p">,</span> <span class="n">xhi</span><span class="p">,</span> <span class="n">ylo</span><span class="p">,</span> <span class="n">yhi</span><span class="p">,</span> <span class="n">zlo</span><span class="p">,</span> <span class="n">zhi</span><span class="p">))</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>In contrast, methods of PyLammps accept parameters directly and will convert
|
||||
them automatically to a final command string.</p>
|
||||
<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="n">L</span><span class="o">.</span><span class="n">region</span><span class="p">(</span><span class="s2">"box block"</span><span class="p">,</span> <span class="n">xlo</span><span class="p">,</span> <span class="n">xhi</span><span class="p">,</span> <span class="n">ylo</span><span class="p">,</span> <span class="n">yhi</span><span class="p">,</span> <span class="n">zlo</span><span class="p">,</span> <span class="n">zhi</span><span class="p">)</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>Using these facilities, the example shown for the lammps API can be rewritten as follows:</p>
|
||||
<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>
|
||||
<span class="n">L</span> <span class="o">=</span> <span class="n">PyLammps</span><span class="p">()</span>
|
||||
|
||||
<span class="c1"># read commands from file 'in.melt'</span>
|
||||
<span class="n">L</span><span class="o">.</span><span class="n">file</span><span class="p">(</span><span class="s1">'in.melt'</span><span class="p">)</span>
|
||||
|
||||
<span class="c1"># issue a single command</span>
|
||||
<span class="n">L</span><span class="o">.</span><span class="n">variable</span><span class="p">(</span><span class="s1">'zpos'</span><span class="p">,</span> <span class="s1">'index'</span><span class="p">,</span> <span class="mf">1.0</span><span class="p">)</span>
|
||||
|
||||
<span class="c1"># create 10 groups with 10 atoms each</span>
|
||||
<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">group</span><span class="p">(</span><span class="sa">f</span><span class="s2">"g</span><span class="si">{</span><span class="n">i</span><span class="si">}</span><span class="s2">"</span><span class="p">,</span> <span class="s2">"id"</span><span class="p">,</span> <span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="mi">10</span><span class="o">*</span><span class="n">i</span><span class="o">+</span><span class="mi">1</span><span class="si">}</span><span class="s2">:</span><span class="si">{</span><span class="mi">10</span><span class="o">*</span><span class="p">(</span><span class="n">i</span><span class="o">+</span><span class="mi">1</span><span class="p">)</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
|
||||
|
||||
<span class="n">L</span><span class="o">.</span><span class="n">clear</span><span class="p">()</span>
|
||||
<span class="n">L</span><span class="o">.</span><span class="n">region</span><span class="p">(</span><span class="s2">"box block"</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">2</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">2</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">2</span><span class="p">)</span>
|
||||
<span class="n">L</span><span class="o">.</span><span class="n">create_box</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="s2">"box"</span><span class="p">)</span>
|
||||
<span class="n">L</span><span class="o">.</span><span class="n">create_atoms</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="s2">"single"</span><span class="p">,</span> <span class="mf">1.0</span><span class="p">,</span> <span class="mf">1.0</span><span class="p">,</span> <span class="s2">"$</span><span class="si">{zpos}</span><span class="s2">"</span><span class="p">)</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div></div>
|
||||
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|
||||
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||||
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Reference in New Issue
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