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<h1>Source code for MMTK.ForceFields.SPCEFF</h1><div class="highlight"><pre>
<span class="c"># SPCE force field</span>
<span class="c">#</span>
<span class="c"># Written by Konrad Hinsen</span>
<span class="c">#</span>
<span class="sd">"""</span>
<span class="sd">SPC/E force field for water simulations</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</span> <span class="kn">import</span> <span class="n">MMForceField</span>
<span class="k">class</span> <span class="nc">SPCEParameters</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
<span class="n">atom_type_property</span> <span class="o">=</span> <span class="s">'spce_atom_type'</span>
<span class="n">charge_property</span> <span class="o">=</span> <span class="s">'spce_charge'</span>
<span class="n">lennard_jones_1_4</span> <span class="o">=</span> <span class="mf">1.</span>
<span class="n">electrostatic_1_4</span> <span class="o">=</span> <span class="mf">1.</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="k">if</span> <span class="nb">type</span> <span class="o">==</span> <span class="s">'O'</span><span class="p">:</span>
<span class="c"># TIP3: 0.6363936, 0.315075240657</span>
<span class="k">return</span> <span class="p">(</span><span class="mf">0.650169580819</span><span class="p">,</span> <span class="mf">0.31655578902</span><span class="p">,</span> <span class="mi">0</span><span class="p">)</span>
<span class="k">elif</span> <span class="nb">type</span> <span class="o">==</span> <span class="s">'H'</span><span class="p">:</span>
<span class="k">return</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="mi">0</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s">'Unknown atom type '</span> <span class="o">+</span> <span class="nb">type</span><span class="p">)</span>
<span class="c"># Bond and angle parameters from:</span>
<span class="c"># O. Telemann, B. Jonsson, S. Engstrom</span>
<span class="c"># Mol. Phys. 60(1), 193-203 (1987)</span>
<span class="k">def</span> <span class="nf">bondParameters</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">at1</span><span class="p">,</span> <span class="n">at2</span><span class="p">):</span>
<span class="k">if</span> <span class="n">at1</span> <span class="o">==</span> <span class="s">'O'</span> <span class="ow">or</span> <span class="n">at2</span> <span class="o">==</span> <span class="s">'O'</span><span class="p">:</span>
<span class="k">return</span> <span class="p">(</span><span class="mf">0.1</span><span class="p">,</span> <span class="mf">463700.</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">return</span> <span class="p">(</span><span class="mf">0.163298086184</span><span class="p">,</span> <span class="mf">0.</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">bondAngleParameters</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">at1</span><span class="p">,</span> <span class="n">at2</span><span class="p">,</span> <span class="n">at3</span><span class="p">):</span>
<span class="k">if</span> <span class="n">at2</span> <span class="o">==</span> <span class="s">'O'</span><span class="p">:</span>
<span class="k">return</span> <span class="p">(</span><span class="mf">1.91061193216</span><span class="p">,</span> <span class="mf">383.</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">return</span> <span class="p">(</span><span class="mf">0.615490360716</span><span class="p">,</span> <span class="mf">0.</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">dihedralParameters</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">at1</span><span class="p">,</span> <span class="n">at2</span><span class="p">,</span> <span class="n">at3</span><span class="p">,</span> <span class="n">at4</span><span class="p">):</span>
<span class="k">return</span> <span class="p">[(</span><span class="mi">1</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">improperParameters</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">at1</span><span class="p">,</span> <span class="n">at2</span><span class="p">,</span> <span class="n">at3</span><span class="p">,</span> <span class="n">at4</span><span class="p">):</span>
<span class="k">return</span> <span class="p">[(</span><span class="mi">1</span><span class="p">,</span> <span class="mf">0.</span><span class="p">,</span> <span class="mf">0.</span><span class="p">)]</span>
<div class="viewcode-block" id="SPCEForceField"><a class="viewcode-back" href="../../../modules.html#MMTK.ForceFields.SPCEFF.SPCEForceField">[docs]</a><span class="k">class</span> <span class="nc">SPCEForceField</span><span class="p">(</span><span class="n">MMForceField</span><span class="o">.</span><span class="n">MMForceField</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Force field for water simulations with the SPC/E model</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">lj_options</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">es_options</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :param lj_options: parameters for Lennard-Jones</span>
<span class="sd"> interactions; one of:</span>
<span class="sd"> * a number, specifying the cutoff</span>
<span class="sd"> * None, meaning the default method</span>
<span class="sd"> (no cutoff; inclusion of all</span>
<span class="sd"> pairs, using the minimum-image</span>
<span class="sd"> conventions for periodic universes)</span>
<span class="sd"> * a dictionary with an entry "method"</span>
<span class="sd"> which specifies the calculation</span>
<span class="sd"> method as either "direct" (all pair</span>
<span class="sd"> terms) or "cutoff", with the cutoff</span>
<span class="sd"> specified by the dictionary</span>
<span class="sd"> entry "cutoff".</span>
<span class="sd"> :param es_options: parameters for electrostatic</span>
<span class="sd"> interactions; one of:</span>
<span class="sd"> * a number, specifying the cutoff</span>
<span class="sd"> * None, meaning the default method</span>
<span class="sd"> (all pairs without cutoff for</span>
<span class="sd"> non-periodic system, Ewald summation</span>
<span class="sd"> for periodic systems)</span>
<span class="sd"> * a dictionary with an entry "method"</span>
<span class="sd"> which specifies the calculation</span>
<span class="sd"> method as either "direct" (all pair</span>
<span class="sd"> terms), "cutoff" (with the cutoff</span>
<span class="sd"> specified by the dictionary</span>
<span class="sd"> entry "cutoff"), "ewald" (Ewald</span>
<span class="sd"> summation, only for periodic</span>
<span class="sd"> universes), "screened" or</span>
<span class="sd"> "multipole" (fast-multipole method).</span>
<span class="sd"> """</span>
<span class="n">MMForceField</span><span class="o">.</span><span class="n">MMForceField</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">'SPCE'</span><span class="p">,</span> <span class="n">SPCEParameters</span><span class="p">(),</span>
<span class="n">lj_options</span><span class="p">,</span> <span class="n">es_options</span><span class="p">)</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">lj_options</span><span class="p">,</span> <span class="n">es_options</span><span class="p">)</span></div>
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