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<h1>Source code for MMTK.ForceFields.LennardJonesFF</h1><div class="highlight"><pre>
<span class="c"># A Lennard-Jones force fields for simple liquids</span>
<span class="c">#</span>
<span class="c"># Written by Konrad Hinsen</span>
<span class="c">#</span>
<span class="sd">"""</span>
<span class="sd">Lennard-Jones force field for simple liquids</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">MMTK.ForceFields.NonBondedInteractions</span> <span class="kn">import</span> <span class="n">LJForceField</span>
<span class="kn">from</span> <span class="nn">Scientific.Geometry</span> <span class="kn">import</span> <span class="n">Vector</span>
<span class="kn">import</span> <span class="nn">copy</span>
<span class="c">#</span>
<span class="c"># The force field class</span>
<span class="c">#</span>
<div class="viewcode-block" id="LennardJonesForceField"><a class="viewcode-back" href="../../../modules.html#MMTK.ForceFields.LennardJonesFF.LennardJonesForceField">[docs]</a><span class="k">class</span> <span class="nc">LennardJonesForceField</span><span class="p">(</span><span class="n">LJForceField</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Lennard-Jones force field</span>
<span class="sd"> The Lennard-Jones parameters are taken from the atom attributes</span>
<span class="sd"> LJ_radius and LJ_energy. The pair interaction energy has the form</span>
<span class="sd"> U(r)=4*LJ_energy*((LJ_radius/r)**12-(LJ_radius/r)**6).</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">cutoff</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :param cutoff: a cutoff value or None, meaning no cutoff.</span>
<span class="sd"> Pair interactions in periodic systems are calculated</span>
<span class="sd"> using the minimum-image convention; the cutoff should</span>
<span class="sd"> therefore never be larger than half the smallest edge</span>
<span class="sd"> length of the elementary cell.</span>
<span class="sd"> :type cutoff: 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">cutoff</span><span class="p">,</span> <span class="p">)</span>
<span class="n">LJForceField</span><span class="o">.</span><span class="n">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s">'LJ'</span><span class="p">,</span> <span class="n">cutoff</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">lj_14_factor</span> <span class="o">=</span> <span class="mf">1.</span>
<span class="k">def</span> <span class="nf">ready</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">global_data</span><span class="p">):</span>
<span class="k">return</span> <span class="bp">True</span>
<span class="k">def</span> <span class="nf">collectParameters</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">universe</span><span class="p">,</span> <span class="n">global_data</span><span class="p">):</span>
<span class="k">if</span> <span class="ow">not</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">global_data</span><span class="p">,</span> <span class="s">'lj_parameters'</span><span class="p">):</span>
<span class="n">parameters</span> <span class="o">=</span> <span class="p">{}</span>
<span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">universe</span><span class="p">:</span>
<span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">o</span><span class="o">.</span><span class="n">atomList</span><span class="p">():</span>
<span class="n">parameters</span><span class="p">[</span><span class="n">a</span><span class="o">.</span><span class="n">symbol</span><span class="p">]</span> <span class="o">=</span> <span class="p">(</span><span class="n">a</span><span class="o">.</span><span class="n">LJ_energy</span><span class="p">,</span> <span class="n">a</span><span class="o">.</span><span class="n">LJ_radius</span><span class="p">,</span> <span class="mi">0</span><span class="p">)</span>
<span class="n">global_data</span><span class="o">.</span><span class="n">lj_parameters</span> <span class="o">=</span> <span class="n">parameters</span>
<span class="k">def</span> <span class="nf">_atomType</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="nb">object</span><span class="p">,</span> <span class="n">atom</span><span class="p">,</span> <span class="n">global_data</span><span class="p">):</span>
<span class="k">return</span> <span class="n">atom</span><span class="o">.</span><span class="n">symbol</span>
<span class="k">def</span> <span class="nf">_ljParameters</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="nb">type</span><span class="p">,</span> <span class="n">global_data</span><span class="p">):</span>
<span class="k">return</span> <span class="n">global_data</span><span class="o">.</span><span class="n">lj_parameters</span><span class="p">[</span><span class="nb">type</span><span class="p">]</span>
<span class="k">def</span> <span class="nf">evaluatorParameters</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">universe</span><span class="p">,</span> <span class="n">subset1</span><span class="p">,</span> <span class="n">subset2</span><span class="p">,</span> <span class="n">global_data</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">collectParameters</span><span class="p">(</span><span class="n">universe</span><span class="p">,</span> <span class="n">global_data</span><span class="p">)</span>
<span class="k">return</span> <span class="n">LJForceField</span><span class="o">.</span><span class="n">evaluatorParameters</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">universe</span><span class="p">,</span> <span class="n">subset1</span><span class="p">,</span>
<span class="n">subset2</span><span class="p">,</span> <span class="n">global_data</span><span class="p">)</span></div>
</pre></div>
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