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<h1>Source code for MMTK.Universe</h1><div class="highlight"><pre>
<span class="c"># This module implements the various types of universes</span>
<span class="c"># (infinite, periodic etc.). A universe defines the</span>
<span class="c"># geometry of space, the force field, and external interactions</span>
<span class="c"># (boundary conditions, external fields, etc.)</span>
<span class="c">#</span>
<span class="c"># Written by Konrad Hinsen</span>
<span class="c">#</span>
<span class="sd">"""</span>
<span class="sd">Universes</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</span> <span class="kn">import</span> <span class="n">Bonds</span><span class="p">,</span> <span class="n">ChemicalObjects</span><span class="p">,</span> <span class="n">Collections</span><span class="p">,</span> <span class="n">Environment</span><span class="p">,</span> \
<span class="n">Random</span><span class="p">,</span> <span class="n">Utility</span><span class="p">,</span> <span class="n">ParticleProperties</span><span class="p">,</span> <span class="n">Visualization</span>
<span class="kn">from</span> <span class="nn">Scientific.Geometry</span> <span class="kn">import</span> <span class="n">Transformation</span>
<span class="kn">from</span> <span class="nn">Scientific.Geometry</span> <span class="kn">import</span> <span class="n">Vector</span><span class="p">,</span> <span class="n">isVector</span>
<span class="kn">from</span> <span class="nn">Scientific</span> <span class="kn">import</span> <span class="n">N</span>
<span class="kn">import</span> <span class="nn">copy</span>
<span class="k">try</span><span class="p">:</span>
<span class="kn">import</span> <span class="nn">threading</span>
<span class="k">if</span> <span class="ow">not</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">threading</span><span class="p">,</span> <span class="s">'Thread'</span><span class="p">):</span>
<span class="n">threading</span> <span class="o">=</span> <span class="bp">None</span>
<span class="k">except</span> <span class="ne">ImportError</span><span class="p">:</span>
<span class="n">threading</span> <span class="o">=</span> <span class="bp">None</span>
<span class="c">#</span>
<span class="c"># The base class for all universes.</span>
<span class="c">#</span>
<div class="viewcode-block" id="Universe"><a class="viewcode-back" href="../../modules.html#MMTK.Universe.Universe">[docs]</a><span class="k">class</span> <span class="nc">Universe</span><span class="p">(</span><span class="n">Collections</span><span class="o">.</span><span class="n">GroupOfAtoms</span><span class="p">,</span> <span class="n">Visualization</span><span class="o">.</span><span class="n">Viewable</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Universe</span>
<span class="sd"> A universe represents a complete model of a chemical system, i.e.</span>
<span class="sd"> the molecules, their environment (topology, boundary conditions,</span>
<span class="sd"> thermostats, etc.), and optionally a force field.</span>
<span class="sd"> The class Universe is an abstract base class that defines</span>
<span class="sd"> properties common to all kinds of universes. To create universe</span>
<span class="sd"> objects, use one of its subclasses.</span>
<span class="sd"> In addition to the methods listed below, universe objects support</span>
<span class="sd"> the following operations (u is any universe object, o is any</span>
<span class="sd"> chemical object):</span>
<span class="sd"> * len(u) yields the number of chemical objects in the universe</span>
<span class="sd"> * u[i] returns object number i</span>
<span class="sd"> * u.name = o adds o to the universe and also makes it accessible as</span>
<span class="sd"> an attribute</span>
<span class="sd"> * del u.name removes the object that was assigned to u.name from</span>
<span class="sd"> the universe</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">forcefield</span><span class="p">,</span> <span class="n">properties</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_forcefield</span> <span class="o">=</span> <span class="n">forcefield</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_evaluator</span> <span class="o">=</span> <span class="p">{}</span>
<span class="bp">self</span><span class="o">.</span><span class="n">name</span> <span class="o">=</span> <span class="s">''</span>
<span class="k">if</span> <span class="n">properties</span><span class="o">.</span><span class="n">has_key</span><span class="p">(</span><span class="s">'name'</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">name</span> <span class="o">=</span> <span class="n">properties</span><span class="p">[</span><span class="s">'name'</span><span class="p">]</span>
<span class="k">del</span> <span class="n">properties</span><span class="p">[</span><span class="s">'name'</span><span class="p">]</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_objects</span> <span class="o">=</span> <span class="n">Collections</span><span class="o">.</span><span class="n">Collection</span><span class="p">()</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_environment</span> <span class="o">=</span> <span class="p">[]</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_configuration</span> <span class="o">=</span> <span class="bp">None</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_masses</span> <span class="o">=</span> <span class="bp">None</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_atom_properties</span> <span class="o">=</span> <span class="p">{}</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_atoms</span> <span class="o">=</span> <span class="bp">None</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_bond_database</span> <span class="o">=</span> <span class="bp">None</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_bond_pairs</span> <span class="o">=</span> <span class="bp">None</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_version</span> <span class="o">=</span> <span class="mi">0</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_np</span> <span class="o">=</span> <span class="bp">None</span>
<span class="n">is_universe</span> <span class="o">=</span> <span class="bp">True</span>
<span class="n">is_periodic</span> <span class="o">=</span> <span class="bp">False</span>
<span class="n">is_orthogonal</span> <span class="o">=</span> <span class="bp">False</span>
<span class="k">def</span> <span class="nf">__getstate__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="n">state</span> <span class="o">=</span> <span class="n">copy</span><span class="o">.</span><span class="n">copy</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">__dict__</span><span class="p">)</span>
<span class="n">state</span><span class="p">[</span><span class="s">'_evaluator'</span><span class="p">]</span> <span class="o">=</span> <span class="p">{}</span>
<span class="n">state</span><span class="p">[</span><span class="s">'_configuration'</span><span class="p">]</span> <span class="o">=</span> <span class="bp">None</span>
<span class="k">del</span> <span class="n">state</span><span class="p">[</span><span class="s">'_masses'</span><span class="p">]</span>
<span class="k">del</span> <span class="n">state</span><span class="p">[</span><span class="s">'_bond_database'</span><span class="p">]</span>
<span class="k">del</span> <span class="n">state</span><span class="p">[</span><span class="s">'_bond_pairs'</span><span class="p">]</span>
<span class="k">del</span> <span class="n">state</span><span class="p">[</span><span class="s">'_np'</span><span class="p">]</span>
<span class="k">del</span> <span class="n">state</span><span class="p">[</span><span class="s">'_spec'</span><span class="p">]</span>
<span class="k">return</span> <span class="n">state</span>
<span class="k">def</span> <span class="nf">__setstate__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">state</span><span class="p">):</span>
<span class="n">state</span><span class="p">[</span><span class="s">'_np'</span><span class="p">]</span> <span class="o">=</span> <span class="bp">None</span>
<span class="n">state</span><span class="p">[</span><span class="s">'_atoms'</span><span class="p">]</span> <span class="o">=</span> <span class="bp">None</span>
<span class="n">state</span><span class="p">[</span><span class="s">'_bond_database'</span><span class="p">]</span> <span class="o">=</span> <span class="bp">None</span>
<span class="n">state</span><span class="p">[</span><span class="s">'_bond_pairs'</span><span class="p">]</span> <span class="o">=</span> <span class="bp">None</span>
<span class="bp">self</span><span class="o">.</span><span class="n">__dict__</span><span class="p">[</span><span class="s">'_environment'</span><span class="p">]</span> <span class="o">=</span> <span class="p">[]</span>
<span class="k">if</span> <span class="n">state</span><span class="o">.</span><span class="n">has_key</span><span class="p">(</span><span class="s">'atom_properties'</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">__dict__</span><span class="p">[</span><span class="s">'_atom_properties'</span><span class="p">]</span> <span class="o">=</span> <span class="n">state</span><span class="p">[</span><span class="s">'atom_properties'</span><span class="p">]</span>
<span class="k">del</span> <span class="n">state</span><span class="p">[</span><span class="s">'atom_properties'</span><span class="p">]</span>
<span class="k">for</span> <span class="n">attr</span><span class="p">,</span> <span class="n">value</span> <span class="ow">in</span> <span class="n">state</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
<span class="bp">self</span><span class="o">.</span><span class="n">__dict__</span><span class="p">[</span><span class="n">attr</span><span class="p">]</span> <span class="o">=</span> <span class="n">value</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_evaluator</span> <span class="o">=</span> <span class="p">{}</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_masses</span> <span class="o">=</span> <span class="bp">None</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_createSpec</span><span class="p">()</span>
<span class="k">def</span> <span class="nf">__len__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_objects</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">__getitem__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">item</span><span class="p">):</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_objects</span><span class="p">[</span><span class="n">item</span><span class="p">]</span>
<span class="k">def</span> <span class="nf">__setattr__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">attr</span><span class="p">,</span> <span class="n">value</span><span class="p">):</span>
<span class="k">if</span> <span class="n">attr</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">!=</span> <span class="s">'_'</span> <span class="ow">and</span> <span class="bp">self</span><span class="o">.</span><span class="n">__dict__</span><span class="o">.</span><span class="n">has_key</span><span class="p">(</span><span class="n">attr</span><span class="p">):</span>
<span class="k">try</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">removeObject</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">__dict__</span><span class="p">[</span><span class="n">attr</span><span class="p">])</span>
<span class="k">except</span> <span class="ne">ValueError</span><span class="p">:</span>
<span class="k">pass</span>
<span class="bp">self</span><span class="o">.</span><span class="n">__dict__</span><span class="p">[</span><span class="n">attr</span><span class="p">]</span> <span class="o">=</span> <span class="n">value</span>
<span class="k">if</span> <span class="n">attr</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">!=</span> <span class="s">'_'</span> <span class="ow">and</span> <span class="p">(</span><span class="n">ChemicalObjects</span><span class="o">.</span><span class="n">isChemicalObject</span><span class="p">(</span><span class="n">value</span><span class="p">)</span>
<span class="ow">or</span> <span class="n">Environment</span><span class="o">.</span><span class="n">isEnvironmentObject</span><span class="p">(</span><span class="n">value</span><span class="p">)):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">addObject</span><span class="p">(</span><span class="n">value</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">__delattr__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">attr</span><span class="p">):</span>
<span class="k">try</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">removeObject</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">__dict__</span><span class="p">[</span><span class="n">attr</span><span class="p">])</span>
<span class="k">except</span> <span class="ne">ValueError</span><span class="p">:</span>
<span class="k">pass</span>
<span class="k">del</span> <span class="bp">self</span><span class="o">.</span><span class="n">__dict__</span><span class="p">[</span><span class="n">attr</span><span class="p">]</span>
<span class="k">def</span> <span class="nf">__repr__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</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="s">' '</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span> <span class="o">+</span> <span class="s">' containing '</span> <span class="o">+</span> \
<span class="sb">`len(self._objects)`</span> <span class="o">+</span> <span class="s">' objects.'</span>
<span class="n">__str__</span> <span class="o">=</span> <span class="n">__repr__</span>
<span class="k">def</span> <span class="nf">__copy__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</span> <span class="n">copy</span><span class="o">.</span><span class="n">deepcopy</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
<div class="viewcode-block" id="Universe.objectList"><a class="viewcode-back" href="../../modules.html#MMTK.Universe.Universe.objectList">[docs]</a> <span class="k">def</span> <span class="nf">objectList</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">klass</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :param klass: an optional class argument</span>
<span class="sd"> :type klass: class</span>
<span class="sd"> :returns: a list of all chemical objects in the universe.</span>
<span class="sd"> If klass is given, only objects that are instances</span>
<span class="sd"> of klass are returned.</span>
<span class="sd"> :rtype: list</span>
<span class="sd"> """</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_objects</span><span class="o">.</span><span class="n">objectList</span><span class="p">(</span><span class="n">klass</span><span class="p">)</span>
</div>
<div class="viewcode-block" id="Universe.environmentObjectList"><a class="viewcode-back" href="../../modules.html#MMTK.Universe.Universe.environmentObjectList">[docs]</a> <span class="k">def</span> <span class="nf">environmentObjectList</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">klass</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :param klass: an optional class argument</span>
<span class="sd"> :type klass: class</span>
<span class="sd"> :returns: a list of all environment objects in the universe.</span>
<span class="sd"> If klass is given, only objects that are instances</span>
<span class="sd"> of klass are returned.</span>
<span class="sd"> :rtype: list</span>
<span class="sd"> """</span>
<span class="k">if</span> <span class="n">klass</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_environment</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">return</span> <span class="nb">filter</span><span class="p">(</span><span class="k">lambda</span> <span class="n">o</span><span class="p">,</span> <span class="n">k</span><span class="o">=</span><span class="n">klass</span><span class="p">:</span> <span class="n">o</span><span class="o">.</span><span class="n">__class__</span> <span class="ow">is</span> <span class="n">k</span><span class="p">,</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_environment</span><span class="p">)</span>
</div>
<div class="viewcode-block" id="Universe.atomList"><a class="viewcode-back" href="../../modules.html#MMTK.Universe.Universe.atomList">[docs]</a> <span class="k">def</span> <span class="nf">atomList</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :returns: a list of all atoms in the universe</span>
<span class="sd"> :rtype: list</span>
<span class="sd"> """</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_atoms</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_atoms</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_objects</span><span class="o">.</span><span class="n">atomList</span><span class="p">()</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_atoms</span>
</div>
<span class="k">def</span> <span class="nf">atomIterator</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_objects</span><span class="o">.</span><span class="n">atomIterator</span><span class="p">()</span>
<span class="k">def</span> <span class="nf">bondedUnits</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_objects</span><span class="o">.</span><span class="n">bondedUnits</span><span class="p">()</span>
<div class="viewcode-block" id="Universe.universe"><a class="viewcode-back" href="../../modules.html#MMTK.Universe.Universe.universe">[docs]</a> <span class="k">def</span> <span class="nf">universe</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :returns: the universe itself</span>
<span class="sd"> """</span>
<span class="k">return</span> <span class="bp">self</span>
</div>
<div class="viewcode-block" id="Universe.addObject"><a class="viewcode-back" href="../../modules.html#MMTK.Universe.Universe.addObject">[docs]</a> <span class="k">def</span> <span class="nf">addObject</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">steal</span> <span class="o">=</span> <span class="bp">False</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Adds object to the universe. If object is a Collection,</span>
<span class="sd"> all elements of the Collection are added to the universe.</span>
<span class="sd"> :param object: the object (chemical or environment) to be added</span>
<span class="sd"> :param steal: if True, permit stealing the object from another</span>
<span class="sd"> universe, otherwise the object must not yet be</span>
<span class="sd"> attached to any universe.</span>
<span class="sd"> :type steal: bool</span>
<span class="sd"> """</span>
<span class="k">if</span> <span class="n">ChemicalObjects</span><span class="o">.</span><span class="n">isChemicalObject</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
<span class="k">if</span> <span class="p">(</span><span class="ow">not</span> <span class="n">steal</span><span class="p">)</span> <span class="ow">and</span> <span class="nb">object</span><span class="o">.</span><span class="n">parent</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span>
<span class="k">if</span> <span class="n">isUniverse</span><span class="p">(</span><span class="nb">object</span><span class="o">.</span><span class="n">parent</span><span class="p">):</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="sb">`object`</span> <span class="o">+</span>
<span class="s">' is already in another universe'</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="sb">`object`</span> <span class="o">+</span> <span class="s">' is part of another object'</span><span class="p">)</span>
<span class="nb">object</span><span class="o">.</span><span class="n">parent</span> <span class="o">=</span> <span class="bp">self</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_objects</span><span class="o">.</span><span class="n">addObject</span><span class="p">(</span><span class="nb">object</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_changed</span><span class="p">(</span><span class="bp">True</span><span class="p">)</span>
<span class="k">elif</span> <span class="n">Environment</span><span class="o">.</span><span class="n">isEnvironmentObject</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
<span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_environment</span><span class="p">:</span>
<span class="n">o</span><span class="o">.</span><span class="n">checkCompatibilityWith</span><span class="p">(</span><span class="nb">object</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_environment</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">object</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_changed</span><span class="p">(</span><span class="bp">False</span><span class="p">)</span>
<span class="k">elif</span> <span class="n">Collections</span><span class="o">.</span><span class="n">isCollection</span><span class="p">(</span><span class="nb">object</span><span class="p">)</span> \
<span class="ow">or</span> <span class="n">Utility</span><span class="o">.</span><span class="n">isSequenceObject</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
<span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="nb">object</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">addObject</span><span class="p">(</span><span class="n">o</span><span class="p">,</span> <span class="n">steal</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">TypeError</span><span class="p">(</span><span class="nb">repr</span><span class="p">(</span><span class="nb">object</span><span class="p">)</span> <span class="o">+</span> <span class="s">' cannot be added to a universe'</span><span class="p">)</span>
</div>
<div class="viewcode-block" id="Universe.removeObject"><a class="viewcode-back" href="../../modules.html#MMTK.Universe.Universe.removeObject">[docs]</a> <span class="k">def</span> <span class="nf">removeObject</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="sd">"""</span>
<span class="sd"> Removes object from the universe. If object is a Collection,</span>
<span class="sd"> each of its elements is removed. The object to be removed must</span>
<span class="sd"> be in the universe.</span>
<span class="sd"> :param object: the object (chemical or environment) to be removed</span>
<span class="sd"> """</span>
<span class="k">if</span> <span class="n">ChemicalObjects</span><span class="o">.</span><span class="n">isChemicalObject</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
<span class="k">if</span> <span class="nb">object</span><span class="o">.</span><span class="n">parent</span> <span class="o">!=</span> <span class="bp">self</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="sb">`object`</span> <span class="o">+</span> <span class="s">' is not in this universe.'</span><span class="p">)</span>
<span class="nb">object</span><span class="o">.</span><span class="n">parent</span> <span class="o">=</span> <span class="bp">None</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_objects</span><span class="o">.</span><span class="n">removeObject</span><span class="p">(</span><span class="nb">object</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_changed</span><span class="p">(</span><span class="bp">True</span><span class="p">)</span>
<span class="k">elif</span> <span class="n">Collections</span><span class="o">.</span><span class="n">isCollection</span><span class="p">(</span><span class="nb">object</span><span class="p">)</span> \
<span class="ow">or</span> <span class="p">(</span><span class="n">Utility</span><span class="o">.</span><span class="n">isSequenceObject</span><span class="p">(</span><span class="nb">object</span><span class="p">)</span>
<span class="c"># Strings are nasty because their elements are strings</span>
<span class="c"># as well. This creates infinite recursion without</span>
<span class="c"># this special-case handling.</span>
<span class="ow">and</span> <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="nb">object</span><span class="p">,</span> <span class="nb">basestring</span><span class="p">)):</span>
<span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="nb">object</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">removeObject</span><span class="p">(</span><span class="n">o</span><span class="p">)</span>
<span class="k">elif</span> <span class="n">Environment</span><span class="o">.</span><span class="n">isEnvironmentObject</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_environment</span><span class="o">.</span><span class="n">remove</span><span class="p">(</span><span class="nb">object</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_changed</span><span class="p">(</span><span class="bp">False</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="sb">`object`</span> <span class="o">+</span> <span class="s">' is not in this universe.'</span><span class="p">)</span>
</div>
<div class="viewcode-block" id="Universe.selectShell"><a class="viewcode-back" href="../../modules.html#MMTK.Universe.Universe.selectShell">[docs]</a> <span class="k">def</span> <span class="nf">selectShell</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">point</span><span class="p">,</span> <span class="n">r1</span><span class="p">,</span> <span class="n">r2</span><span class="o">=</span><span class="mf">0.</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :param point: a point in space</span>
<span class="sd"> :type point: Scientific.Geometry.Vector</span>
<span class="sd"> :param r1: one of the radii of a spherical shell</span>
<span class="sd"> :type r1: float</span>
<span class="sd"> :param r2: the other of the two radii of a spherical shell</span>
<span class="sd"> :type r2: float</span>
<span class="sd"> :returns: a Collection of all objects in the universe whose</span>
<span class="sd"> distance from point lies between r1 and r2.</span>
<span class="sd"> """</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_objects</span><span class="o">.</span><span class="n">selectShell</span><span class="p">(</span><span class="n">point</span><span class="p">,</span> <span class="n">r1</span><span class="p">,</span> <span class="n">r2</span><span class="p">)</span>
</div>
<div class="viewcode-block" id="Universe.selectBox"><a class="viewcode-back" href="../../modules.html#MMTK.Universe.Universe.selectBox">[docs]</a> <span class="k">def</span> <span class="nf">selectBox</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">p1</span><span class="p">,</span> <span class="n">p2</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :param p1: one corner of a box in space</span>
<span class="sd"> :type p1: Scientific.Geometry.Vector</span>
<span class="sd"> :param p2: the other corner of a box in space</span>
<span class="sd"> :type p2: Scientific.Geometry.Vector</span>
<span class="sd"> :returns: a Collection of all objects in the universe that lie</span>
<span class="sd"> within the box whose diagonally opposite corners are</span>
<span class="sd"> given by p1 and p2.</span>
<span class="sd"> """</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_objects</span><span class="o">.</span><span class="n">selectBox</span><span class="p">(</span><span class="n">p1</span><span class="p">,</span> <span class="n">p2</span><span class="p">)</span>
</div>
<span class="k">def</span> <span class="nf">_changed</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">system_size_changed</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_evaluator</span> <span class="o">=</span> <span class="p">{}</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_bond_database</span> <span class="o">=</span> <span class="bp">None</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_version</span> <span class="o">+=</span> <span class="mi">1</span>
<span class="k">if</span> <span class="n">system_size_changed</span><span class="p">:</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_configuration</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span>
<span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">atomList</span><span class="p">():</span>
<span class="n">a</span><span class="o">.</span><span class="n">unsetArray</span><span class="p">()</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_configuration</span> <span class="o">=</span> <span class="bp">None</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_masses</span> <span class="o">=</span> <span class="bp">None</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_atom_properties</span> <span class="o">=</span> <span class="p">{}</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_atoms</span> <span class="o">=</span> <span class="bp">None</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_np</span> <span class="o">=</span> <span class="bp">None</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_bond_pairs</span> <span class="o">=</span> <span class="bp">None</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_configuration</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_configuration</span><span class="o">.</span><span class="n">version</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_version</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_masses</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_masses</span><span class="o">.</span><span class="n">version</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_version</span>
<div class="viewcode-block" id="Universe.acquireReadStateLock"><a class="viewcode-back" href="../../modules.html#MMTK.Universe.Universe.acquireReadStateLock">[docs]</a> <span class="k">def</span> <span class="nf">acquireReadStateLock</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Acquire the universe read state lock. Any application that</span>
<span class="sd"> uses threading must acquire this lock prior to accessing the</span>
<span class="sd"> current state of the universe, in particular its configuration</span>
<span class="sd"> (particle positions). This guarantees the consistency of the</span>
<span class="sd"> data; while any thread holds the read state lock, no other</span>
<span class="sd"> thread can obtain the write state lock that permits modifying</span>
<span class="sd"> the state. The read state lock should be released as soon as</span>
<span class="sd"> possible.</span>
<span class="sd"> The read state lock can be acquired only if no thread holds</span>
<span class="sd"> the write state lock. If the read state lock cannot be</span>
<span class="sd"> acquired immediately, the thread will be blocked until</span>
<span class="sd"> it becomes available. Any number of threads can acquire</span>
<span class="sd"> the read state lock simultaneously.</span>
<span class="sd"> """</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_spec</span><span class="o">.</span><span class="n">stateLock</span><span class="p">(</span><span class="mi">1</span><span class="p">)</span>
</div>
<div class="viewcode-block" id="Universe.acquireWriteStateLock"><a class="viewcode-back" href="../../modules.html#MMTK.Universe.Universe.acquireWriteStateLock">[docs]</a> <span class="k">def</span> <span class="nf">acquireWriteStateLock</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Acquire the universe write state lock. Any application that</span>
<span class="sd"> uses threading must acquire this lock prior to modifying the</span>
<span class="sd"> current state of the universe, in particular its configuration</span>
<span class="sd"> (particle positions). This guarantees the consistency of the</span>
<span class="sd"> data; while any thread holds the write state lock, no other</span>
<span class="sd"> thread can obtain the read state lock that permits accessing</span>
<span class="sd"> the state. The write state lock should be released as soon as</span>
<span class="sd"> possible.</span>
<span class="sd"> The write state lock can be acquired only if no other thread</span>
<span class="sd"> holds either the read state lock or the write state lock. If</span>
<span class="sd"> the write state lock cannot be acquired immediately, the</span>
<span class="sd"> thread will be blocked until it becomes available.</span>
<span class="sd"> """</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_spec</span><span class="o">.</span><span class="n">stateLock</span><span class="p">(</span><span class="o">-</span><span class="mi">1</span><span class="p">)</span>
</div>
<div class="viewcode-block" id="Universe.releaseReadStateLock"><a class="viewcode-back" href="../../modules.html#MMTK.Universe.Universe.releaseReadStateLock">[docs]</a> <span class="k">def</span> <span class="nf">releaseReadStateLock</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">write</span><span class="o">=</span><span class="bp">False</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Release the universe read state lock.</span>
<span class="sd"> """</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_spec</span><span class="o">.</span><span class="n">stateLock</span><span class="p">(</span><span class="mi">2</span><span class="p">)</span>
</div>
<div class="viewcode-block" id="Universe.releaseWriteStateLock"><a class="viewcode-back" href="../../modules.html#MMTK.Universe.Universe.releaseWriteStateLock">[docs]</a> <span class="k">def</span> <span class="nf">releaseWriteStateLock</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">write</span><span class="o">=</span><span class="bp">False</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Release the universe write state lock.</span>
<span class="sd"> """</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_spec</span><span class="o">.</span><span class="n">stateLock</span><span class="p">(</span><span class="o">-</span><span class="mi">2</span><span class="p">)</span>
</div>
<div class="viewcode-block" id="Universe.acquireConfigurationChangeLock"><a class="viewcode-back" href="../../modules.html#MMTK.Universe.Universe.acquireConfigurationChangeLock">[docs]</a> <span class="k">def</span> <span class="nf">acquireConfigurationChangeLock</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">waitflag</span><span class="o">=</span><span class="bp">True</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Acquire the configuration change lock. This lock should be</span>
<span class="sd"> acquired before starting an algorithm that changes the</span>
<span class="sd"> configuration continuously, e.g. minimization or molecular dynamics</span>
<span class="sd"> algorithms. This guarantees the proper order of execution when</span>
<span class="sd"> several such operations are started in succession. For example,</span>
<span class="sd"> when a minimization should be followed by a dynamics run,</span>
<span class="sd"> the use of this flag permits both operations to be started</span>
<span class="sd"> as background tasks which will be executed one after the other,</span>
<span class="sd"> permitting other threads to run in parallel.</span>
<span class="sd"> The configuration change lock should not be confused with</span>
<span class="sd"> the universe state lock. The former guarantees the proper</span>
<span class="sd"> sequence of long-running algorithms, whereas the latter</span>
<span class="sd"> guarantees the consistency of the data. A dynamics algorithm,</span>
<span class="sd"> for example, keeps the configuration change lock from the</span>
<span class="sd"> beginning to the end, but acquires the universe state lock</span>
<span class="sd"> only immediately before modifying configuration and velocities,</span>
<span class="sd"> and releases it immediately afterwards.</span>
<span class="sd"> :param waitflag: if true, the method waits until the lock</span>
<span class="sd"> becomes available; this is the most common mode.</span>
<span class="sd"> If false, the method returns immediately even</span>
<span class="sd"> if another thread holds the lock.</span>
<span class="sd"> :type waitflag: bool</span>
<span class="sd"> :returns: a flag indicating if the lock was successfully</span>
<span class="sd"> acquired (1) or not (0).</span>
<span class="sd"> :rtype: int</span>
<span class="sd"> """</span>
<span class="k">if</span> <span class="n">waitflag</span><span class="p">:</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_spec</span><span class="o">.</span><span class="n">configurationChangeLock</span><span class="p">(</span><span class="mi">1</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_spec</span><span class="o">.</span><span class="n">configurationChangeLock</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span>
</div>
<div class="viewcode-block" id="Universe.releaseConfigurationChangeLock"><a class="viewcode-back" href="../../modules.html#MMTK.Universe.Universe.releaseConfigurationChangeLock">[docs]</a> <span class="k">def</span> <span class="nf">releaseConfigurationChangeLock</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Releases the configuration change lock.</span>
<span class="sd"> """</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_spec</span><span class="o">.</span><span class="n">configurationChangeLock</span><span class="p">(</span><span class="mi">2</span><span class="p">)</span>
</div>
<div class="viewcode-block" id="Universe.setForceField"><a class="viewcode-back" href="../../modules.html#MMTK.Universe.Universe.setForceField">[docs]</a> <span class="k">def</span> <span class="nf">setForceField</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">forcefield</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :param forcefield: the new forcefield for this universe</span>
<span class="sd"> :type forcefield: :class:`~MMTK.ForceFields.ForceField.ForceField`</span>
<span class="sd"> """</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_forcefield</span> <span class="o">=</span> <span class="n">forcefield</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_evaluator</span> <span class="o">=</span> <span class="p">{}</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_bond_database</span> <span class="o">=</span> <span class="bp">None</span>
</div>
<span class="k">def</span> <span class="nf">position</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">conf</span><span class="p">):</span>
<span class="k">if</span> <span class="n">ChemicalObjects</span><span class="o">.</span><span class="n">isChemicalObject</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
<span class="k">return</span> <span class="nb">object</span><span class="o">.</span><span class="n">position</span><span class="p">(</span><span class="n">conf</span><span class="p">)</span>
<span class="k">elif</span> <span class="n">isVector</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
<span class="k">return</span> <span class="nb">object</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">return</span> <span class="n">Vector</span><span class="p">(</span><span class="nb">object</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">numberOfAtoms</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_objects</span><span class="o">.</span><span class="n">numberOfAtoms</span><span class="p">()</span>
<span class="k">def</span> <span class="nf">numberOfPoints</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_np</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_np</span> <span class="o">=</span> <span class="n">Collections</span><span class="o">.</span><span class="n">GroupOfAtoms</span><span class="o">.</span><span class="n">numberOfPoints</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_np</span>
<span class="n">numberOfCartesianCoordinates</span> <span class="o">=</span> <span class="n">numberOfPoints</span>
<div class="viewcode-block" id="Universe.configuration"><a class="viewcode-back" href="../../modules.html#MMTK.Universe.Universe.configuration">[docs]</a> <span class="k">def</span> <span class="nf">configuration</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :returns: the configuration object describing the current</span>
<span class="sd"> configuration of the universe. Note that this is not a</span>
<span class="sd"> copy of the current state, but a reference: the positions</span>
<span class="sd"> in the configuration object will change when coordinate</span>
<span class="sd"> changes are applied to the universe in whatever way.</span>
<span class="sd"> :rtype: :class:`~MMTK.ParticleProperties.Configuration`</span>
<span class="sd"> """</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_configuration</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">np</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">numberOfAtoms</span><span class="p">()</span>
<span class="n">coordinates</span> <span class="o">=</span> <span class="n">N</span><span class="o">.</span><span class="n">zeros</span><span class="p">((</span><span class="n">np</span><span class="p">,</span> <span class="mi">3</span><span class="p">),</span> <span class="n">N</span><span class="o">.</span><span class="n">Float</span><span class="p">)</span>
<span class="n">index_map</span> <span class="o">=</span> <span class="p">{}</span>
<span class="n">redef</span> <span class="o">=</span> <span class="p">[]</span>
<span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">atomList</span><span class="p">():</span>
<span class="k">if</span> <span class="n">a</span><span class="o">.</span><span class="n">index</span> <span class="ow">is</span> <span class="bp">None</span> <span class="ow">or</span> <span class="n">a</span><span class="o">.</span><span class="n">index</span> <span class="o">>=</span> <span class="n">np</span><span class="p">:</span>
<span class="n">redef</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">a</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">if</span> <span class="n">index_map</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">a</span><span class="o">.</span><span class="n">index</span><span class="p">,</span> <span class="bp">None</span><span class="p">)</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">index_map</span><span class="p">[</span><span class="n">a</span><span class="o">.</span><span class="n">index</span><span class="p">]</span> <span class="o">=</span> <span class="n">a</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">redef</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">a</span><span class="p">)</span>
<span class="n">free_indices</span> <span class="o">=</span> <span class="p">[</span><span class="n">i</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">xrange</span><span class="p">(</span><span class="n">np</span><span class="p">)</span>
<span class="k">if</span> <span class="n">index_map</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="bp">None</span><span class="p">)</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">]</span>
<span class="k">assert</span> <span class="nb">len</span><span class="p">(</span><span class="n">free_indices</span><span class="p">)</span> <span class="o">==</span> <span class="nb">len</span><span class="p">(</span><span class="n">redef</span><span class="p">)</span>
<span class="k">for</span> <span class="n">a</span><span class="p">,</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span><span class="n">redef</span><span class="p">,</span> <span class="n">free_indices</span><span class="p">):</span>
<span class="n">a</span><span class="o">.</span><span class="n">index</span> <span class="o">=</span> <span class="n">i</span>
<span class="c"># At this point a.index runs from 0 to np-1 in the universe.</span>
<span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">atomList</span><span class="p">():</span>
<span class="k">if</span> <span class="n">a</span><span class="o">.</span><span class="n">array</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="k">try</span><span class="p">:</span>
<span class="n">coordinates</span><span class="p">[</span><span class="n">a</span><span class="o">.</span><span class="n">index</span><span class="p">,</span> <span class="p">:]</span> <span class="o">=</span> <span class="n">a</span><span class="o">.</span><span class="n">pos</span><span class="o">.</span><span class="n">array</span>
<span class="k">del</span> <span class="n">a</span><span class="o">.</span><span class="n">pos</span>
<span class="k">except</span> <span class="ne">AttributeError</span><span class="p">:</span>
<span class="n">coordinates</span><span class="p">[</span><span class="n">a</span><span class="o">.</span><span class="n">index</span><span class="p">,</span> <span class="p">:]</span> <span class="o">=</span> <span class="n">Utility</span><span class="o">.</span><span class="n">undefined</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">coordinates</span><span class="p">[</span><span class="n">a</span><span class="o">.</span><span class="n">index</span><span class="p">,</span> <span class="p">:]</span> <span class="o">=</span> <span class="n">a</span><span class="o">.</span><span class="n">array</span><span class="p">[</span><span class="n">a</span><span class="o">.</span><span class="n">index</span><span class="p">,</span> <span class="p">:]</span>
<span class="n">a</span><span class="o">.</span><span class="n">array</span> <span class="o">=</span> <span class="n">coordinates</span>
<span class="c"># Define configuration object.</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_configuration</span> <span class="o">=</span> <span class="mi">1</span> <span class="c"># a hack to prevent endless recursion</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_configuration</span> <span class="o">=</span> \
<span class="n">ParticleProperties</span><span class="o">.</span><span class="n">Configuration</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">coordinates</span><span class="p">)</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_configuration</span>
</div>
<div class="viewcode-block" id="Universe.copyConfiguration"><a class="viewcode-back" href="../../modules.html#MMTK.Universe.Universe.copyConfiguration">[docs]</a> <span class="k">def</span> <span class="nf">copyConfiguration</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> This operation is thread-safe; it won't return inconsistent</span>
<span class="sd"> data even when another thread is modifying the configuration.</span>
<span class="sd"> :returns: a copy of the current configuration</span>
<span class="sd"> :rtype: :class:`~MMTK.ParticleProperties.Configuration`</span>
<span class="sd"> """</span>
<span class="bp">self</span><span class="o">.</span><span class="n">acquireReadStateLock</span><span class="p">()</span>
<span class="k">try</span><span class="p">:</span>
<span class="n">conf</span> <span class="o">=</span> <span class="n">copy</span><span class="o">.</span><span class="n">copy</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">configuration</span><span class="p">())</span>
<span class="k">finally</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">releaseReadStateLock</span><span class="p">()</span>
<span class="k">return</span> <span class="n">conf</span>
</div>
<span class="k">def</span> <span class="nf">atomNames</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">configuration</span><span class="p">()</span>
<span class="n">names</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">numberOfAtoms</span><span class="p">()</span><span class="o">*</span><span class="p">[</span><span class="bp">None</span><span class="p">]</span>
<span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">atomList</span><span class="p">():</span>
<span class="n">names</span><span class="p">[</span><span class="n">a</span><span class="o">.</span><span class="n">index</span><span class="p">]</span> <span class="o">=</span> <span class="n">a</span><span class="o">.</span><span class="n">fullName</span><span class="p">()</span>
<span class="k">return</span> <span class="n">names</span>
<div class="viewcode-block" id="Universe.setConfiguration"><a class="viewcode-back" href="../../modules.html#MMTK.Universe.Universe.setConfiguration">[docs]</a> <span class="k">def</span> <span class="nf">setConfiguration</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">configuration</span><span class="p">,</span> <span class="n">block</span><span class="o">=</span><span class="bp">True</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Update the current configuration of the universe by copying</span>
<span class="sd"> the given input configuration.</span>
<span class="sd"> </span>
<span class="sd"> :param configuration: the new configuration</span>
<span class="sd"> :type configuration: :class:`~MMTK.ParticleProperties.Configuration`</span>
<span class="sd"> :param block: if True, the operation blocks other threads</span>
<span class="sd"> from accessing the configuration before the update</span>
<span class="sd"> is completed. If False, it is assumed that the</span>
<span class="sd"> caller takes care of locking.</span>
<span class="sd"> :type block: bool</span>
<span class="sd"> """</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">ParticleProperties</span><span class="o">.</span><span class="n">isConfiguration</span><span class="p">(</span><span class="n">configuration</span><span class="p">):</span>
<span class="k">raise</span> <span class="ne">TypeError</span><span class="p">(</span><span class="s">'not a universe configuration'</span><span class="p">)</span>
<span class="n">conf</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">configuration</span><span class="p">()</span>
<span class="k">if</span> <span class="n">block</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">acquireWriteStateLock</span><span class="p">()</span>
<span class="k">try</span><span class="p">:</span>
<span class="n">conf</span><span class="o">.</span><span class="n">assign</span><span class="p">(</span><span class="n">configuration</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">setCellParameters</span><span class="p">(</span><span class="n">configuration</span><span class="o">.</span><span class="n">cell_parameters</span><span class="p">)</span>
<span class="k">finally</span><span class="p">:</span>
<span class="k">if</span> <span class="n">block</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">releaseWriteStateLock</span><span class="p">()</span>
</div>
<div class="viewcode-block" id="Universe.addToConfiguration"><a class="viewcode-back" href="../../modules.html#MMTK.Universe.Universe.addToConfiguration">[docs]</a> <span class="k">def</span> <span class="nf">addToConfiguration</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">displacement</span><span class="p">,</span> <span class="n">block</span><span class="o">=</span><span class="bp">True</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Update the current configuration of the universe by adding</span>
<span class="sd"> the given displacement vector.</span>
<span class="sd"> </span>
<span class="sd"> :param displacement: the displacement vector for each atom</span>
<span class="sd"> :type displacement: :class:`~MMTK.ParticleProperties.ParticleVector`</span>
<span class="sd"> :param block: if True, the operation blocks other threads</span>
<span class="sd"> from accessing the configuration before the update</span>
<span class="sd"> is completed. If False, it is assumed that the</span>
<span class="sd"> caller takes care of locking.</span>
<span class="sd"> :type block: bool</span>
<span class="sd"> """</span>
<span class="n">conf</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">configuration</span><span class="p">()</span>
<span class="k">if</span> <span class="n">block</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">acquireWriteStateLock</span><span class="p">()</span>
<span class="k">try</span><span class="p">:</span>
<span class="n">conf</span><span class="o">.</span><span class="n">assign</span><span class="p">(</span><span class="n">conf</span><span class="o">+</span><span class="n">displacement</span><span class="p">)</span>
<span class="k">finally</span><span class="p">:</span>
<span class="k">if</span> <span class="n">block</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">releaseWriteStateLock</span><span class="p">()</span>
</div>
<div class="viewcode-block" id="Universe.getParticleScalar"><a class="viewcode-back" href="../../modules.html#MMTK.Universe.Universe.getParticleScalar">[docs]</a> <span class="k">def</span> <span class="nf">getParticleScalar</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="p">,</span> <span class="n">datatype</span> <span class="o">=</span> <span class="n">N</span><span class="o">.</span><span class="n">Float</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :param name: the name of an atom attribute</span>
<span class="sd"> :type name: str</span>
<span class="sd"> :param datatype: the datatype of the array allocated to hold the data</span>
<span class="sd"> :returns: the values of the attribute 'name' for each atom</span>
<span class="sd"> in the universe.</span>
<span class="sd"> :rtype: :class:`~MMTK.ParticleProperties.ParticleScalar`</span>
<span class="sd"> """</span>
<span class="n">conf</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">configuration</span><span class="p">()</span>
<span class="n">array</span> <span class="o">=</span> <span class="n">N</span><span class="o">.</span><span class="n">zeros</span><span class="p">((</span><span class="nb">len</span><span class="p">(</span><span class="n">conf</span><span class="p">),),</span> <span class="n">datatype</span><span class="p">)</span>
<span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">atomList</span><span class="p">():</span>
<span class="n">array</span><span class="p">[</span><span class="n">a</span><span class="o">.</span><span class="n">index</span><span class="p">]</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">a</span><span class="p">,</span> <span class="n">name</span><span class="p">)</span>
<span class="k">return</span> <span class="n">ParticleProperties</span><span class="o">.</span><span class="n">ParticleScalar</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">array</span><span class="p">)</span></div>
<span class="n">getAtomScalarArray</span> <span class="o">=</span> <span class="n">getParticleScalar</span>
<div class="viewcode-block" id="Universe.getParticleBoolean"><a class="viewcode-back" href="../../modules.html#MMTK.Universe.Universe.getParticleBoolean">[docs]</a> <span class="k">def</span> <span class="nf">getParticleBoolean</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :param name: the name of an atom attribute</span>
<span class="sd"> :type name: str</span>
<span class="sd"> :returns: the values of the boolean attribute 'name' for each atom</span>
<span class="sd"> in the universe, or False for atoms that do not have</span>
<span class="sd"> the attribute.</span>
<span class="sd"> :rtype: :class:`~MMTK.ParticleProperties.ParticleScalar`</span>
<span class="sd"> """</span>
<span class="n">conf</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">configuration</span><span class="p">()</span>
<span class="n">array</span> <span class="o">=</span> <span class="n">N</span><span class="o">.</span><span class="n">zeros</span><span class="p">((</span><span class="nb">len</span><span class="p">(</span><span class="n">conf</span><span class="p">),),</span> <span class="n">N</span><span class="o">.</span><span class="n">Int</span><span class="p">)</span>
<span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">atomList</span><span class="p">():</span>
<span class="k">try</span><span class="p">:</span>
<span class="n">array</span><span class="p">[</span><span class="n">a</span><span class="o">.</span><span class="n">index</span><span class="p">]</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">a</span><span class="p">,</span> <span class="n">name</span><span class="p">)</span>
<span class="k">except</span> <span class="ne">AttributeError</span><span class="p">:</span> <span class="k">pass</span>
<span class="k">return</span> <span class="n">ParticleProperties</span><span class="o">.</span><span class="n">ParticleScalar</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">array</span><span class="p">)</span></div>
<span class="n">getAtomBooleanArray</span> <span class="o">=</span> <span class="n">getParticleBoolean</span>
<div class="viewcode-block" id="Universe.masses"><a class="viewcode-back" href="../../modules.html#MMTK.Universe.Universe.masses">[docs]</a> <span class="k">def</span> <span class="nf">masses</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :returns: the masses of all atoms in the universe</span>
<span class="sd"> :rtype: :class:`~MMTK.ParticleProperties.ParticleScalar`</span>
<span class="sd"> """</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_masses</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_masses</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">getParticleScalar</span><span class="p">(</span><span class="s">'_mass'</span><span class="p">)</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_masses</span>
</div>
<div class="viewcode-block" id="Universe.charges"><a class="viewcode-back" href="../../modules.html#MMTK.Universe.Universe.charges">[docs]</a> <span class="k">def</span> <span class="nf">charges</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Return the atomic charges defined by the universe's</span>
<span class="sd"> force field.</span>
<span class="sd"> :returns: the charges of all atoms in the universe</span>
<span class="sd"> :rtype: :class:`~MMTK.ParticleProperties.ParticleScalar`</span>
<span class="sd"> """</span>
<span class="n">ff</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_forcefield</span>
<span class="k">if</span> <span class="n">ff</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s">"no force field defined"</span><span class="p">)</span>
<span class="k">return</span> <span class="n">ff</span><span class="o">.</span><span class="n">charges</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
</div>
<div class="viewcode-block" id="Universe.velocities"><a class="viewcode-back" href="../../modules.html#MMTK.Universe.Universe.velocities">[docs]</a> <span class="k">def</span> <span class="nf">velocities</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :returns: the current velocities of all atoms, or None if</span>
<span class="sd"> no velocities are defined. Note that this is not a</span>
<span class="sd"> copy of the current state but a reference to it;</span>
<span class="sd"> its data will change whenever any changes are made</span>
<span class="sd"> to the current velocities.</span>
<span class="sd"> :rtype: :class:`~MMTK.ParticleProperties.ParticleVector`</span>
<span class="sd"> """</span>
<span class="k">try</span><span class="p">:</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_atom_properties</span><span class="p">[</span><span class="s">'velocity'</span><span class="p">]</span>
<span class="k">except</span> <span class="ne">KeyError</span><span class="p">:</span>
<span class="k">return</span> <span class="bp">None</span>
</div>
<div class="viewcode-block" id="Universe.setVelocities"><a class="viewcode-back" href="../../modules.html#MMTK.Universe.Universe.setVelocities">[docs]</a> <span class="k">def</span> <span class="nf">setVelocities</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">velocities</span><span class="p">,</span> <span class="n">block</span><span class="o">=</span><span class="bp">True</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Update the current velocities of the universe by copying</span>
<span class="sd"> the given input velocities.</span>
<span class="sd"> </span>
<span class="sd"> :param velocities: the new velocities, or None to remove</span>
<span class="sd"> the velocity definition from the universe</span>
<span class="sd"> :type velocities: :class:`~MMTK.ParticleProperties.ParticleVector`</span>
<span class="sd"> :param block: if True, the operation blocks other threads</span>
<span class="sd"> from accessing the configuration before the update</span>
<span class="sd"> is completed. If False, it is assumed that the</span>
<span class="sd"> caller takes care of locking.</span>
<span class="sd"> :type block: bool</span>
<span class="sd"> """</span>
<span class="k">if</span> <span class="n">velocities</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="k">try</span><span class="p">:</span>
<span class="k">del</span> <span class="bp">self</span><span class="o">.</span><span class="n">_atom_properties</span><span class="p">[</span><span class="s">'velocity'</span><span class="p">]</span>
<span class="k">except</span> <span class="ne">KeyError</span><span class="p">:</span>
<span class="k">pass</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">try</span><span class="p">:</span>
<span class="n">v</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_atom_properties</span><span class="p">[</span><span class="s">'velocity'</span><span class="p">]</span>
<span class="k">except</span> <span class="ne">KeyError</span><span class="p">:</span>
<span class="n">v</span> <span class="o">=</span> <span class="n">ParticleProperties</span><span class="o">.</span><span class="n">ParticleVector</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_atom_properties</span><span class="p">[</span><span class="s">'velocity'</span><span class="p">]</span> <span class="o">=</span> <span class="n">v</span>
<span class="k">if</span> <span class="n">block</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">acquireWriteStateLock</span><span class="p">()</span>
<span class="k">try</span><span class="p">:</span>
<span class="n">v</span><span class="o">.</span><span class="n">assign</span><span class="p">(</span><span class="n">velocities</span><span class="p">)</span>
<span class="k">finally</span><span class="p">:</span>
<span class="k">if</span> <span class="n">block</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">releaseWriteStateLock</span><span class="p">()</span>
</div>
<div class="viewcode-block" id="Universe.initializeVelocitiesToTemperature"><a class="viewcode-back" href="../../modules.html#MMTK.Universe.Universe.initializeVelocitiesToTemperature">[docs]</a> <span class="k">def</span> <span class="nf">initializeVelocitiesToTemperature</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="sd">"""</span>
<span class="sd"> Generate random velocities for all atoms from a Boltzmann</span>
<span class="sd"> distribution.</span>
<span class="sd"> :param temperature: the reference temperature for the Boltzmann</span>
<span class="sd"> distribution</span>
<span class="sd"> :type temperature: float</span>
<span class="sd"> """</span>
<span class="bp">self</span><span class="o">.</span><span class="n">configuration</span><span class="p">()</span>
<span class="n">masses</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">masses</span><span class="p">()</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_atom_properties</span><span class="o">.</span><span class="n">has_key</span><span class="p">(</span><span class="s">'velocity'</span><span class="p">):</span>
<span class="k">del</span> <span class="bp">self</span><span class="o">.</span><span class="n">_atom_properties</span><span class="p">[</span><span class="s">'velocity'</span><span class="p">]</span>
<span class="n">fixed</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">getParticleBoolean</span><span class="p">(</span><span class="s">'fixed'</span><span class="p">)</span>
<span class="n">np</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">numberOfPoints</span><span class="p">()</span>
<span class="n">velocities</span> <span class="o">=</span> <span class="n">N</span><span class="o">.</span><span class="n">zeros</span><span class="p">((</span><span class="n">np</span><span class="p">,</span> <span class="mi">3</span><span class="p">),</span> <span class="n">N</span><span class="o">.</span><span class="n">Float</span><span class="p">)</span>
<span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">xrange</span><span class="p">(</span><span class="n">np</span><span class="p">):</span>
<span class="n">m</span> <span class="o">=</span> <span class="n">masses</span><span class="p">[</span><span class="n">i</span><span class="p">]</span>
<span class="k">if</span> <span class="n">m</span> <span class="o">></span> <span class="mf">0.</span> <span class="ow">and</span> <span class="ow">not</span> <span class="n">fixed</span><span class="p">[</span><span class="n">i</span><span class="p">]:</span>
<span class="n">velocities</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">=</span> <span class="n">Random</span><span class="o">.</span><span class="n">randomVelocity</span><span class="p">(</span><span class="n">temperature</span><span class="p">,</span>
<span class="n">m</span><span class="p">)</span><span class="o">.</span><span class="n">array</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_atom_properties</span><span class="p">[</span><span class="s">'velocity'</span><span class="p">]</span> <span class="o">=</span> \
<span class="n">ParticleProperties</span><span class="o">.</span><span class="n">ParticleVector</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">velocities</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">adjustVelocitiesToConstraints</span><span class="p">()</span>
</div>
<div class="viewcode-block" id="Universe.scaleVelocitiesToTemperature"><a class="viewcode-back" href="../../modules.html#MMTK.Universe.Universe.scaleVelocitiesToTemperature">[docs]</a> <span class="k">def</span> <span class="nf">scaleVelocitiesToTemperature</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">block</span><span class="o">=</span><span class="bp">True</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Scale all velocities by a common factor in order to obtain</span>
<span class="sd"> the specified temperature.</span>
<span class="sd"> :param temperature: the reference temperature</span>
<span class="sd"> :type temperature: float</span>
<span class="sd"> :param block: if True, the operation blocks other threads</span>
<span class="sd"> from accessing the configuration before the update</span>
<span class="sd"> is completed. If False, it is assumed that the</span>
<span class="sd"> caller takes care of locking.</span>
<span class="sd"> :type block: bool</span>
<span class="sd"> """</span>
<span class="n">velocities</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">velocities</span><span class="p">()</span>
<span class="n">factor</span> <span class="o">=</span> <span class="n">N</span><span class="o">.</span><span class="n">sqrt</span><span class="p">(</span><span class="n">temperature</span><span class="o">/</span><span class="bp">self</span><span class="o">.</span><span class="n">temperature</span><span class="p">())</span>
<span class="k">if</span> <span class="n">block</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">acquireWriteStateLock</span><span class="p">()</span>
<span class="k">try</span><span class="p">:</span>
<span class="n">velocities</span><span class="o">.</span><span class="n">scaleBy</span><span class="p">(</span><span class="n">factor</span><span class="p">)</span>
<span class="k">finally</span><span class="p">:</span>
<span class="k">if</span> <span class="n">block</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">releaseWriteStateLock</span><span class="p">()</span>
</div>
<span class="k">def</span> <span class="nf">degreesOfFreedom</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</span> <span class="n">GroupOfAtoms</span><span class="o">.</span><span class="n">degreesOfFreedom</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> \
<span class="o">-</span> <span class="bp">self</span><span class="o">.</span><span class="n">numberOfDistanceConstraints</span><span class="p">()</span>
<div class="viewcode-block" id="Universe.distanceConstraintList"><a class="viewcode-back" href="../../modules.html#MMTK.Universe.Universe.distanceConstraintList">[docs]</a> <span class="k">def</span> <span class="nf">distanceConstraintList</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :returns: the list of distance constraints</span>
<span class="sd"> :rtype: list</span>
<span class="sd"> """</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_objects</span><span class="o">.</span><span class="n">distanceConstraintList</span><span class="p">()</span>
</div>
<div class="viewcode-block" id="Universe.numberOfDistanceConstraints"><a class="viewcode-back" href="../../modules.html#MMTK.Universe.Universe.numberOfDistanceConstraints">[docs]</a> <span class="k">def</span> <span class="nf">numberOfDistanceConstraints</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :returns: the number of distance constraints</span>
<span class="sd"> :rtype: int</span>
<span class="sd"> """</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_objects</span><span class="o">.</span><span class="n">numberOfDistanceConstraints</span><span class="p">()</span>
</div>
<div class="viewcode-block" id="Universe.setBondConstraints"><a class="viewcode-back" href="../../modules.html#MMTK.Universe.Universe.setBondConstraints">[docs]</a> <span class="k">def</span> <span class="nf">setBondConstraints</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Sets distance constraints for all bonds.</span>
<span class="sd"> """</span>
<span class="bp">self</span><span class="o">.</span><span class="n">configuration</span><span class="p">()</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_objects</span><span class="o">.</span><span class="n">setBondConstraints</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">enforceConstraints</span><span class="p">()</span>
</div>
<div class="viewcode-block" id="Universe.removeDistanceConstraints"><a class="viewcode-back" href="../../modules.html#MMTK.Universe.Universe.removeDistanceConstraints">[docs]</a> <span class="k">def</span> <span class="nf">removeDistanceConstraints</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Removes all distance constraints.</span>
<span class="sd"> """</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_objects</span><span class="o">.</span><span class="n">removeDistanceConstraints</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
</div>
<div class="viewcode-block" id="Universe.enforceConstraints"><a class="viewcode-back" href="../../modules.html#MMTK.Universe.Universe.enforceConstraints">[docs]</a> <span class="k">def</span> <span class="nf">enforceConstraints</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">configuration</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">velocities</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Enforces the previously defined distance constraints</span>
<span class="sd"> by modifying the configuration and velocities.</span>
<span class="sd"> :param configuration: the configuration in which the</span>
<span class="sd"> constraints are enforced</span>
<span class="sd"> (None for current configuration)</span>
<span class="sd"> :type configuration: :class:`~MMTK.ParticleProperties.Configuration`</span>
<span class="sd"> :param velocities: the velocities in which the</span>
<span class="sd"> constraints are enforced</span>
<span class="sd"> (None for current velocities)</span>
<span class="sd"> :type velocities: :class:`~MMTK.ParticleProperties.ParticleVector`</span>
<span class="sd"> """</span>
<span class="kn">from</span> <span class="nn">MMTK</span> <span class="kn">import</span> <span class="n">Dynamics</span>
<span class="n">Dynamics</span><span class="o">.</span><span class="n">enforceConstraints</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">configuration</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">adjustVelocitiesToConstraints</span><span class="p">(</span><span class="n">velocities</span><span class="p">)</span>
</div>
<div class="viewcode-block" id="Universe.adjustVelocitiesToConstraints"><a class="viewcode-back" href="../../modules.html#MMTK.Universe.Universe.adjustVelocitiesToConstraints">[docs]</a> <span class="k">def</span> <span class="nf">adjustVelocitiesToConstraints</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">velocities</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">block</span><span class="o">=</span><span class="bp">True</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Modifies the velocities to be compatible with</span>
<span class="sd"> the distance constraints, i.e. projects out the velocity</span>
<span class="sd"> components along the constrained distances.</span>
<span class="sd"> :param velocities: the velocities in which the</span>
<span class="sd"> constraints are enforced</span>
<span class="sd"> (None for current velocities)</span>
<span class="sd"> :type velocities: :class:`~MMTK.ParticleProperties.ParticleVector`</span>
<span class="sd"> :param block: if True, the operation blocks other threads</span>
<span class="sd"> from accessing the configuration before the update</span>
<span class="sd"> is completed. If False, it is assumed that the</span>
<span class="sd"> caller takes care of locking.</span>
<span class="sd"> :type block: bool</span>
<span class="sd"> """</span>
<span class="kn">from</span> <span class="nn">MMTK</span> <span class="kn">import</span> <span class="n">Dynamics</span>
<span class="k">if</span> <span class="n">velocities</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">velocities</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">velocities</span><span class="p">()</span>
<span class="k">if</span> <span class="n">velocities</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span>
<span class="k">if</span> <span class="n">block</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">acquireWriteStateLock</span><span class="p">()</span>
<span class="k">try</span><span class="p">:</span>
<span class="n">Dynamics</span><span class="o">.</span><span class="n">projectVelocities</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">velocities</span><span class="p">)</span>
<span class="k">finally</span><span class="p">:</span>
<span class="k">if</span> <span class="n">block</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">releaseWriteStateLock</span><span class="p">()</span>
</div>
<span class="k">def</span> <span class="nf">bondLengthDatabase</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_bond_database</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_bond_database</span> <span class="o">=</span> <span class="bp">None</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_bond_database</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">ff</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_forcefield</span>
<span class="k">try</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_bond_database</span> <span class="o">=</span> <span class="n">ff</span><span class="o">.</span><span class="n">bondLengthDatabase</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
<span class="k">except</span> <span class="ne">AttributeError</span><span class="p">:</span>
<span class="k">pass</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_bond_database</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_bond_database</span> <span class="o">=</span> <span class="n">Bonds</span><span class="o">.</span><span class="n">DummyBondLengthDatabase</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_bond_database</span>
<div class="viewcode-block" id="Universe.forcefield"><a class="viewcode-back" href="../../modules.html#MMTK.Universe.Universe.forcefield">[docs]</a> <span class="k">def</span> <span class="nf">forcefield</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :returns: the force field</span>
<span class="sd"> :rtype: :class:`~MMTK.ForceFields.ForceField.ForceField`</span>
<span class="sd"> """</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_forcefield</span>
</div>
<span class="k">def</span> <span class="nf">energyEvaluatorParameters</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">subset1</span> <span class="o">=</span> <span class="bp">None</span><span class="p">,</span> <span class="n">subset2</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">configuration</span><span class="p">()</span>
<span class="kn">from</span> <span class="nn">MMTK.ForceFields</span> <span class="kn">import</span> <span class="n">ForceField</span>
<span class="n">ffdata</span> <span class="o">=</span> <span class="n">ForceField</span><span class="o">.</span><span class="n">ForceFieldData</span><span class="p">()</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_forcefield</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">subset1</span><span class="p">,</span> <span class="n">subset2</span><span class="p">,</span>
<span class="n">ffdata</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">energyEvaluator</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">subset1</span> <span class="o">=</span> <span class="bp">None</span><span class="p">,</span> <span class="n">subset2</span> <span class="o">=</span> <span class="bp">None</span><span class="p">,</span>
<span class="n">threads</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">mpi_communicator</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_forcefield</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s">"no force field defined"</span><span class="p">)</span>
<span class="k">try</span><span class="p">:</span>
<span class="nb">eval</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_evaluator</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">threads</span><span class="p">)]</span>
<span class="k">except</span> <span class="ne">KeyError</span><span class="p">:</span>
<span class="kn">from</span> <span class="nn">MMTK.ForceFields</span> <span class="kn">import</span> <span class="n">ForceField</span>
<span class="nb">eval</span> <span class="o">=</span> <span class="n">ForceField</span><span class="o">.</span><span class="n">EnergyEvaluator</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">_forcefield</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">threads</span><span class="p">,</span> <span class="n">mpi_communicator</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_evaluator</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">threads</span><span class="p">)]</span> <span class="o">=</span> <span class="nb">eval</span>
<span class="k">return</span> <span class="nb">eval</span>
<div class="viewcode-block" id="Universe.energy"><a class="viewcode-back" href="../../modules.html#MMTK.Universe.Universe.energy">[docs]</a> <span class="k">def</span> <span class="nf">energy</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">subset1</span> <span class="o">=</span> <span class="bp">None</span><span class="p">,</span> <span class="n">subset2</span> <span class="o">=</span> <span class="bp">None</span><span class="p">,</span> <span class="n">small_change</span><span class="o">=</span><span class="bp">False</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :param subset1: a subset of a universe, or None</span>
<span class="sd"> :type subset1: :class:`~MMTK.ChemicalObjects.ChemicalObject`</span>
<span class="sd"> :param subset2: a subset of a universe, or None</span>
<span class="sd"> :type subset2: :class:`~MMTK.ChemicalObjects.ChemicalObject`</span>
<span class="sd"> :param small_change: if True, algorithms optimized for small</span>
<span class="sd"> configurational changes relative to the last</span>
<span class="sd"> evaluation may be used.</span>
<span class="sd"> :type small_change: bool</span>
<span class="sd"> :returns: the potential energy of interaction between the atoms</span>
<span class="sd"> in subset1 and the atoms in subset2. If subset2 is None,</span>
<span class="sd"> the interactions within subset1 are calculated. It both</span>
<span class="sd"> subsets are None, the potential energy of the whole</span>
<span class="sd"> universe is returned.</span>
<span class="sd"> :rtype: float</span>
<span class="sd"> """</span>
<span class="nb">eval</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">energyEvaluator</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="k">return</span> <span class="nb">eval</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="n">small_change</span><span class="p">)</span>
</div>
<div class="viewcode-block" id="Universe.energyAndGradients"><a class="viewcode-back" href="../../modules.html#MMTK.Universe.Universe.energyAndGradients">[docs]</a> <span class="k">def</span> <span class="nf">energyAndGradients</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">subset1</span> <span class="o">=</span> <span class="bp">None</span><span class="p">,</span> <span class="n">subset2</span> <span class="o">=</span> <span class="bp">None</span><span class="p">,</span>
<span class="n">small_change</span><span class="o">=</span><span class="bp">False</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :returns: the energy and the energy gradients</span>
<span class="sd"> :rtype: (float, :class:`~MMTK.ParticleProperties.ParticleVector`)</span>
<span class="sd"> """</span>
<span class="nb">eval</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">energyEvaluator</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="k">return</span> <span class="nb">eval</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="n">small_change</span><span class="p">)</span>
</div>
<div class="viewcode-block" id="Universe.energyAndForceConstants"><a class="viewcode-back" href="../../modules.html#MMTK.Universe.Universe.energyAndForceConstants">[docs]</a> <span class="k">def</span> <span class="nf">energyAndForceConstants</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">subset1</span> <span class="o">=</span> <span class="bp">None</span><span class="p">,</span> <span class="n">subset2</span> <span class="o">=</span> <span class="bp">None</span><span class="p">,</span>
<span class="n">small_change</span><span class="o">=</span><span class="bp">False</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :returns: the energy and the force constants</span>
<span class="sd"> :rtype: (float, :class:`~MMTK.ParticleProperties.SymmetricPairTensor`)</span>
<span class="sd"> """</span>
<span class="nb">eval</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">energyEvaluator</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">e</span><span class="p">,</span> <span class="n">g</span><span class="p">,</span> <span class="n">fc</span> <span class="o">=</span> <span class="nb">eval</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="n">small_change</span><span class="p">)</span>
<span class="k">return</span> <span class="n">e</span><span class="p">,</span> <span class="n">fc</span>
</div>
<div class="viewcode-block" id="Universe.energyGradientsAndForceConstants"><a class="viewcode-back" href="../../modules.html#MMTK.Universe.Universe.energyGradientsAndForceConstants">[docs]</a> <span class="k">def</span> <span class="nf">energyGradientsAndForceConstants</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">subset1</span> <span class="o">=</span> <span class="bp">None</span><span class="p">,</span> <span class="n">subset2</span> <span class="o">=</span> <span class="bp">None</span><span class="p">,</span>
<span class="n">small_change</span><span class="o">=</span><span class="bp">False</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :returns: the energy, its gradients, and the force constants</span>
<span class="sd"> :rtype: (float, :class:`~MMTK.ParticleProperties.ParticleVector`,</span>
<span class="sd"> :class:`~MMTK.ParticleProperties.SymmetricPairTensor`)</span>
<span class="sd"> """</span>
<span class="nb">eval</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">energyEvaluator</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="k">return</span> <span class="nb">eval</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="n">small_change</span><span class="p">)</span>
</div>
<div class="viewcode-block" id="Universe.energyTerms"><a class="viewcode-back" href="../../modules.html#MMTK.Universe.Universe.energyTerms">[docs]</a> <span class="k">def</span> <span class="nf">energyTerms</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">subset1</span> <span class="o">=</span> <span class="bp">None</span><span class="p">,</span> <span class="n">subset2</span> <span class="o">=</span> <span class="bp">None</span><span class="p">,</span> <span class="n">small_change</span><span class="o">=</span><span class="bp">False</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :returns: a dictionary containing the energy values for each</span>
<span class="sd"> energy term separately. The energy terms are defined by the</span>
<span class="sd"> force field.</span>
<span class="sd"> :rtype: dict</span>
<span class="sd"> """</span>
<span class="nb">eval</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">energyEvaluator</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="nb">eval</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="n">small_change</span><span class="p">)</span>
<span class="k">return</span> <span class="nb">eval</span><span class="o">.</span><span class="n">lastEnergyTerms</span><span class="p">()</span>
</div>
<div class="viewcode-block" id="Universe.configurationDifference"><a class="viewcode-back" href="../../modules.html#MMTK.Universe.Universe.configurationDifference">[docs]</a> <span class="k">def</span> <span class="nf">configurationDifference</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">conf1</span><span class="p">,</span> <span class="n">conf2</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :param conf1: a configuration</span>
<span class="sd"> :type conf1: :class:`~MMTK.ParticleProperties.Configuration`</span>
<span class="sd"> :param conf2: a configuration</span>
<span class="sd"> :type conf2: :class:`~MMTK.ParticleProperties.Configuration`</span>
<span class="sd"> :returns: the difference vector between the two configurations</span>
<span class="sd"> for each atom, taking into account the universe</span>
<span class="sd"> topology (e.g. minimum-image convention).</span>
<span class="sd"> :rtype: :class:`~MMTK.ParticleProperties.ParticleVector`</span>
<span class="sd"> """</span>
<span class="n">d</span> <span class="o">=</span> <span class="n">conf2</span><span class="o">-</span><span class="n">conf1</span>
<span class="n">cell</span> <span class="o">=</span> <span class="n">conf1</span><span class="o">.</span><span class="n">cell_parameters</span>
<span class="k">if</span> <span class="n">cell</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_spec</span><span class="o">.</span><span class="n">foldCoordinatesIntoBox</span><span class="p">(</span><span class="n">d</span><span class="o">.</span><span class="n">array</span><span class="p">)</span>
<span class="k">return</span> <span class="n">d</span>
</div>
<div class="viewcode-block" id="Universe.distanceVector"><a class="viewcode-back" href="../../modules.html#MMTK.Universe.Universe.distanceVector">[docs]</a> <span class="k">def</span> <span class="nf">distanceVector</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">p1</span><span class="p">,</span> <span class="n">p2</span><span class="p">,</span> <span class="n">conf</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :param p1: a vector or a chemical object whose position is taken</span>
<span class="sd"> :param p2: a vector or a chemical object whose position is taken</span>
<span class="sd"> :param conf: a configuration (None for the current configuration)</span>
<span class="sd"> :returns: the distance vector between p1 and p2 (i.e. the</span>
<span class="sd"> vector from p1 to p2) in the configuration conf,</span>
<span class="sd"> taking into account the universe's topology.</span>
<span class="sd"> """</span>
<span class="n">p1</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">position</span><span class="p">(</span><span class="n">p1</span><span class="p">,</span> <span class="n">conf</span><span class="p">)</span>
<span class="n">p2</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">position</span><span class="p">(</span><span class="n">p2</span><span class="p">,</span> <span class="n">conf</span><span class="p">)</span>
<span class="k">if</span> <span class="n">conf</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="k">return</span> <span class="n">Vector</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_spec</span><span class="o">.</span><span class="n">distanceVector</span><span class="p">(</span><span class="n">p1</span><span class="o">.</span><span class="n">array</span><span class="p">,</span> <span class="n">p2</span><span class="o">.</span><span class="n">array</span><span class="p">))</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">cell</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_fixCellParameters</span><span class="p">(</span><span class="n">conf</span><span class="o">.</span><span class="n">cell_parameters</span><span class="p">)</span>
<span class="k">if</span> <span class="n">cell</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="k">return</span> <span class="n">Vector</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_spec</span><span class="o">.</span><span class="n">distanceVector</span><span class="p">(</span><span class="n">p1</span><span class="o">.</span><span class="n">array</span><span class="p">,</span> <span class="n">p2</span><span class="o">.</span><span class="n">array</span><span class="p">))</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">return</span> <span class="n">Vector</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_spec</span><span class="o">.</span><span class="n">distanceVector</span><span class="p">(</span><span class="n">p1</span><span class="o">.</span><span class="n">array</span><span class="p">,</span> <span class="n">p2</span><span class="o">.</span><span class="n">array</span><span class="p">,</span>
<span class="n">cell</span><span class="p">))</span>
</div>
<div class="viewcode-block" id="Universe.distance"><a class="viewcode-back" href="../../modules.html#MMTK.Universe.Universe.distance">[docs]</a> <span class="k">def</span> <span class="nf">distance</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">p1</span><span class="p">,</span> <span class="n">p2</span><span class="p">,</span> <span class="n">conf</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :param p1: a vector or a chemical object whose position is taken</span>
<span class="sd"> :param p2: a vector or a chemical object whose position is taken</span>
<span class="sd"> :param conf: a configuration (None for the current configuration)</span>
<span class="sd"> :returns: the distance between p1 and p2, i.e. the length</span>
<span class="sd"> of the distance vector</span>
<span class="sd"> :rtype: float</span>
<span class="sd"> """</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">distanceVector</span><span class="p">(</span><span class="n">p1</span><span class="p">,</span> <span class="n">p2</span><span class="p">,</span> <span class="n">conf</span><span class="p">)</span><span class="o">.</span><span class="n">length</span><span class="p">()</span>
</div>
<div class="viewcode-block" id="Universe.angle"><a class="viewcode-back" href="../../modules.html#MMTK.Universe.Universe.angle">[docs]</a> <span class="k">def</span> <span class="nf">angle</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">p1</span><span class="p">,</span> <span class="n">p2</span><span class="p">,</span> <span class="n">p3</span><span class="p">,</span> <span class="n">conf</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :param p1: a vector or a chemical object whose position is taken</span>
<span class="sd"> :param p2: a vector or a chemical object whose position is taken</span>
<span class="sd"> :param p3: a vector or a chemical object whose position is taken</span>
<span class="sd"> :param conf: a configuration (None for the current configuration)</span>
<span class="sd"> :returns: the angle between the distance vectors p1-p2 and p3-p2</span>
<span class="sd"> :rtype: float</span>
<span class="sd"> """</span>
<span class="n">v1</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">distanceVector</span><span class="p">(</span><span class="n">p2</span><span class="p">,</span> <span class="n">p1</span><span class="p">,</span> <span class="n">conf</span><span class="p">)</span>
<span class="n">v2</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">distanceVector</span><span class="p">(</span><span class="n">p2</span><span class="p">,</span> <span class="n">p3</span><span class="p">,</span> <span class="n">conf</span><span class="p">)</span>
<span class="k">return</span> <span class="n">v1</span><span class="o">.</span><span class="n">angle</span><span class="p">(</span><span class="n">v2</span><span class="p">)</span>
</div>
<div class="viewcode-block" id="Universe.dihedral"><a class="viewcode-back" href="../../modules.html#MMTK.Universe.Universe.dihedral">[docs]</a> <span class="k">def</span> <span class="nf">dihedral</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">p1</span><span class="p">,</span> <span class="n">p2</span><span class="p">,</span> <span class="n">p3</span><span class="p">,</span> <span class="n">p4</span><span class="p">,</span> <span class="n">conf</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :param p1: a vector or a chemical object whose position is taken</span>
<span class="sd"> :param p2: a vector or a chemical object whose position is taken</span>
<span class="sd"> :param p3: a vector or a chemical object whose position is taken</span>
<span class="sd"> :param p4: a vector or a chemical object whose position is taken</span>
<span class="sd"> :param conf: a configuration (None for the current configuration)</span>
<span class="sd"> :returns: the dihedral angle between the plane containing the</span>
<span class="sd"> distance vectors p1-p2 and p3-p2 and the plane containing</span>
<span class="sd"> the distance vectors p2-p3 and p4-p3</span>
<span class="sd"> :rtype: float</span>
<span class="sd"> """</span>
<span class="n">v1</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">distanceVector</span><span class="p">(</span><span class="n">p2</span><span class="p">,</span> <span class="n">p1</span><span class="p">,</span> <span class="n">conf</span><span class="p">)</span>
<span class="n">v2</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">distanceVector</span><span class="p">(</span><span class="n">p3</span><span class="p">,</span> <span class="n">p2</span><span class="p">,</span> <span class="n">conf</span><span class="p">)</span>
<span class="n">v3</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">distanceVector</span><span class="p">(</span><span class="n">p3</span><span class="p">,</span> <span class="n">p4</span><span class="p">,</span> <span class="n">conf</span><span class="p">)</span>
<span class="n">a</span> <span class="o">=</span> <span class="n">v1</span><span class="o">.</span><span class="n">cross</span><span class="p">(</span><span class="n">v2</span><span class="p">)</span><span class="o">.</span><span class="n">normal</span><span class="p">()</span>
<span class="n">b</span> <span class="o">=</span> <span class="n">v3</span><span class="o">.</span><span class="n">cross</span><span class="p">(</span><span class="n">v2</span><span class="p">)</span><span class="o">.</span><span class="n">normal</span><span class="p">()</span>
<span class="n">cos</span> <span class="o">=</span> <span class="n">a</span><span class="o">*</span><span class="n">b</span>
<span class="n">sin</span> <span class="o">=</span> <span class="n">b</span><span class="o">.</span><span class="n">cross</span><span class="p">(</span><span class="n">a</span><span class="p">)</span><span class="o">*</span><span class="n">v2</span><span class="o">/</span><span class="n">v2</span><span class="o">.</span><span class="n">length</span><span class="p">()</span>
<span class="k">return</span> <span class="n">Transformation</span><span class="o">.</span><span class="n">angleFromSineAndCosine</span><span class="p">(</span><span class="n">sin</span><span class="p">,</span> <span class="n">cos</span><span class="p">)</span>
</div>
<span class="k">def</span> <span class="nf">_deleteAtom</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">atom</span><span class="p">):</span>
<span class="k">pass</span>
<div class="viewcode-block" id="Universe.basisVectors"><a class="viewcode-back" href="../../modules.html#MMTK.Universe.Universe.basisVectors">[docs]</a> <span class="k">def</span> <span class="nf">basisVectors</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :returns: the basis vectors of the elementary cell of a periodic</span>
<span class="sd"> universe, or None for a non-periodic universe</span>
<span class="sd"> :rtype: NoneType or list</span>
<span class="sd"> """</span>
<span class="k">return</span> <span class="bp">None</span>
</div>
<div class="viewcode-block" id="Universe.reciprocalBasisVectors"><a class="viewcode-back" href="../../modules.html#MMTK.Universe.Universe.reciprocalBasisVectors">[docs]</a> <span class="k">def</span> <span class="nf">reciprocalBasisVectors</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :returns: the reciprocal basis vectors of the elementary cell of</span>
<span class="sd"> a periodic universe, or None for a non-periodic universe</span>
<span class="sd"> :rtype: NoneType or list</span>
<span class="sd"> """</span>
<span class="k">return</span> <span class="bp">None</span>
</div>
<span class="k">def</span> <span class="nf">cellParameters</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</span> <span class="bp">None</span>
<span class="k">def</span> <span class="nf">setCellParameters</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">parameters</span><span class="p">):</span>
<span class="k">if</span> <span class="n">parameters</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s">'incompatible cell parameters'</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">_fixCellParameters</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">cell_parameters</span><span class="p">):</span>
<span class="k">return</span> <span class="n">cell_parameters</span>
<div class="viewcode-block" id="Universe.cellVolume"><a class="viewcode-back" href="../../modules.html#MMTK.Universe.Universe.cellVolume">[docs]</a> <span class="k">def</span> <span class="nf">cellVolume</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :returns: the volume of the elementary cell of a periodic</span>
<span class="sd"> universe, None for a non-periodic universe</span>
<span class="sd"> :rtype: NoneType or float</span>
<span class="sd"> """</span>
<span class="k">return</span> <span class="bp">None</span>
</div>
<div class="viewcode-block" id="Universe.largestDistance"><a class="viewcode-back" href="../../modules.html#MMTK.Universe.Universe.largestDistance">[docs]</a> <span class="k">def</span> <span class="nf">largestDistance</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :returns: the largest possible distance between any two points</span>
<span class="sd"> that can be represented independent of orientation, i.e. the</span>
<span class="sd"> radius of the largest sphere that fits into the simulation</span>
<span class="sd"> cell. Returns None if no such upper limit exists.</span>
<span class="sd"> :rtype: NoneType or float</span>
<span class="sd"> """</span>
<span class="k">return</span> <span class="bp">None</span>
</div>
<div class="viewcode-block" id="Universe.contiguousObjectOffset"><a class="viewcode-back" href="../../modules.html#MMTK.Universe.Universe.contiguousObjectOffset">[docs]</a> <span class="k">def</span> <span class="nf">contiguousObjectOffset</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">objects</span> <span class="o">=</span> <span class="bp">None</span><span class="p">,</span> <span class="n">conf</span> <span class="o">=</span> <span class="bp">None</span><span class="p">,</span>
<span class="n">box_coordinates</span> <span class="o">=</span> <span class="bp">False</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :param objects: a list of chemical objects, or None for all</span>
<span class="sd"> objects in the universe</span>
<span class="sd"> :type objects: list</span>
<span class="sd"> :param conf: a configuration (None for the current configuration)</span>
<span class="sd"> :param box_coordinates: use box coordinates rather than real ones</span>
<span class="sd"> :type box_coordinates: bool</span>
<span class="sd"> :returns: a set of displacement vectors relative to</span>
<span class="sd"> the conf which, when added to the configuration,</span>
<span class="sd"> create a configuration in which none of the objects</span>
<span class="sd"> is split across the edge of the elementary cell.</span>
<span class="sd"> For nonperiodic universes the return value is None.</span>
<span class="sd"> :rtype: :class:`~MMTK.ParticleProperties.ParticleVector`</span>
<span class="sd"> """</span>
<span class="k">return</span> <span class="bp">None</span>
</div>
<div class="viewcode-block" id="Universe.contiguousObjectConfiguration"><a class="viewcode-back" href="../../modules.html#MMTK.Universe.Universe.contiguousObjectConfiguration">[docs]</a> <span class="k">def</span> <span class="nf">contiguousObjectConfiguration</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">objects</span> <span class="o">=</span> <span class="bp">None</span><span class="p">,</span> <span class="n">conf</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :param objects: a list of chemical objects, or None for all</span>
<span class="sd"> objects in the universe</span>
<span class="sd"> :type objects: list</span>
<span class="sd"> :param conf: a configuration (None for the current configuration)</span>
<span class="sd"> :returns: configuration conf (default: current configuration)</span>
<span class="sd"> corrected by the contiguous object offsets for that</span>
<span class="sd"> configuration.</span>
<span class="sd"> :rtype: :class:`~MMTK.ParticleProperties.Configuration`</span>
<span class="sd"> """</span>
<span class="k">if</span> <span class="n">conf</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">conf</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">configuration</span><span class="p">()</span>
<span class="n">offset</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">contiguousObjectOffset</span><span class="p">(</span><span class="n">objects</span><span class="p">,</span> <span class="n">conf</span><span class="p">)</span>
<span class="k">if</span> <span class="n">offset</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span>
<span class="k">return</span> <span class="n">conf</span> <span class="o">+</span> <span class="n">offset</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">return</span> <span class="n">copy</span><span class="o">.</span><span class="n">copy</span><span class="p">(</span><span class="n">conf</span><span class="p">)</span>
</div>
<div class="viewcode-block" id="Universe.realToBoxCoordinates"><a class="viewcode-back" href="../../modules.html#MMTK.Universe.Universe.realToBoxCoordinates">[docs]</a> <span class="k">def</span> <span class="nf">realToBoxCoordinates</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">vector</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Box coordinates are defined only for periodic universes;</span>
<span class="sd"> their components have values between -0.5 and 0.5; these</span>
<span class="sd"> extreme values correspond to the walls of the simulation box.</span>
<span class="sd"> :param vector: a point in the universe</span>
<span class="sd"> :returns: the box coordinate equivalent of vector, or the original</span>
<span class="sd"> vector if no box coordinate system exists</span>
<span class="sd"> :rtype: Scientific.Geometry.Vector</span>
<span class="sd"> """</span>
<span class="k">return</span> <span class="n">vector</span>
</div>
<div class="viewcode-block" id="Universe.boxToRealCoordinates"><a class="viewcode-back" href="../../modules.html#MMTK.Universe.Universe.boxToRealCoordinates">[docs]</a> <span class="k">def</span> <span class="nf">boxToRealCoordinates</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">vector</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :param vector: a point in the universe expressed in box coordinates</span>
<span class="sd"> :returns: the real-space equivalent of vector</span>
<span class="sd"> :rtype: Scientific.Geometry.Vector</span>
<span class="sd"> """</span>
<span class="k">return</span> <span class="n">vector</span>
</div>
<span class="k">def</span> <span class="nf">_realToBoxPointArray</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">array</span><span class="p">,</span> <span class="n">parameters</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span>
<span class="k">return</span> <span class="n">array</span>
<span class="k">def</span> <span class="nf">_boxToRealPointArray</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">array</span><span class="p">,</span> <span class="n">parameters</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span>
<span class="k">return</span> <span class="n">array</span>
<div class="viewcode-block" id="Universe.cartesianToFractional"><a class="viewcode-back" href="../../modules.html#MMTK.Universe.Universe.cartesianToFractional">[docs]</a> <span class="k">def</span> <span class="nf">cartesianToFractional</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">vector</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Fractional coordinates are defined only for periodic universes;</span>
<span class="sd"> their components have values between 0. and 1.</span>
<span class="sd"> :param vector: a point in the universe</span>
<span class="sd"> :type vector: Scientific.Geometry.Vector</span>
<span class="sd"> :returns: the fractional coordinate equivalent of vector</span>
<span class="sd"> :rtype: Scientific.N.array_type</span>
<span class="sd"> """</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s">"Universe is not periodic"</span><span class="p">)</span>
</div>
<span class="k">def</span> <span class="nf">cartesianToFractionalMatrix</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s">"Universe is not periodic"</span><span class="p">)</span>
<div class="viewcode-block" id="Universe.fractionalToCartesian"><a class="viewcode-back" href="../../modules.html#MMTK.Universe.Universe.fractionalToCartesian">[docs]</a> <span class="k">def</span> <span class="nf">fractionalToCartesian</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">array</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Fractional coordinates are defined only for periodic universes;</span>
<span class="sd"> their components have values between 0. and 1.</span>
<span class="sd"> :param array: an array of fractional coordinates</span>
<span class="sd"> :type array: Scientific.N.array_type</span>
<span class="sd"> :returns: the real-space equivalent of vector</span>
<span class="sd"> :rtype: Scientific.Geometry.Vector</span>
<span class="sd"> """</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s">"Universe is not periodic"</span><span class="p">)</span>
</div>
<span class="k">def</span> <span class="nf">fractionalToCartesianMatrix</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s">"Universe is not periodic"</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">foldCoordinatesIntoBox</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</span>
<div class="viewcode-block" id="Universe.randomPoint"><a class="viewcode-back" href="../../modules.html#MMTK.Universe.Universe.randomPoint">[docs]</a> <span class="k">def</span> <span class="nf">randomPoint</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :returns: a random point from a uniform distribution within</span>
<span class="sd"> the universe. This operation is defined only for</span>
<span class="sd"> finite-volume universes, e.g. periodic universes.</span>
<span class="sd"> :rtype: Scientific.Geometry.Vector</span>
<span class="sd"> """</span>
<span class="k">raise</span> <span class="ne">TypeError</span><span class="p">(</span><span class="s">"undefined operation"</span><span class="p">)</span>
</div>
<div class="viewcode-block" id="Universe.map"><a class="viewcode-back" href="../../modules.html#MMTK.Universe.Universe.map">[docs]</a> <span class="k">def</span> <span class="nf">map</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">function</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Apply a function to all objects in the universe and</span>
<span class="sd"> return the list of the results. If the results are chemical</span>
<span class="sd"> objects, a Collection object is returned instead of a list.</span>
<span class="sd"> :param function: the function to be applied</span>
<span class="sd"> :type function: callable</span>
<span class="sd"> :returns: the list or collection of the results</span>
<span class="sd"> """</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_objects</span><span class="o">.</span><span class="n">map</span><span class="p">(</span><span class="n">function</span><span class="p">)</span>
</div>
<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="n">objects</span> <span class="o">=</span> <span class="bp">None</span><span class="p">,</span> <span class="n">index_map</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
<span class="k">if</span> <span class="n">objects</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">objects</span> <span class="o">=</span> <span class="bp">self</span>
<span class="n">attributes</span> <span class="o">=</span> <span class="p">{}</span>
<span class="k">for</span> <span class="n">attr</span> <span class="ow">in</span> <span class="nb">dir</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">if</span> <span class="n">attr</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">!=</span> <span class="s">'_'</span><span class="p">:</span>
<span class="nb">object</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">attr</span><span class="p">)</span>
<span class="k">if</span> <span class="n">ChemicalObjects</span><span class="o">.</span><span class="n">isChemicalObject</span><span class="p">(</span><span class="nb">object</span><span class="p">)</span> \
<span class="ow">or</span> <span class="n">Environment</span><span class="o">.</span><span class="n">isEnvironmentObject</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
<span class="n">attributes</span><span class="p">[</span><span class="nb">object</span><span class="p">]</span> <span class="o">=</span> <span class="n">attr</span>
<span class="n">items</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">objects</span><span class="o">.</span><span class="n">objectList</span><span class="p">():</span>
<span class="n">attr</span> <span class="o">=</span> <span class="n">attributes</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">o</span><span class="p">,</span> <span class="bp">None</span><span class="p">)</span>
<span class="k">if</span> <span class="n">attr</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">items</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">repr</span><span class="p">(</span><span class="n">attr</span><span class="p">))</span>
<span class="n">items</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">o</span><span class="o">.</span><span class="n">description</span><span class="p">(</span><span class="n">index_map</span><span class="p">))</span>
<span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_environment</span><span class="p">:</span>
<span class="n">attr</span> <span class="o">=</span> <span class="n">attributes</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">o</span><span class="p">,</span> <span class="bp">None</span><span class="p">)</span>
<span class="k">if</span> <span class="n">attr</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">items</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">repr</span><span class="p">(</span><span class="n">attr</span><span class="p">))</span>
<span class="n">items</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">o</span><span class="o">.</span><span class="n">description</span><span class="p">())</span>
<span class="k">try</span><span class="p">:</span>
<span class="n">classname</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">classname_for_trajectories</span>
<span class="k">except</span> <span class="ne">AttributeError</span><span class="p">:</span>
<span class="n">classname</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="n">s</span> <span class="o">=</span> <span class="s">'c(</span><span class="si">%s</span><span class="s">,[</span><span class="si">%s</span><span class="s">])'</span> <span class="o">%</span> \
<span class="p">(</span><span class="sb">`classname + self._descriptionArguments()`</span><span class="p">,</span>
<span class="s">','</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">items</span><span class="p">))</span>
<span class="k">return</span> <span class="n">s</span>
<span class="k">def</span> <span class="nf">_graphics</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">conf</span><span class="p">,</span> <span class="n">distance_fn</span><span class="p">,</span> <span class="n">model</span><span class="p">,</span> <span class="n">module</span><span class="p">,</span> <span class="n">options</span><span class="p">):</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_objects</span><span class="o">.</span><span class="n">_graphics</span><span class="p">(</span><span class="n">conf</span><span class="p">,</span> <span class="n">distance_fn</span><span class="p">,</span> <span class="n">model</span><span class="p">,</span>
<span class="n">module</span><span class="p">,</span> <span class="n">options</span><span class="p">)</span>
<div class="viewcode-block" id="Universe.setFromTrajectory"><a class="viewcode-back" href="../../modules.html#MMTK.Universe.Universe.setFromTrajectory">[docs]</a> <span class="k">def</span> <span class="nf">setFromTrajectory</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">trajectory</span><span class="p">,</span> <span class="n">step</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Set the state of the universe to the one stored in a trajectory.</span>
<span class="sd"> This operation is thread-safe; it blocks other threads that</span>
<span class="sd"> want to access the configuration or velocities while the data is</span>
<span class="sd"> being updated.</span>
<span class="sd"> :param trajectory: a trajectory object for this universe</span>
<span class="sd"> :type trajectory: :class:`~MMTK.Trajectory.Trajectory`</span>
<span class="sd"> :param step: a step number, or None for the default step</span>
<span class="sd"> (0 for a standard trajectory, the last written</span>
<span class="sd"> step for a restart trajectory)</span>
<span class="sd"> :type step: int</span>
<span class="sd"> """</span>
<span class="k">if</span> <span class="n">step</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">step</span> <span class="o">=</span> <span class="n">trajectory</span><span class="o">.</span><span class="n">defaultStep</span><span class="p">()</span>
<span class="bp">self</span><span class="o">.</span><span class="n">acquireWriteStateLock</span><span class="p">()</span>
<span class="k">try</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">setConfiguration</span><span class="p">(</span><span class="n">trajectory</span><span class="o">.</span><span class="n">configuration</span><span class="p">[</span><span class="n">step</span><span class="p">],</span> <span class="bp">False</span><span class="p">)</span>
<span class="n">vel</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">velocities</span><span class="p">()</span>
<span class="k">try</span><span class="p">:</span>
<span class="n">vel_tr</span> <span class="o">=</span> <span class="n">trajectory</span><span class="o">.</span><span class="n">velocities</span><span class="p">[</span><span class="n">step</span><span class="p">]</span>
<span class="k">except</span> <span class="ne">AttributeError</span><span class="p">:</span>
<span class="k">if</span> <span class="n">vel</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">Utility</span><span class="o">.</span><span class="n">warning</span><span class="p">(</span><span class="s">"velocities were not modified because "</span> <span class="o">+</span>
<span class="s">"the trajectory does not contain "</span> <span class="o">+</span>
<span class="s">"velocity data."</span><span class="p">)</span>
<span class="k">return</span>
<span class="k">if</span> <span class="n">vel</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_atom_properties</span><span class="p">[</span><span class="s">'velocity'</span><span class="p">]</span> <span class="o">=</span> <span class="n">vel_tr</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">vel</span><span class="o">.</span><span class="n">assign</span><span class="p">(</span><span class="n">vel_tr</span><span class="p">)</span>
<span class="k">finally</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">releaseWriteStateLock</span><span class="p">()</span>
<span class="c">#</span>
<span class="c"># More efficient reimplementations of methods in Collections.GroupOfAtoms</span>
<span class="c">#</span></div>
<span class="k">def</span> <span class="nf">numberOfFixedAtoms</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">getParticleBoolean</span><span class="p">(</span><span class="s">'fixed'</span><span class="p">)</span><span class="o">.</span><span class="n">sumOverParticles</span><span class="p">()</span>
<span class="k">def</span> <span class="nf">degreesOfFreedom</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</span> <span class="mi">3</span><span class="o">*</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">numberOfAtoms</span><span class="p">()</span><span class="o">-</span><span class="bp">self</span><span class="o">.</span><span class="n">numberOfFixedAtoms</span><span class="p">())</span> \
<span class="o">-</span> <span class="bp">self</span><span class="o">.</span><span class="n">numberOfDistanceConstraints</span><span class="p">()</span>
<span class="k">def</span> <span class="nf">mass</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">masses</span><span class="p">()</span><span class="o">.</span><span class="n">sumOverParticles</span><span class="p">()</span>
<span class="k">def</span> <span class="nf">centerOfMass</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">conf</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
<span class="n">m</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">masses</span><span class="p">()</span>
<span class="k">if</span> <span class="n">conf</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">conf</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">configuration</span><span class="p">()</span>
<span class="k">return</span> <span class="p">(</span><span class="n">m</span><span class="o">*</span><span class="n">conf</span><span class="p">)</span><span class="o">.</span><span class="n">sumOverParticles</span><span class="p">()</span><span class="o">/</span><span class="n">m</span><span class="o">.</span><span class="n">sumOverParticles</span><span class="p">()</span>
<span class="k">def</span> <span class="nf">kineticEnergy</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">velocities</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
<span class="k">if</span> <span class="n">velocities</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">velocities</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">velocities</span><span class="p">()</span>
<span class="k">return</span> <span class="mf">0.5</span><span class="o">*</span><span class="n">velocities</span><span class="o">.</span><span class="n">massWeightedDotProduct</span><span class="p">(</span><span class="n">velocities</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">momentum</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">velocities</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
<span class="k">if</span> <span class="n">velocities</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">velocities</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">velocities</span><span class="p">()</span>
<span class="k">return</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">masses</span><span class="p">()</span><span class="o">*</span><span class="n">velocities</span><span class="p">)</span><span class="o">.</span><span class="n">sumOverParticles</span><span class="p">()</span>
<span class="k">def</span> <span class="nf">translateBy</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">vector</span><span class="p">):</span>
<span class="n">conf</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">configuration</span><span class="p">()</span><span class="o">.</span><span class="n">array</span>
<span class="n">N</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">conf</span><span class="p">,</span> <span class="n">vector</span><span class="o">.</span><span class="n">array</span><span class="p">[</span><span class="n">N</span><span class="o">.</span><span class="n">NewAxis</span><span class="p">,</span> <span class="p">:],</span> <span class="n">conf</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">applyTransformation</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="n">conf</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">configuration</span><span class="p">()</span><span class="o">.</span><span class="n">array</span>
<span class="n">rot</span> <span class="o">=</span> <span class="n">t</span><span class="o">.</span><span class="n">rotation</span><span class="p">()</span><span class="o">.</span><span class="n">tensor</span><span class="o">.</span><span class="n">array</span>
<span class="n">conf</span><span class="p">[:]</span> <span class="o">=</span> <span class="n">N</span><span class="o">.</span><span class="n">dot</span><span class="p">(</span><span class="n">conf</span><span class="p">,</span> <span class="n">N</span><span class="o">.</span><span class="n">transpose</span><span class="p">(</span><span class="n">rot</span><span class="p">))</span>
<span class="n">N</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">conf</span><span class="p">,</span> <span class="n">t</span><span class="o">.</span><span class="n">translation</span><span class="p">()</span><span class="o">.</span><span class="n">vector</span><span class="o">.</span><span class="n">array</span><span class="p">[</span><span class="n">N</span><span class="o">.</span><span class="n">NewAxis</span><span class="p">,</span> <span class="p">:],</span> <span class="n">conf</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">writeXML</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="nb">file</span><span class="p">):</span>
<span class="nb">file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">'<?xml version="1.0" encoding="ISO-8859-1" '</span> <span class="o">+</span>
<span class="s">'standalone="yes"?></span><span class="se">\n\n</span><span class="s">'</span><span class="p">)</span>
<span class="nb">file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">'<molecularsystem></span><span class="se">\n\n</span><span class="s">'</span><span class="p">)</span>
<span class="nb">file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">'<templates></span><span class="se">\n\n</span><span class="s">'</span><span class="p">)</span>
<span class="n">memo</span> <span class="o">=</span> <span class="p">{</span><span class="s">'counter'</span><span class="p">:</span> <span class="mi">1</span><span class="p">}</span>
<span class="n">instances</span> <span class="o">=</span> <span class="p">[]</span>
<span class="n">atoms</span> <span class="o">=</span> <span class="p">[]</span>
<span class="k">for</span> <span class="nb">object</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_objects</span><span class="o">.</span><span class="n">objectList</span><span class="p">():</span>
<span class="n">instances</span> <span class="o">=</span> <span class="n">instances</span> <span class="o">+</span> <span class="nb">object</span><span class="o">.</span><span class="n">writeXML</span><span class="p">(</span><span class="nb">file</span><span class="p">,</span> <span class="n">memo</span><span class="p">,</span> <span class="mi">1</span><span class="p">)</span>
<span class="n">atoms</span> <span class="o">=</span> <span class="n">atoms</span> <span class="o">+</span> <span class="nb">object</span><span class="o">.</span><span class="n">getXMLAtomOrder</span><span class="p">()</span>
<span class="nb">file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">'</span><span class="se">\n</span><span class="s"></templates></span><span class="se">\n\n</span><span class="s">'</span><span class="p">)</span>
<span class="nb">file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">'<universe </span><span class="si">%s</span><span class="s">></span><span class="se">\n</span><span class="s">'</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">XMLSpec</span><span class="p">())</span>
<span class="k">for</span> <span class="n">instance</span> <span class="ow">in</span> <span class="n">instances</span><span class="p">:</span>
<span class="nb">file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">' '</span><span class="p">)</span>
<span class="nb">file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">instance</span><span class="p">)</span>
<span class="nb">file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">'</span><span class="se">\n</span><span class="s">'</span><span class="p">)</span>
<span class="n">conf</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">configuration</span><span class="p">()</span>
<span class="k">if</span> <span class="n">conf</span><span class="o">.</span><span class="n">hasValidPositions</span><span class="p">():</span>
<span class="nb">file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">' <configuration></span><span class="se">\n</span><span class="s">'</span><span class="p">)</span>
<span class="nb">file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">' <atomArray units="units:nm"</span><span class="se">\n</span><span class="s">'</span><span class="p">)</span>
<span class="nb">file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">' x3="'</span><span class="p">)</span>
<span class="k">for</span> <span class="n">atom</span> <span class="ow">in</span> <span class="n">atoms</span><span class="p">:</span>
<span class="nb">file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">conf</span><span class="p">[</span><span class="n">atom</span><span class="p">][</span><span class="mi">0</span><span class="p">]))</span>
<span class="nb">file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">' '</span><span class="p">)</span>
<span class="nb">file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">'"</span><span class="se">\n</span><span class="s">'</span><span class="p">)</span>
<span class="nb">file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">' y3="'</span><span class="p">)</span>
<span class="k">for</span> <span class="n">atom</span> <span class="ow">in</span> <span class="n">atoms</span><span class="p">:</span>
<span class="nb">file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">conf</span><span class="p">[</span><span class="n">atom</span><span class="p">][</span><span class="mi">1</span><span class="p">]))</span>
<span class="nb">file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">' '</span><span class="p">)</span>
<span class="nb">file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">'"</span><span class="se">\n</span><span class="s">'</span><span class="p">)</span>
<span class="nb">file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">' z3="'</span><span class="p">)</span>
<span class="k">for</span> <span class="n">atom</span> <span class="ow">in</span> <span class="n">atoms</span><span class="p">:</span>
<span class="nb">file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">conf</span><span class="p">[</span><span class="n">atom</span><span class="p">][</span><span class="mi">2</span><span class="p">]))</span>
<span class="nb">file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">' '</span><span class="p">)</span>
<span class="nb">file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">'"</span><span class="se">\n</span><span class="s">'</span><span class="p">)</span>
<span class="nb">file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">' /></span><span class="se">\n</span><span class="s">'</span><span class="p">)</span>
<span class="nb">file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">' </configuration></span><span class="se">\n</span><span class="s">'</span><span class="p">)</span>
<span class="nb">file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">'</universe></span><span class="se">\n\n</span><span class="s">'</span><span class="p">)</span>
<span class="nb">file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">'</molecularsystem></span><span class="se">\n</span><span class="s">'</span><span class="p">)</span>
<span class="c">#</span>
<span class="c"># Infinite universes</span>
<span class="c">#</span></div>
<div class="viewcode-block" id="InfiniteUniverse"><a class="viewcode-back" href="../../modules.html#MMTK.Universe.InfiniteUniverse">[docs]</a><span class="k">class</span> <span class="nc">InfiniteUniverse</span><span class="p">(</span><span class="n">Universe</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Infinite (unbounded and nonperiodic) universe.</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">forcefield</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="o">**</span><span class="n">properties</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :param forcefield: a force field, or None for no force field</span>
<span class="sd"> :type forcefield: :class:`~MMTK.ForceFields.ForceField.ForceField`</span>
<span class="sd"> """</span>
<span class="n">Universe</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="n">forcefield</span><span class="p">,</span> <span class="n">properties</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_createSpec</span><span class="p">()</span>
<span class="k">def</span> <span class="nf">CdistanceFunction</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="kn">from</span> <span class="nn">MMTK_universe</span> <span class="kn">import</span> <span class="n">infinite_universe_distance_function</span>
<span class="k">return</span> <span class="n">infinite_universe_distance_function</span><span class="p">,</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">CcorrectionFunction</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="kn">from</span> <span class="nn">MMTK_universe</span> <span class="kn">import</span> <span class="n">infinite_universe_correction_function</span>
<span class="k">return</span> <span class="n">infinite_universe_correction_function</span><span class="p">,</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">CvolumeFunction</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="kn">from</span> <span class="nn">MMTK_universe</span> <span class="kn">import</span> <span class="n">infinite_universe_volume_function</span>
<span class="k">return</span> <span class="n">infinite_universe_volume_function</span><span class="p">,</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">CboxTransformationFunction</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</span> <span class="bp">None</span><span class="p">,</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">_createSpec</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="kn">from</span> <span class="nn">MMTK_universe</span> <span class="kn">import</span> <span class="n">InfiniteUniverseSpec</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_spec</span> <span class="o">=</span> <span class="n">InfiniteUniverseSpec</span><span class="p">()</span>
<span class="k">def</span> <span class="nf">_descriptionArguments</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_forcefield</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="k">return</span> <span class="s">'()'</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">return</span> <span class="s">'(</span><span class="si">%s</span><span class="s">)'</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">_forcefield</span><span class="o">.</span><span class="n">description</span><span class="p">()</span>
<span class="k">def</span> <span class="nf">XMLSpec</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</span> <span class="s">'topology="infinite"'</span>
<span class="c">#</span>
<span class="c"># 3D periodic universe base class</span>
<span class="c">#</span></div>
<span class="k">class</span> <span class="nc">Periodic3DUniverse</span><span class="p">(</span><span class="n">Universe</span><span class="p">):</span>
<span class="n">is_periodic</span> <span class="o">=</span> <span class="bp">True</span>
<span class="k">def</span> <span class="nf">setVolume</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">volume</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Multiplies all edge lengths by the same factor such that the cell</span>
<span class="sd"> volume becomes equal to the specified value.</span>
<span class="sd"> :param volume: the desired volume</span>
<span class="sd"> :type volume: float</span>
<span class="sd"> """</span>
<span class="n">factor</span> <span class="o">=</span> <span class="p">(</span><span class="n">volume</span><span class="o">/</span><span class="bp">self</span><span class="o">.</span><span class="n">cellVolume</span><span class="p">())</span><span class="o">**</span><span class="p">(</span><span class="mf">1.</span><span class="o">/</span><span class="mf">3.</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">scaleSize</span><span class="p">(</span><span class="n">factor</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">foldCoordinatesIntoBox</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_spec</span><span class="o">.</span><span class="n">foldCoordinatesIntoBox</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">configuration</span><span class="p">()</span><span class="o">.</span><span class="n">array</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">basisVectors</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</span> <span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">boxToRealCoordinates</span><span class="p">(</span><span class="n">Vector</span><span class="p">(</span><span class="mf">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="bp">self</span><span class="o">.</span><span class="n">boxToRealCoordinates</span><span class="p">(</span><span class="n">Vector</span><span class="p">(</span><span class="mf">0.</span><span class="p">,</span> <span class="mf">1.</span><span class="p">,</span> <span class="mf">0.</span><span class="p">)),</span>
<span class="bp">self</span><span class="o">.</span><span class="n">boxToRealCoordinates</span><span class="p">(</span><span class="n">Vector</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="mf">1.</span><span class="p">))]</span>
<span class="k">def</span> <span class="nf">cartesianToFractional</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">vector</span><span class="p">):</span>
<span class="n">r1</span><span class="p">,</span> <span class="n">r2</span><span class="p">,</span> <span class="n">r3</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">reciprocalBasisVectors</span><span class="p">()</span>
<span class="k">return</span> <span class="n">N</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="n">r1</span><span class="o">*</span><span class="n">vector</span><span class="p">,</span> <span class="n">r2</span><span class="o">*</span><span class="n">vector</span><span class="p">,</span> <span class="n">r3</span><span class="o">*</span><span class="n">vector</span><span class="p">])</span>
<span class="k">def</span> <span class="nf">cartesianToFractionalMatrix</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</span> <span class="n">N</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">reciprocalBasisVectors</span><span class="p">())</span>
<span class="k">def</span> <span class="nf">fractionalToCartesian</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">array</span><span class="p">):</span>
<span class="n">e1</span><span class="p">,</span> <span class="n">e2</span><span class="p">,</span> <span class="n">e3</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">basisVectors</span><span class="p">()</span>
<span class="k">return</span> <span class="n">array</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">*</span><span class="n">e1</span> <span class="o">+</span> <span class="n">array</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">*</span><span class="n">e2</span> <span class="o">+</span> <span class="n">array</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span><span class="o">*</span><span class="n">e3</span>
<span class="k">def</span> <span class="nf">fractionalToCartesianMatrix</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</span> <span class="n">N</span><span class="o">.</span><span class="n">transpose</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">basisVectors</span><span class="p">())</span>
<span class="k">def</span> <span class="nf">randomPoint</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">boxToRealCoordinates</span><span class="p">(</span><span class="n">Random</span><span class="o">.</span><span class="n">randomPointInBox</span><span class="p">(</span><span class="mf">1.</span><span class="p">,</span> <span class="mf">1.</span><span class="p">,</span> <span class="mf">1.</span><span class="p">))</span>
<span class="k">def</span> <span class="nf">contiguousObjectOffset</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">objects</span> <span class="o">=</span> <span class="bp">None</span><span class="p">,</span> <span class="n">conf</span> <span class="o">=</span> <span class="bp">None</span><span class="p">,</span>
<span class="n">box_coordinates</span> <span class="o">=</span> <span class="mi">0</span><span class="p">):</span>
<span class="kn">from</span> <span class="nn">MMTK_universe</span> <span class="kn">import</span> <span class="n">contiguous_object_offset</span>
<span class="k">if</span> <span class="n">objects</span> <span class="ow">is</span> <span class="bp">None</span> <span class="ow">or</span> <span class="n">objects</span> <span class="o">==</span> <span class="bp">self</span> <span class="ow">or</span> <span class="n">objects</span> <span class="o">==</span> <span class="p">[</span><span class="bp">self</span><span class="p">]:</span>
<span class="n">default</span> <span class="o">=</span> <span class="bp">True</span>
<span class="n">objects</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_objects</span><span class="o">.</span><span class="n">objectList</span><span class="p">()</span>
<span class="n">pairs</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_bond_pairs</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">default</span> <span class="o">=</span> <span class="bp">False</span>
<span class="n">pairs</span> <span class="o">=</span> <span class="bp">None</span>
<span class="k">if</span> <span class="n">conf</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">conf</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">configuration</span><span class="p">()</span>
<span class="n">cell</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_fixCellParameters</span><span class="p">(</span><span class="n">conf</span><span class="o">.</span><span class="n">cell_parameters</span><span class="p">)</span>
<span class="n">offset</span> <span class="o">=</span> <span class="n">ParticleProperties</span><span class="o">.</span><span class="n">ParticleVector</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
<span class="k">if</span> <span class="n">pairs</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">pairs</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">objects</span><span class="p">:</span>
<span class="n">new_object</span> <span class="o">=</span> <span class="bp">True</span>
<span class="k">if</span> <span class="n">ChemicalObjects</span><span class="o">.</span><span class="n">isChemicalObject</span><span class="p">(</span><span class="n">o</span><span class="p">):</span>
<span class="n">units</span> <span class="o">=</span> <span class="n">o</span><span class="o">.</span><span class="n">bondedUnits</span><span class="p">()</span>
<span class="k">elif</span> <span class="n">Collections</span><span class="o">.</span><span class="n">isCollection</span><span class="p">(</span><span class="n">o</span><span class="p">)</span> <span class="ow">or</span> <span class="n">isUniverse</span><span class="p">(</span><span class="n">o</span><span class="p">):</span>
<span class="n">units</span> <span class="o">=</span> <span class="nb">set</span><span class="p">([</span><span class="n">u</span>
<span class="k">for</span> <span class="n">element</span> <span class="ow">in</span> <span class="n">o</span>
<span class="k">for</span> <span class="n">u</span> <span class="ow">in</span> <span class="n">element</span><span class="o">.</span><span class="n">topLevelChemicalObject</span><span class="p">()</span>
<span class="o">.</span><span class="n">bondedUnits</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="nb">str</span><span class="p">(</span><span class="n">o</span><span class="p">)</span> <span class="o">+</span> <span class="s">" not a chemical object"</span><span class="p">)</span>
<span class="k">for</span> <span class="n">bu</span> <span class="ow">in</span> <span class="n">units</span><span class="p">:</span>
<span class="n">atoms</span> <span class="o">=</span> <span class="p">[</span><span class="n">a</span><span class="o">.</span><span class="n">index</span> <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">bu</span><span class="o">.</span><span class="n">atomsWithDefinedPositions</span><span class="p">()]</span>
<span class="n">mpairs</span> <span class="o">=</span> <span class="n">bu</span><span class="o">.</span><span class="n">traverseBondTree</span><span class="p">(</span><span class="k">lambda</span> <span class="n">a</span><span class="p">:</span> <span class="n">a</span><span class="o">.</span><span class="n">index</span><span class="p">)</span>
<span class="n">mpairs</span> <span class="o">=</span> <span class="p">[(</span><span class="n">a1</span><span class="p">,</span> <span class="n">a2</span><span class="p">)</span> <span class="k">for</span> <span class="p">(</span><span class="n">a1</span><span class="p">,</span> <span class="n">a2</span><span class="p">)</span> <span class="ow">in</span> <span class="n">mpairs</span>
<span class="k">if</span> <span class="n">a1</span> <span class="ow">in</span> <span class="n">atoms</span> <span class="ow">and</span> <span class="n">a2</span> <span class="ow">in</span> <span class="n">atoms</span><span class="p">]</span>
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">mpairs</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
<span class="n">mpairs</span> <span class="o">=</span> <span class="n">Utility</span><span class="o">.</span><span class="n">pairs</span><span class="p">(</span><span class="n">atoms</span><span class="p">)</span>
<span class="n">new_object</span> <span class="o">=</span> <span class="bp">False</span>
<span class="n">pairs</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span><span class="n">mpairs</span><span class="p">)</span>
<span class="n">pairs</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">pairs</span><span class="p">)</span>
<span class="k">if</span> <span class="n">default</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_bond_pairs</span> <span class="o">=</span> <span class="n">pairs</span>
<span class="k">if</span> <span class="n">cell</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">contiguous_object_offset</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_spec</span><span class="p">,</span> <span class="n">pairs</span><span class="p">,</span> <span class="n">conf</span><span class="o">.</span><span class="n">array</span><span class="p">,</span>
<span class="n">offset</span><span class="o">.</span><span class="n">array</span><span class="p">,</span> <span class="n">box_coordinates</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">contiguous_object_offset</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_spec</span><span class="p">,</span> <span class="n">pairs</span><span class="p">,</span> <span class="n">conf</span><span class="o">.</span><span class="n">array</span><span class="p">,</span>
<span class="n">offset</span><span class="o">.</span><span class="n">array</span><span class="p">,</span> <span class="n">box_coordinates</span><span class="p">,</span> <span class="n">cell</span><span class="p">)</span>
<span class="k">return</span> <span class="n">offset</span>
<span class="k">def</span> <span class="nf">_graphics</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">conf</span><span class="p">,</span> <span class="n">distance_fn</span><span class="p">,</span> <span class="n">model</span><span class="p">,</span> <span class="n">module</span><span class="p">,</span> <span class="n">options</span><span class="p">):</span>
<span class="n">objects</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_objects</span><span class="o">.</span><span class="n">_graphics</span><span class="p">(</span><span class="n">conf</span><span class="p">,</span> <span class="n">distance_fn</span><span class="p">,</span> <span class="n">model</span><span class="p">,</span>
<span class="n">module</span><span class="p">,</span> <span class="n">options</span><span class="p">)</span>
<span class="n">v1</span><span class="p">,</span> <span class="n">v2</span><span class="p">,</span> <span class="n">v3</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">basisVectors</span><span class="p">()</span>
<span class="n">p</span> <span class="o">=</span> <span class="o">-</span><span class="mf">0.5</span><span class="o">*</span><span class="p">(</span><span class="n">v1</span><span class="o">+</span><span class="n">v2</span><span class="o">+</span><span class="n">v3</span><span class="p">)</span>
<span class="n">color</span> <span class="o">=</span> <span class="n">options</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s">'color'</span><span class="p">,</span> <span class="s">'white'</span><span class="p">)</span>
<span class="n">material</span> <span class="o">=</span> <span class="n">module</span><span class="o">.</span><span class="n">EmissiveMaterial</span><span class="p">(</span><span class="n">color</span><span class="p">)</span>
<span class="n">objects</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">module</span><span class="o">.</span><span class="n">Line</span><span class="p">(</span><span class="n">p</span><span class="p">,</span> <span class="n">p</span><span class="o">+</span><span class="n">v1</span><span class="p">,</span> <span class="n">material</span><span class="o">=</span><span class="n">material</span><span class="p">))</span>
<span class="n">objects</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">module</span><span class="o">.</span><span class="n">Line</span><span class="p">(</span><span class="n">p</span><span class="p">,</span> <span class="n">p</span><span class="o">+</span><span class="n">v2</span><span class="p">,</span> <span class="n">material</span><span class="o">=</span><span class="n">material</span><span class="p">))</span>
<span class="n">objects</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">module</span><span class="o">.</span><span class="n">Line</span><span class="p">(</span><span class="n">p</span><span class="o">+</span><span class="n">v1</span><span class="p">,</span> <span class="n">p</span><span class="o">+</span><span class="n">v1</span><span class="o">+</span><span class="n">v2</span><span class="p">,</span> <span class="n">material</span><span class="o">=</span><span class="n">material</span><span class="p">))</span>
<span class="n">objects</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">module</span><span class="o">.</span><span class="n">Line</span><span class="p">(</span><span class="n">p</span><span class="o">+</span><span class="n">v2</span><span class="p">,</span> <span class="n">p</span><span class="o">+</span><span class="n">v1</span><span class="o">+</span><span class="n">v2</span><span class="p">,</span> <span class="n">material</span><span class="o">=</span><span class="n">material</span><span class="p">))</span>
<span class="n">objects</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">module</span><span class="o">.</span><span class="n">Line</span><span class="p">(</span><span class="n">p</span><span class="p">,</span> <span class="n">p</span><span class="o">+</span><span class="n">v3</span><span class="p">,</span> <span class="n">material</span><span class="o">=</span><span class="n">material</span><span class="p">))</span>
<span class="n">objects</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">module</span><span class="o">.</span><span class="n">Line</span><span class="p">(</span><span class="n">p</span><span class="o">+</span><span class="n">v1</span><span class="p">,</span> <span class="n">p</span><span class="o">+</span><span class="n">v1</span><span class="o">+</span><span class="n">v3</span><span class="p">,</span> <span class="n">material</span><span class="o">=</span><span class="n">material</span><span class="p">))</span>
<span class="n">objects</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">module</span><span class="o">.</span><span class="n">Line</span><span class="p">(</span><span class="n">p</span><span class="o">+</span><span class="n">v2</span><span class="p">,</span> <span class="n">p</span><span class="o">+</span><span class="n">v2</span><span class="o">+</span><span class="n">v3</span><span class="p">,</span> <span class="n">material</span><span class="o">=</span><span class="n">material</span><span class="p">))</span>
<span class="n">objects</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">module</span><span class="o">.</span><span class="n">Line</span><span class="p">(</span><span class="n">p</span><span class="o">+</span><span class="n">v1</span><span class="o">+</span><span class="n">v2</span><span class="p">,</span> <span class="n">p</span><span class="o">+</span><span class="n">v1</span><span class="o">+</span><span class="n">v2</span><span class="o">+</span><span class="n">v3</span><span class="p">,</span> <span class="n">material</span><span class="o">=</span><span class="n">material</span><span class="p">))</span>
<span class="n">objects</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">module</span><span class="o">.</span><span class="n">Line</span><span class="p">(</span><span class="n">p</span><span class="o">+</span><span class="n">v3</span><span class="p">,</span> <span class="n">p</span><span class="o">+</span><span class="n">v1</span><span class="o">+</span><span class="n">v3</span><span class="p">,</span> <span class="n">material</span><span class="o">=</span><span class="n">material</span><span class="p">))</span>
<span class="n">objects</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">module</span><span class="o">.</span><span class="n">Line</span><span class="p">(</span><span class="n">p</span><span class="o">+</span><span class="n">v3</span><span class="p">,</span> <span class="n">p</span><span class="o">+</span><span class="n">v2</span><span class="o">+</span><span class="n">v3</span><span class="p">,</span> <span class="n">material</span><span class="o">=</span><span class="n">material</span><span class="p">))</span>
<span class="n">objects</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">module</span><span class="o">.</span><span class="n">Line</span><span class="p">(</span><span class="n">p</span><span class="o">+</span><span class="n">v1</span><span class="o">+</span><span class="n">v3</span><span class="p">,</span> <span class="n">p</span><span class="o">+</span><span class="n">v1</span><span class="o">+</span><span class="n">v2</span><span class="o">+</span><span class="n">v3</span><span class="p">,</span> <span class="n">material</span><span class="o">=</span><span class="n">material</span><span class="p">))</span>
<span class="n">objects</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">module</span><span class="o">.</span><span class="n">Line</span><span class="p">(</span><span class="n">p</span><span class="o">+</span><span class="n">v2</span><span class="o">+</span><span class="n">v3</span><span class="p">,</span> <span class="n">p</span><span class="o">+</span><span class="n">v1</span><span class="o">+</span><span class="n">v2</span><span class="o">+</span><span class="n">v3</span><span class="p">,</span> <span class="n">material</span><span class="o">=</span><span class="n">material</span><span class="p">))</span>
<span class="k">return</span> <span class="n">objects</span>
<span class="c">#</span>
<span class="c"># Orthorhombic universe with periodic boundary conditions</span>
<span class="c">#</span>
<div class="viewcode-block" id="OrthorhombicPeriodicUniverse"><a class="viewcode-back" href="../../modules.html#MMTK.Universe.OrthorhombicPeriodicUniverse">[docs]</a><span class="k">class</span> <span class="nc">OrthorhombicPeriodicUniverse</span><span class="p">(</span><span class="n">Periodic3DUniverse</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Periodic universe with orthorhombic elementary cell.</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">size</span> <span class="o">=</span> <span class="bp">None</span><span class="p">,</span> <span class="n">forcefield</span> <span class="o">=</span> <span class="bp">None</span><span class="p">,</span> <span class="o">**</span><span class="n">properties</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :param size: a sequence of length three specifying the edge</span>
<span class="sd"> lengths along the x, y, and z directions</span>
<span class="sd"> :param forcefield: a force field, or None for no force field</span>
<span class="sd"> :type forcefield: :class:`~MMTK.ForceFields.ForceField.ForceField`</span>
<span class="sd"> """</span>
<span class="n">Universe</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="n">forcefield</span><span class="p">,</span> <span class="n">properties</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">data</span> <span class="o">=</span> <span class="n">N</span><span class="o">.</span><span class="n">zeros</span><span class="p">((</span><span class="mi">3</span><span class="p">,),</span> <span class="n">N</span><span class="o">.</span><span class="n">Float</span><span class="p">)</span>
<span class="k">if</span> <span class="n">size</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">setSize</span><span class="p">(</span><span class="n">size</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_createSpec</span><span class="p">()</span>
<span class="n">is_orthogonal</span> <span class="o">=</span> <span class="bp">True</span>
<span class="k">def</span> <span class="nf">__setstate__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">state</span><span class="p">):</span>
<span class="n">Universe</span><span class="o">.</span><span class="n">__setstate__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">state</span><span class="p">)</span>
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="o">.</span><span class="n">shape</span><span class="p">)</span> <span class="o">==</span> <span class="mi">2</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">data</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
<span class="k">def</span> <span class="nf">setSize</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">size</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[:]</span> <span class="o">=</span> <span class="n">size</span>
<div class="viewcode-block" id="OrthorhombicPeriodicUniverse.scaleSize"><a class="viewcode-back" href="../../modules.html#MMTK.Universe.OrthorhombicPeriodicUniverse.scaleSize">[docs]</a> <span class="k">def</span> <span class="nf">scaleSize</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">factor</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Multiplies all edge lengths by a factor.</span>
<span class="sd"> :param factor: the scale factor</span>
<span class="sd"> :type factor: float</span>
<span class="sd"> """</span>
<span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[:]</span> <span class="o">=</span> <span class="n">factor</span><span class="o">*</span><span class="bp">self</span><span class="o">.</span><span class="n">data</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_spec</span><span class="o">.</span><span class="n">foldCoordinatesIntoBox</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">configuration</span><span class="p">()</span><span class="o">.</span><span class="n">array</span><span class="p">)</span>
</div>
<span class="k">def</span> <span class="nf">setCellParameters</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">parameters</span><span class="p">):</span>
<span class="k">if</span> <span class="n">parameters</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[:]</span> <span class="o">=</span> <span class="n">parameters</span>
<span class="k">def</span> <span class="nf">realToBoxCoordinates</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">vector</span><span class="p">):</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="n">vector</span>
<span class="k">return</span> <span class="n">Vector</span><span class="p">(</span><span class="n">x</span><span class="o">/</span><span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span>
<span class="n">y</span><span class="o">/</span><span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span>
<span class="n">z</span><span class="o">/</span><span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span>
<span class="k">def</span> <span class="nf">boxToRealCoordinates</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">vector</span><span class="p">):</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="n">vector</span>
<span class="k">return</span> <span class="n">Vector</span><span class="p">(</span><span class="n">x</span><span class="o">*</span><span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span>
<span class="n">y</span><span class="o">*</span><span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span>
<span class="n">z</span><span class="o">*</span><span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span>
<span class="k">def</span> <span class="nf">_realToBoxPointArray</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">array</span><span class="p">,</span> <span class="n">parameters</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span>
<span class="k">if</span> <span class="n">parameters</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">parameters</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span>
<span class="k">if</span> <span class="n">parameters</span><span class="o">.</span><span class="n">shape</span> <span class="o">==</span> <span class="p">(</span><span class="mi">3</span><span class="p">,):</span>
<span class="n">parameters</span> <span class="o">=</span> <span class="n">parameters</span><span class="p">[</span><span class="n">N</span><span class="o">.</span><span class="n">NewAxis</span><span class="p">,</span> <span class="p">:]</span>
<span class="k">return</span> <span class="n">array</span><span class="o">/</span><span class="n">parameters</span>
<span class="k">def</span> <span class="nf">_boxToRealPointArray</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">array</span><span class="p">,</span> <span class="n">parameters</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span>
<span class="k">if</span> <span class="n">parameters</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">parameters</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span>
<span class="k">if</span> <span class="n">parameters</span><span class="o">.</span><span class="n">shape</span> <span class="o">==</span> <span class="p">(</span><span class="mi">3</span><span class="p">,):</span>
<span class="n">parameters</span> <span class="o">=</span> <span class="n">parameters</span><span class="p">[</span><span class="n">N</span><span class="o">.</span><span class="n">NewAxis</span><span class="p">,</span> <span class="p">:]</span>
<span class="k">return</span> <span class="n">array</span><span class="o">*</span><span class="n">parameters</span>
<span class="k">def</span> <span class="nf">CdistanceFunction</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="kn">from</span> <span class="nn">MMTK_universe</span> <span class="kn">import</span> <span class="n">orthorhombic_universe_distance_function</span>
<span class="k">return</span> <span class="n">orthorhombic_universe_distance_function</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span>
<span class="k">def</span> <span class="nf">CcorrectionFunction</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="kn">from</span> <span class="nn">MMTK_universe</span> <span class="kn">import</span> <span class="n">orthorhombic_universe_correction_function</span>
<span class="k">return</span> <span class="n">orthorhombic_universe_correction_function</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span>
<span class="k">def</span> <span class="nf">CvolumeFunction</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="kn">from</span> <span class="nn">MMTK_universe</span> <span class="kn">import</span> <span class="n">orthorhombic_universe_volume_function</span>
<span class="k">return</span> <span class="n">orthorhombic_universe_volume_function</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span>
<span class="k">def</span> <span class="nf">CboxTransformationFunction</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="kn">from</span> <span class="nn">MMTK_universe</span> <span class="kn">import</span> <span class="n">orthorhombic_universe_box_transformation</span>
<span class="k">return</span> <span class="n">orthorhombic_universe_box_transformation</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span>
<span class="k">def</span> <span class="nf">cellParameters</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span>
<span class="k">def</span> <span class="nf">reciprocalBasisVectors</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</span> <span class="p">[</span><span class="n">Vector</span><span class="p">(</span><span class="mf">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="o">/</span><span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span>
<span class="n">Vector</span><span class="p">(</span><span class="mf">0.</span><span class="p">,</span> <span class="mf">1.</span><span class="p">,</span> <span class="mf">0.</span><span class="p">)</span><span class="o">/</span><span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span>
<span class="n">Vector</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="mf">1.</span><span class="p">)</span><span class="o">/</span><span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="mi">2</span><span class="p">]]</span>
<span class="k">def</span> <span class="nf">cellVolume</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</span> <span class="n">N</span><span class="o">.</span><span class="n">multiply</span><span class="o">.</span><span class="n">reduce</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">largestDistance</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</span> <span class="mf">0.5</span><span class="o">*</span><span class="n">N</span><span class="o">.</span><span class="n">minimum</span><span class="o">.</span><span class="n">reduce</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">_createSpec</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="kn">from</span> <span class="nn">MMTK_universe</span> <span class="kn">import</span> <span class="n">OrthorhombicPeriodicUniverseSpec</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_spec</span> <span class="o">=</span> <span class="n">OrthorhombicPeriodicUniverseSpec</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">_descriptionArguments</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_forcefield</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="k">return</span> <span class="s">'((0.,0.,0.),)'</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">return</span> <span class="s">'((0.,0.,0.),</span><span class="si">%s</span><span class="s">)'</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">_forcefield</span><span class="o">.</span><span class="n">description</span><span class="p">()</span>
<span class="k">def</span> <span class="nf">XMLSpec</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</span> <span class="s">'topology="periodic3d" '</span> <span class="o">+</span> \
<span class="s">'cellshape="orthorhombic" '</span> <span class="o">+</span> \
<span class="p">(</span><span class="s">'cellsize="</span><span class="si">%f</span><span class="s"> </span><span class="si">%f</span><span class="s"> </span><span class="si">%f</span><span class="s">" '</span> <span class="o">%</span> <span class="nb">tuple</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">))</span> <span class="o">+</span> \
<span class="s">'units="units:nm"'</span>
<span class="c">#</span>
<span class="c"># Cubic universe with periodic boundary conditions</span>
<span class="c">#</span></div>
<div class="viewcode-block" id="CubicPeriodicUniverse"><a class="viewcode-back" href="../../modules.html#MMTK.Universe.CubicPeriodicUniverse">[docs]</a><span class="k">class</span> <span class="nc">CubicPeriodicUniverse</span><span class="p">(</span><span class="n">OrthorhombicPeriodicUniverse</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Periodic universe with cubic elementary cell.</span>
<span class="sd"> """</span>
<div class="viewcode-block" id="CubicPeriodicUniverse.setSize"><a class="viewcode-back" href="../../modules.html#MMTK.Universe.CubicPeriodicUniverse.setSize">[docs]</a> <span class="k">def</span> <span class="nf">setSize</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">size</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Set the edge length to a given value.</span>
<span class="sd"> :param size: the new size</span>
<span class="sd"> :type size: float</span>
<span class="sd"> """</span>
<span class="n">OrthorhombicPeriodicUniverse</span><span class="o">.</span><span class="n">setSize</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="mi">3</span><span class="o">*</span><span class="p">(</span><span class="n">size</span><span class="p">,))</span>
</div>
<span class="k">def</span> <span class="nf">_descriptionArguments</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_forcefield</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="k">return</span> <span class="s">'(0.)'</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">return</span> <span class="s">'(0.,</span><span class="si">%s</span><span class="s">)'</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">_forcefield</span><span class="o">.</span><span class="n">description</span><span class="p">()</span>
<span class="c">#</span>
<span class="c"># Parallelepipedic universe with periodic boundary conditions</span>
<span class="c">#</span></div>
<div class="viewcode-block" id="ParallelepipedicPeriodicUniverse"><a class="viewcode-back" href="../../modules.html#MMTK.Universe.ParallelepipedicPeriodicUniverse">[docs]</a><span class="k">class</span> <span class="nc">ParallelepipedicPeriodicUniverse</span><span class="p">(</span><span class="n">Periodic3DUniverse</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Periodic universe with parallelepipedic elementary cell.</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">shape</span> <span class="o">=</span> <span class="bp">None</span><span class="p">,</span> <span class="n">forcefield</span> <span class="o">=</span> <span class="bp">None</span><span class="p">,</span> <span class="o">**</span><span class="n">properties</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :param shape: the basis vectors</span>
<span class="sd"> :type shape: sequence of Scientific.Geometry.Vector</span>
<span class="sd"> :param forcefield: a force field, or None for no force field</span>
<span class="sd"> :type forcefield: :class:`~MMTK.ForceFields.ForceField.ForceField`</span>
<span class="sd"> """</span>
<span class="n">Universe</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="n">forcefield</span><span class="p">,</span> <span class="n">properties</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">data</span> <span class="o">=</span> <span class="n">N</span><span class="o">.</span><span class="n">zeros</span><span class="p">((</span><span class="mi">19</span><span class="p">,),</span> <span class="n">N</span><span class="o">.</span><span class="n">Float</span><span class="p">)</span>
<span class="k">if</span> <span class="n">shape</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">setShape</span><span class="p">(</span><span class="n">shape</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_createSpec</span><span class="p">()</span>
<span class="n">is_periodic</span> <span class="o">=</span> <span class="bp">True</span>
<span class="k">def</span> <span class="nf">setShape</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">shape</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[:</span><span class="mi">9</span><span class="p">]</span> <span class="o">=</span> <span class="n">N</span><span class="o">.</span><span class="n">ravel</span><span class="p">(</span><span class="n">N</span><span class="o">.</span><span class="n">transpose</span><span class="p">([</span><span class="nb">list</span><span class="p">(</span><span class="n">s</span><span class="p">)</span> <span class="k">for</span> <span class="n">s</span> <span class="ow">in</span> <span class="n">shape</span><span class="p">]))</span>
<span class="kn">from</span> <span class="nn">MMTK_universe</span> <span class="kn">import</span> <span class="n">parallelepiped_invert</span>
<span class="n">parallelepiped_invert</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">)</span>
<div class="viewcode-block" id="ParallelepipedicPeriodicUniverse.scaleSize"><a class="viewcode-back" href="../../modules.html#MMTK.Universe.ParallelepipedicPeriodicUniverse.scaleSize">[docs]</a> <span class="k">def</span> <span class="nf">scaleSize</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">factor</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Multiplies all edge lengths by a factor.</span>
<span class="sd"> :param factor: the scale factor</span>
<span class="sd"> :type factor: float</span>
<span class="sd"> """</span>
<span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[:</span><span class="mi">9</span><span class="p">]</span> <span class="o">=</span> <span class="n">factor</span><span class="o">*</span><span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[:</span><span class="mi">9</span><span class="p">]</span>
<span class="kn">from</span> <span class="nn">MMTK_universe</span> <span class="kn">import</span> <span class="n">parallelepiped_invert</span>
<span class="n">parallelepiped_invert</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_spec</span><span class="o">.</span><span class="n">foldCoordinatesIntoBox</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">configuration</span><span class="p">()</span><span class="o">.</span><span class="n">array</span><span class="p">)</span>
</div>
<span class="k">def</span> <span class="nf">setCellParameters</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">parameters</span><span class="p">):</span>
<span class="k">if</span> <span class="n">parameters</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[:</span><span class="mi">9</span><span class="p">]</span> <span class="o">=</span> <span class="n">parameters</span>
<span class="kn">from</span> <span class="nn">MMTK_universe</span> <span class="kn">import</span> <span class="n">parallelepiped_invert</span>
<span class="n">parallelepiped_invert</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">_fixCellParameters</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">cell_parameters</span><span class="p">):</span>
<span class="n">full_parameters</span> <span class="o">=</span> <span class="mf">0.</span><span class="o">*</span><span class="bp">self</span><span class="o">.</span><span class="n">data</span>
<span class="n">full_parameters</span><span class="p">[:</span><span class="mi">9</span><span class="p">]</span> <span class="o">=</span> <span class="n">cell_parameters</span>
<span class="kn">from</span> <span class="nn">MMTK_universe</span> <span class="kn">import</span> <span class="n">parallelepiped_invert</span>
<span class="n">parallelepiped_invert</span><span class="p">(</span><span class="n">full_parameters</span><span class="p">)</span>
<span class="k">return</span> <span class="n">full_parameters</span>
<span class="k">def</span> <span class="nf">realToBoxCoordinates</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">vector</span><span class="p">):</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="n">vector</span>
<span class="k">return</span> <span class="n">Vector</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="mi">0</span><span class="o">+</span><span class="mi">9</span><span class="p">]</span><span class="o">*</span><span class="n">x</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="mi">1</span><span class="o">+</span><span class="mi">9</span><span class="p">]</span><span class="o">*</span><span class="n">y</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="mi">2</span><span class="o">+</span><span class="mi">9</span><span class="p">]</span><span class="o">*</span><span class="n">z</span><span class="p">,</span>
<span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="mi">3</span><span class="o">+</span><span class="mi">9</span><span class="p">]</span><span class="o">*</span><span class="n">x</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="mi">4</span><span class="o">+</span><span class="mi">9</span><span class="p">]</span><span class="o">*</span><span class="n">y</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="mi">5</span><span class="o">+</span><span class="mi">9</span><span class="p">]</span><span class="o">*</span><span class="n">z</span><span class="p">,</span>
<span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="mi">6</span><span class="o">+</span><span class="mi">9</span><span class="p">]</span><span class="o">*</span><span class="n">x</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="mi">7</span><span class="o">+</span><span class="mi">9</span><span class="p">]</span><span class="o">*</span><span class="n">y</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="mi">8</span><span class="o">+</span><span class="mi">9</span><span class="p">]</span><span class="o">*</span><span class="n">z</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">boxToRealCoordinates</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">vector</span><span class="p">):</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="n">vector</span>
<span class="k">return</span> <span class="n">Vector</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">*</span><span class="n">x</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">*</span><span class="n">y</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span><span class="o">*</span><span class="n">z</span><span class="p">,</span>
<span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span><span class="o">*</span><span class="n">x</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="mi">4</span><span class="p">]</span><span class="o">*</span><span class="n">y</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="mi">5</span><span class="p">]</span><span class="o">*</span><span class="n">z</span><span class="p">,</span>
<span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="mi">6</span><span class="p">]</span><span class="o">*</span><span class="n">x</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="mi">7</span><span class="p">]</span><span class="o">*</span><span class="n">y</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="mi">8</span><span class="p">]</span><span class="o">*</span><span class="n">z</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">_realToBoxPointArray</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">array</span><span class="p">,</span> <span class="n">parameters</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span>
<span class="k">if</span> <span class="n">parameters</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">matrix</span> <span class="o">=</span> <span class="n">N</span><span class="o">.</span><span class="n">reshape</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="mi">9</span><span class="p">:</span><span class="mi">18</span><span class="p">],</span> <span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="mi">3</span><span class="p">,</span> <span class="mi">3</span><span class="p">))</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">parameters</span> <span class="o">=</span> <span class="n">N</span><span class="o">.</span><span class="n">concatenate</span><span class="p">([</span><span class="n">parameters</span><span class="p">,</span> <span class="n">N</span><span class="o">.</span><span class="n">zeros</span><span class="p">((</span><span class="mi">10</span><span class="p">,),</span> <span class="n">N</span><span class="o">.</span><span class="n">Float</span><span class="p">)])</span>
<span class="kn">from</span> <span class="nn">MMTK_universe</span> <span class="kn">import</span> <span class="n">parallelepiped_invert</span>
<span class="n">parallelepiped_invert</span><span class="p">(</span><span class="n">parameters</span><span class="p">)</span>
<span class="n">matrix</span> <span class="o">=</span> <span class="n">N</span><span class="o">.</span><span class="n">reshape</span><span class="p">(</span><span class="n">parameters</span><span class="p">[</span><span class="mi">9</span><span class="p">:</span><span class="mi">18</span><span class="p">],</span> <span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="mi">3</span><span class="p">,</span> <span class="mi">3</span><span class="p">))</span>
<span class="k">return</span> <span class="n">N</span><span class="o">.</span><span class="n">add</span><span class="o">.</span><span class="n">reduce</span><span class="p">(</span><span class="n">matrix</span><span class="o">*</span><span class="n">array</span><span class="p">[:,</span> <span class="n">N</span><span class="o">.</span><span class="n">NewAxis</span><span class="p">,</span> <span class="p">:],</span> <span class="n">axis</span><span class="o">=-</span><span class="mi">1</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">_boxToRealPointArray</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">array</span><span class="p">,</span> <span class="n">parameters</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span>
<span class="k">if</span> <span class="n">parameters</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">parameters</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[:</span><span class="mi">9</span><span class="p">]</span>
<span class="n">matrix</span> <span class="o">=</span> <span class="n">N</span><span class="o">.</span><span class="n">reshape</span><span class="p">(</span><span class="n">parameters</span><span class="p">,</span> <span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="mi">3</span><span class="p">,</span> <span class="mi">3</span><span class="p">))</span>
<span class="k">return</span> <span class="n">N</span><span class="o">.</span><span class="n">add</span><span class="o">.</span><span class="n">reduce</span><span class="p">(</span><span class="n">matrix</span><span class="o">*</span><span class="n">array</span><span class="p">[:,</span> <span class="n">N</span><span class="o">.</span><span class="n">NewAxis</span><span class="p">,</span> <span class="p">:],</span> <span class="n">axis</span><span class="o">=-</span><span class="mi">1</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">CdistanceFunction</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="kn">from</span> <span class="nn">MMTK_universe</span> <span class="kn">import</span> <span class="n">parallelepipedic_universe_distance_function</span>
<span class="k">return</span> <span class="n">parallelepipedic_universe_distance_function</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span>
<span class="k">def</span> <span class="nf">CcorrectionFunction</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="kn">from</span> <span class="nn">MMTK_universe</span> <span class="kn">import</span> <span class="n">parallelepipedic_universe_correction_function</span>
<span class="k">return</span> <span class="n">parallelepipedic_universe_correction_function</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span>
<span class="k">def</span> <span class="nf">CvolumeFunction</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="kn">from</span> <span class="nn">MMTK_universe</span> <span class="kn">import</span> <span class="n">parallelepipedic_universe_volume_function</span>
<span class="k">return</span> <span class="n">parallelepipedic_universe_volume_function</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span>
<span class="k">def</span> <span class="nf">CboxTransformationFunction</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="kn">from</span> <span class="nn">MMTK_universe</span> <span class="kn">import</span> <span class="n">parallelepipedic_universe_box_transformation</span>
<span class="k">return</span> <span class="n">parallelepipedic_universe_box_transformation</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span>
<span class="k">def</span> <span class="nf">cellParameters</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[:</span><span class="mi">9</span><span class="p">]</span>
<span class="k">def</span> <span class="nf">reciprocalBasisVectors</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</span> <span class="p">[</span><span class="n">Vector</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="mi">9</span><span class="p">:</span><span class="mi">12</span><span class="p">]),</span>
<span class="n">Vector</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="mi">12</span><span class="p">:</span><span class="mi">15</span><span class="p">]),</span>
<span class="n">Vector</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="mi">15</span><span class="p">:</span><span class="mi">18</span><span class="p">])]</span>
<span class="k">def</span> <span class="nf">cellVolume</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</span> <span class="nb">abs</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="mi">18</span><span class="p">])</span>
<span class="k">def</span> <span class="nf">largestDistance</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</span> <span class="nb">min</span><span class="p">([</span><span class="mf">0.5</span><span class="o">/</span><span class="n">v</span><span class="o">.</span><span class="n">length</span><span class="p">()</span> <span class="k">for</span> <span class="n">v</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">reciprocalBasisVectors</span><span class="p">()])</span>
<span class="k">def</span> <span class="nf">_createSpec</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="kn">from</span> <span class="nn">MMTK_universe</span> <span class="kn">import</span> <span class="n">ParallelepipedicPeriodicUniverseSpec</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_spec</span> <span class="o">=</span> <span class="n">ParallelepipedicPeriodicUniverseSpec</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">_descriptionArguments</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_forcefield</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="k">return</span> <span class="s">'((Vector(0.,0.,0.),Vector(0.,0.,0.),Vector(0.,0.,0.)))'</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">return</span> <span class="s">'((Vector(0.,0.,0.),Vector(0.,0.,0.),Vector(0.,0.,0.)),</span><span class="si">%s</span><span class="s">)'</span>\
<span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">_forcefield</span><span class="o">.</span><span class="n">description</span><span class="p">()</span>
<span class="k">def</span> <span class="nf">XMLSpec</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</span> <span class="s">'topology="periodic3d" '</span> <span class="o">+</span> \
<span class="s">'cellshape="parallelepipedic" '</span> <span class="o">+</span> \
<span class="p">(</span><span class="s">'cellshape="</span><span class="si">%f</span><span class="s"> </span><span class="si">%f</span><span class="s"> </span><span class="si">%f</span><span class="s"> </span><span class="si">%f</span><span class="s"> </span><span class="si">%f</span><span class="s"> </span><span class="si">%f</span><span class="s"> </span><span class="si">%f</span><span class="s"> </span><span class="si">%f</span><span class="s"> </span><span class="si">%f</span><span class="s">" '</span>
<span class="o">%</span> <span class="nb">tuple</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[:</span><span class="mi">9</span><span class="p">]))</span> <span class="o">+</span> \
<span class="s">'units="units:nm"'</span>
<span class="c">#</span>
<span class="c"># Recognition functions</span>
<span class="c">#</span></div>
<div class="viewcode-block" id="isUniverse"><a class="viewcode-back" href="../../modules.html#MMTK.Universe.isUniverse">[docs]</a><span class="k">def</span> <span class="nf">isUniverse</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :param object: any Python object</span>
<span class="sd"> :returns: True if object is a universe.</span>
<span class="sd"> """</span>
<span class="k">return</span> <span class="nb">isinstance</span><span class="p">(</span><span class="nb">object</span><span class="p">,</span> <span class="n">Universe</span><span class="p">)</span></div>
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