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<h1>Source code for MMTK.Environment</h1><div class="highlight"><pre>
<span class="c"># This module defines environment objects for universes.</span>
<span class="c">#</span>
<span class="c"># Written by Konrad Hinsen</span>
<span class="c">#</span>
<span class="sd">"""</span>
<span class="sd">Environment objects</span>
<span class="sd">Environment objects are objects that define a simulation system without</span>
<span class="sd">being composed of atoms. Examples are thermostats, barostats, external</span>
<span class="sd">fields, etc.</span>
<span class="sd">"""</span>
<span class="n">__docformat__</span> <span class="o">=</span> <span class="s">'restructuredtext'</span>
<span class="kn">from</span> <span class="nn">Scientific</span> <span class="kn">import</span> <span class="n">N</span>
<span class="c">#</span>
<span class="c"># The environment object base class</span>
<span class="c">#</span>
<span class="k">class</span> <span class="nc">EnvironmentObject</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
<span class="n">is_environment_object</span> <span class="o">=</span> <span class="mi">1</span>
<span class="k">def</span> <span class="nf">checkCompatibilityWith</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
<span class="k">pass</span>
<span class="k">def</span> <span class="nf">description</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</span> <span class="s">"o('Environment."</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">__class__</span><span class="o">.</span><span class="n">__name__</span> <span class="o">+</span> \
<span class="sb">`tuple(self.parameters)`</span> <span class="o">+</span> <span class="s">"')"</span>
<span class="c"># Type check</span>
<span class="k">def</span> <span class="nf">isEnvironmentObject</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
<span class="k">return</span> <span class="nb">hasattr</span><span class="p">(</span><span class="nb">object</span><span class="p">,</span> <span class="s">'is_environment_object'</span><span class="p">)</span>
<span class="c">#</span>
<span class="c"># Nose thermostat class</span>
<span class="c">#</span>
<div class="viewcode-block" id="NoseThermostat"><a class="viewcode-back" href="../../modules.html#MMTK.Environment.NoseThermostat">[docs]</a><span class="k">class</span> <span class="nc">NoseThermostat</span><span class="p">(</span><span class="n">EnvironmentObject</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Nose thermostat for Molecular Dynamics</span>
<span class="sd"> A thermostat object can be added to a universe and will then</span>
<span class="sd"> modify the integration algorithm to a simulation of an NVT</span>
<span class="sd"> ensemble.</span>
<span class="sd"> """</span>
<span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">temperature</span><span class="p">,</span> <span class="n">relaxation_time</span> <span class="o">=</span> <span class="mf">0.2</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :param temperature: the temperature set by the thermostat</span>
<span class="sd"> :type temperature: float</span>
<span class="sd"> :param relaxation_time: the relaxation time of the</span>
<span class="sd"> thermostat coordinate</span>
<span class="sd"> :type relaxation_time: float</span>
<span class="sd"> """</span>
<span class="bp">self</span><span class="o">.</span><span class="n">arguments</span> <span class="o">=</span> <span class="p">(</span><span class="n">temperature</span><span class="p">,</span> <span class="n">relaxation_time</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">parameters</span> <span class="o">=</span> <span class="n">N</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="n">temperature</span><span class="p">,</span> <span class="n">relaxation_time</span><span class="p">])</span>
<span class="bp">self</span><span class="o">.</span><span class="n">coordinates</span> <span class="o">=</span> <span class="n">N</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="mf">0.</span><span class="p">,</span> <span class="mf">0.</span><span class="p">])</span>
<span class="k">def</span> <span class="nf">setTemperature</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">temperature</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">parameters</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">=</span> <span class="n">temperature</span>
<span class="k">def</span> <span class="nf">setRelaxationTime</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">t</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">parameters</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">=</span> <span class="n">t</span>
<span class="k">def</span> <span class="nf">checkCompatibilityWith</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
<span class="k">if</span> <span class="n">other</span><span class="o">.</span><span class="n">__class__</span> <span class="ow">is</span> <span class="n">NoseThermostat</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s">"the universe already has a thermostat"</span><span class="p">)</span>
<span class="c">#</span>
<span class="c"># Andersen barostat class</span>
<span class="c">#</span></div>
<div class="viewcode-block" id="AndersenBarostat"><a class="viewcode-back" href="../../modules.html#MMTK.Environment.AndersenBarostat">[docs]</a><span class="k">class</span> <span class="nc">AndersenBarostat</span><span class="p">(</span><span class="n">EnvironmentObject</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Andersen barostat for Molecular Dynamics</span>
<span class="sd"> A barostat object can be added to a universe and will then</span>
<span class="sd"> together with a thermostat object modify the integration algorithm</span>
<span class="sd"> to a simulation of an NPT ensemble.</span>
<span class="sd"> """</span>
<span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">pressure</span><span class="p">,</span> <span class="n">relaxation_time</span> <span class="o">=</span> <span class="mf">1.5</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :param pressure: the pressure set by the barostat</span>
<span class="sd"> :type pressure: float</span>
<span class="sd"> :param relaxation_time: the relaxation time of the</span>
<span class="sd"> barostat coordinate</span>
<span class="sd"> :type relaxation_time: float</span>
<span class="sd"> """</span>
<span class="bp">self</span><span class="o">.</span><span class="n">arguments</span> <span class="o">=</span> <span class="p">(</span><span class="n">pressure</span><span class="p">,</span> <span class="n">relaxation_time</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">parameters</span> <span class="o">=</span> <span class="n">N</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="n">pressure</span><span class="p">,</span> <span class="n">relaxation_time</span><span class="p">])</span>
<span class="bp">self</span><span class="o">.</span><span class="n">coordinates</span> <span class="o">=</span> <span class="n">N</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="mf">0.</span><span class="p">])</span>
<span class="k">def</span> <span class="nf">setPressure</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">pressure</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">parameters</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">=</span> <span class="n">pressure</span>
<span class="k">def</span> <span class="nf">setRelaxationTime</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">t</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">parameters</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">=</span> <span class="n">t</span>
<span class="k">def</span> <span class="nf">checkCompatibilityWith</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
<span class="k">if</span> <span class="n">other</span><span class="o">.</span><span class="n">__class__</span> <span class="ow">is</span> <span class="n">AndersenBarostat</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s">"the universe already has a barostat"</span><span class="p">)</span>
</pre></div></div>
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