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<div class="section" id="simulation-of-liquid-argon">
<h1>Simulation of liquid argon<a class="headerlink" href="#simulation-of-liquid-argon" title="Permalink to this headline">ΒΆ</a></h1>
<div class="highlight-python"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre> 1
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64</pre></div></td><td class="code"><div class="highlight"><pre><span class="c"># Constant-temperature constant-pressure MD simulation of Argon.</span>
<span class="c">#</span>
<span class="kn">from</span> <span class="nn">MMTK</span> <span class="kn">import</span> <span class="o">*</span>
<span class="kn">from</span> <span class="nn">MMTK.ForceFields</span> <span class="kn">import</span> <span class="n">LennardJonesForceField</span>
<span class="kn">from</span> <span class="nn">MMTK.Environment</span> <span class="kn">import</span> <span class="n">NoseThermostat</span><span class="p">,</span> <span class="n">AndersenBarostat</span>
<span class="kn">from</span> <span class="nn">MMTK.Trajectory</span> <span class="kn">import</span> <span class="n">Trajectory</span><span class="p">,</span> <span class="n">TrajectoryOutput</span><span class="p">,</span> <span class="n">LogOutput</span>
<span class="kn">from</span> <span class="nn">MMTK.Dynamics</span> <span class="kn">import</span> <span class="n">VelocityVerletIntegrator</span><span class="p">,</span> <span class="n">VelocityScaler</span><span class="p">,</span> \
<span class="n">TranslationRemover</span><span class="p">,</span> <span class="n">BarostatReset</span>
<span class="kn">import</span> <span class="nn">string</span>
<span class="kn">from</span> <span class="nn">Scientific.IO.TextFile</span> <span class="kn">import</span> <span class="n">TextFile</span>
<span class="c"># Open the configuration file and read the box size.</span>
<span class="n">conf_file</span> <span class="o">=</span> <span class="n">TextFile</span><span class="p">(</span><span class="s">'argon.conf.gz'</span><span class="p">)</span>
<span class="n">lx</span><span class="p">,</span> <span class="n">ly</span><span class="p">,</span> <span class="n">lz</span> <span class="o">=</span> <span class="nb">map</span><span class="p">(</span><span class="n">string</span><span class="o">.</span><span class="n">atof</span><span class="p">,</span> <span class="n">string</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="n">conf_file</span><span class="o">.</span><span class="n">readline</span><span class="p">()))</span>
<span class="c"># Construct a periodic universe using a Lennard-Jones (noble gas) force field</span>
<span class="c"># with a cutoff of 15 Angstrom.</span>
<span class="n">universe</span> <span class="o">=</span> <span class="n">OrthorhombicPeriodicUniverse</span><span class="p">((</span><span class="n">lx</span><span class="o">*</span><span class="n">Units</span><span class="o">.</span><span class="n">Ang</span><span class="p">,</span>
<span class="n">ly</span><span class="o">*</span><span class="n">Units</span><span class="o">.</span><span class="n">Ang</span><span class="p">,</span> <span class="n">lz</span><span class="o">*</span><span class="n">Units</span><span class="o">.</span><span class="n">Ang</span><span class="p">),</span>
<span class="n">LennardJonesForceField</span><span class="p">(</span><span class="mf">15.</span><span class="o">*</span><span class="n">Units</span><span class="o">.</span><span class="n">Ang</span><span class="p">))</span>
<span class="c"># Read the atom positions and construct the atoms.</span>
<span class="k">while</span> <span class="mi">1</span><span class="p">:</span>
<span class="n">line</span> <span class="o">=</span> <span class="n">conf_file</span><span class="o">.</span><span class="n">readline</span><span class="p">()</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">line</span><span class="p">:</span> <span class="k">break</span>
<span class="n">x</span><span class="p">,</span> <span class="n">y</span><span class="p">,</span> <span class="n">z</span> <span class="o">=</span> <span class="nb">map</span><span class="p">(</span><span class="n">string</span><span class="o">.</span><span class="n">atof</span><span class="p">,</span> <span class="n">string</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="n">line</span><span class="p">))</span>
<span class="n">universe</span><span class="o">.</span><span class="n">addObject</span><span class="p">(</span><span class="n">Atom</span><span class="p">(</span><span class="s">'Ar'</span><span class="p">,</span> <span class="n">position</span><span class="o">=</span><span class="n">Vector</span><span class="p">(</span><span class="n">x</span><span class="o">*</span><span class="n">Units</span><span class="o">.</span><span class="n">Ang</span><span class="p">,</span>
<span class="n">y</span><span class="o">*</span><span class="n">Units</span><span class="o">.</span><span class="n">Ang</span><span class="p">,</span> <span class="n">z</span><span class="o">*</span><span class="n">Units</span><span class="o">.</span><span class="n">Ang</span><span class="p">)))</span>
<span class="c"># Define thermodynamic parameters.</span>
<span class="n">temperature</span> <span class="o">=</span> <span class="mf">94.4</span><span class="o">*</span><span class="n">Units</span><span class="o">.</span><span class="n">K</span>
<span class="n">pressure</span> <span class="o">=</span> <span class="mf">1.</span><span class="o">*</span><span class="n">Units</span><span class="o">.</span><span class="n">atm</span>
<span class="c"># Add thermostat and barostat.</span>
<span class="n">universe</span><span class="o">.</span><span class="n">thermostat</span> <span class="o">=</span> <span class="n">NoseThermostat</span><span class="p">(</span><span class="n">temperature</span><span class="p">)</span>
<span class="n">universe</span><span class="o">.</span><span class="n">barostat</span> <span class="o">=</span> <span class="n">AndersenBarostat</span><span class="p">(</span><span class="n">pressure</span><span class="p">)</span>
<span class="c"># Initialize velocities.</span>
<span class="n">universe</span><span class="o">.</span><span class="n">initializeVelocitiesToTemperature</span><span class="p">(</span><span class="n">temperature</span><span class="p">)</span>
<span class="c"># Create trajectory and integrator.</span>
<span class="n">trajectory</span> <span class="o">=</span> <span class="n">Trajectory</span><span class="p">(</span><span class="n">universe</span><span class="p">,</span> <span class="s">"argon_npt.nc"</span><span class="p">,</span> <span class="s">"w"</span><span class="p">,</span> <span class="s">"Argon NPT test"</span><span class="p">)</span>
<span class="n">integrator</span> <span class="o">=</span> <span class="n">VelocityVerletIntegrator</span><span class="p">(</span><span class="n">universe</span><span class="p">,</span> <span class="n">delta_t</span><span class="o">=</span><span class="mi">10</span><span class="o">*</span><span class="n">Units</span><span class="o">.</span><span class="n">fs</span><span class="p">)</span>
<span class="c"># Periodical actions for trajectory output and text log output.</span>
<span class="n">output_actions</span> <span class="o">=</span> <span class="p">[</span><span class="n">TrajectoryOutput</span><span class="p">(</span><span class="n">trajectory</span><span class="p">,</span>
<span class="p">(</span><span class="s">'configuration'</span><span class="p">,</span> <span class="s">'energy'</span><span class="p">,</span> <span class="s">'thermodynamic'</span><span class="p">,</span>
<span class="s">'time'</span><span class="p">,</span> <span class="s">'auxiliary'</span><span class="p">),</span> <span class="mi">0</span><span class="p">,</span> <span class="bp">None</span><span class="p">,</span> <span class="mi">20</span><span class="p">),</span>
<span class="n">LogOutput</span><span class="p">(</span><span class="s">"argon.log"</span><span class="p">,</span> <span class="p">(</span><span class="s">'time'</span><span class="p">,</span> <span class="s">'energy'</span><span class="p">),</span> <span class="mi">0</span><span class="p">,</span> <span class="bp">None</span><span class="p">,</span> <span class="mi">100</span><span class="p">)]</span>
<span class="c"># Do some equilibration steps, rescaling velocities and resetting the</span>
<span class="c"># barostat in regular intervals.</span>
<span class="n">integrator</span><span class="p">(</span><span class="n">steps</span> <span class="o">=</span> <span class="mi">2000</span><span class="p">,</span>
<span class="n">actions</span> <span class="o">=</span> <span class="p">[</span><span class="n">TranslationRemover</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="bp">None</span><span class="p">,</span> <span class="mi">100</span><span class="p">),</span>
<span class="n">VelocityScaler</span><span class="p">(</span><span class="n">temperature</span><span class="p">,</span> <span class="mf">0.1</span><span class="o">*</span><span class="n">temperature</span><span class="p">,</span>
<span class="mi">0</span><span class="p">,</span> <span class="bp">None</span><span class="p">,</span> <span class="mi">100</span><span class="p">),</span>
<span class="n">BarostatReset</span><span class="p">(</span><span class="mi">100</span><span class="p">)]</span> <span class="o">+</span> <span class="n">output_actions</span><span class="p">)</span>
<span class="c"># Do some "production" steps.</span>
<span class="n">integrator</span><span class="p">(</span><span class="n">steps</span> <span class="o">=</span> <span class="mi">2000</span><span class="p">,</span>
<span class="n">actions</span> <span class="o">=</span> <span class="p">[</span><span class="n">TranslationRemover</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="bp">None</span><span class="p">,</span> <span class="mi">100</span><span class="p">)]</span> <span class="o">+</span> <span class="n">output_actions</span><span class="p">)</span>
<span class="c"># Close the trajectory.</span>
<span class="n">trajectory</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
</pre></div>
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