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<h1>Source code for MMTK.Trajectory</h1><div class="highlight"><pre>
<span class="c"># This module implements trajetories and trajectory generators.</span>
<span class="c">#</span>
<span class="c"># Written by Konrad Hinsen</span>
<span class="c">#</span>
<span class="sd">"""</span>
<span class="sd">Trajectory files and their contents</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">Collections</span><span class="p">,</span> <span class="n">Units</span><span class="p">,</span> <span class="n">Universe</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">Vector</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="o">,</span> <span class="nn">os</span><span class="o">,</span> <span class="nn">sys</span>
<span class="c"># Report error if the netCDF module is not available.</span>
<span class="k">try</span><span class="p">:</span>
<span class="kn">from</span> <span class="nn">Scientific.IO</span> <span class="kn">import</span> <span class="n">NetCDF</span>
<span class="k">except</span> <span class="ne">ImportError</span><span class="p">:</span>
<span class="k">raise</span> <span class="n">Utility</span><span class="o">.</span><span class="n">MMTKError</span><span class="p">(</span><span class="s">"Trajectories are not available "</span> <span class="o">+</span>
<span class="s">"because the netCDF module is missing."</span><span class="p">)</span>
<span class="c">#</span>
<span class="c"># Trajectory class</span>
<span class="c">#</span>
<div class="viewcode-block" id="Trajectory"><a class="viewcode-back" href="../../modules.html#MMTK.Trajectory.Trajectory">[docs]</a><span class="k">class</span> <span class="nc">Trajectory</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
<span class="c">#</span>
<span class="c"># Trajectory cache</span>
<span class="c">#</span>
<span class="c"># This cache is maintained for better efficiency in parallel</span>
<span class="c"># processing. The cache contains all trajectories currently open</span>
<span class="c"># for reading. When a trajectory object is unpickled, a trajectory</span>
<span class="c"># from the cache is reused if possible. This means that </span>
<span class="sd">"""</span>
<span class="sd"> Trajectory file</span>
<span class="sd"> The data in a trajectory file can be accessed by step or by</span>
<span class="sd"> variable. If t is a Trajectory object, then:</span>
<span class="sd"> * len(t) is the number of steps</span>
<span class="sd"> * t[i] is the data for step i, in the form of a dictionary that</span>
<span class="sd"> maps variable names to data</span>
<span class="sd"> * t[i:j] and t[i:j:n] return a :class:`~MMTK.Trajectory.SubTrajectory` </span>
<span class="sd"> object that refers to a subset of the total number of steps </span>
<span class="sd"> (no data is copied)</span>
<span class="sd"> * t.variable returns the value of the named variable at all</span>
<span class="sd"> time steps. If the variable is a simple scalar, it is read</span>
<span class="sd"> completely and returned as an array. If the variable contains</span>
<span class="sd"> data for each atom, a :class:`~MMTK.Trajectory.TrajectoryVariable` </span>
<span class="sd"> object is returned from which data at specific steps can be obtained </span>
<span class="sd"> by further indexing operations.</span>
<span class="sd"> The routines that generate trajectories decide what variables</span>
<span class="sd"> are used and what they contain. The most frequently used variable</span>
<span class="sd"> is "configuration", which stores the positions of all atoms.</span>
<span class="sd"> Other common variables are "time", "velocities", "temperature",</span>
<span class="sd"> "pressure", and various energy terms whose name end with "_energy".</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="nb">object</span><span class="p">,</span> <span class="n">filename</span><span class="p">,</span> <span class="n">mode</span> <span class="o">=</span> <span class="s">'r'</span><span class="p">,</span> <span class="n">comment</span> <span class="o">=</span> <span class="bp">None</span><span class="p">,</span>
<span class="n">double_precision</span> <span class="o">=</span> <span class="bp">False</span><span class="p">,</span> <span class="n">cycle</span> <span class="o">=</span> <span class="mi">0</span><span class="p">,</span> <span class="n">block_size</span> <span class="o">=</span> <span class="mi">1</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :param object: the object whose data is stored in the trajectory file.</span>
<span class="sd"> This can be 'None' when opening a file for reading;</span>
<span class="sd"> in that case, a universe object is constructed from the</span>
<span class="sd"> description stored in the trajectory file. This universe</span>
<span class="sd"> object can be accessed via the attribute 'universe'</span>
<span class="sd"> of the trajectory object.</span>
<span class="sd"> :type object: :class:`~MMTK.ChemicalObjects.ChemicalObject`</span>
<span class="sd"> :param filename: the name of the trajectory file</span>
<span class="sd"> :type filename: str</span>
<span class="sd"> :param mode: one of "r" (read-only), "w" (create new file for writing),</span>
<span class="sd"> or "a" (append to existing file or create if the file does</span>
<span class="sd"> not exist)</span>
<span class="sd"> :type mode: str</span>
<span class="sd"> :param comment: optional comment that is stored in the file;</span>
<span class="sd"> allowed only with mode="r"</span>
<span class="sd"> :type comment: str</span>
<span class="sd"> :param double_precision: if True, data in the file is stored using</span>
<span class="sd"> double precision; default is single precision.</span>
<span class="sd"> Note that all I/O via trajectory objects is</span>
<span class="sd"> double precision; conversion from and to</span>
<span class="sd"> single precision file variables is handled</span>
<span class="sd"> automatically.</span>
<span class="sd"> :type double_precision: bool</span>
<span class="sd"> :param cycle: if non-zero, a trajectory is created for a fixed number</span>
<span class="sd"> of steps equal to the value of cycle, and these steps</span>
<span class="sd"> are used cyclically. This is meant for restart</span>
<span class="sd"> trajectories.</span>
<span class="sd"> :type cycle: int</span>
<span class="sd"> :param block_size: an optimization parameter that influences the file</span>
<span class="sd"> structure and the I/O performance for very large</span>
<span class="sd"> files. A block size of 1 is optimal for sequential</span>
<span class="sd"> access to configurations etc., whereas a block size</span>
<span class="sd"> equal to the number of steps is optimal for reading</span>
<span class="sd"> coordinates or scalar variables along the time axis.</span>
<span class="sd"> The default value is 1. Note that older MMTK releases</span>
<span class="sd"> always used a block size of 1 and cannot handle</span>
<span class="sd"> trajectories with different block sizes.</span>
<span class="sd"> :type block_size: int</span>
<span class="sd"> """</span>
<span class="n">filename</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">expanduser</span><span class="p">(</span><span class="n">filename</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">filename</span> <span class="o">=</span> <span class="n">filename</span>
<span class="bp">self</span><span class="o">.</span><span class="n">mode</span> <span class="o">=</span> <span class="n">mode</span>
<span class="k">if</span> <span class="nb">object</span> <span class="ow">is</span> <span class="bp">None</span> <span class="ow">and</span> <span class="n">mode</span> <span class="o">==</span> <span class="s">'r'</span><span class="p">:</span>
<span class="nb">file</span> <span class="o">=</span> <span class="n">NetCDF</span><span class="o">.</span><span class="n">NetCDFFile</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="s">'r'</span><span class="p">)</span>
<span class="n">description</span> <span class="o">=</span> <span class="nb">file</span><span class="o">.</span><span class="n">variables</span><span class="p">[</span><span class="s">'description'</span><span class="p">][:]</span><span class="o">.</span><span class="n">tostring</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">block_size</span> <span class="o">=</span> <span class="nb">file</span><span class="o">.</span><span class="n">dimensions</span><span class="p">[</span><span class="s">'minor_step_number'</span><span class="p">]</span>
<span class="k">except</span> <span class="ne">KeyError</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">block_size</span> <span class="o">=</span> <span class="mi">1</span>
<span class="n">conf</span> <span class="o">=</span> <span class="bp">None</span>
<span class="n">cell</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">block_size</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
<span class="k">try</span><span class="p">:</span>
<span class="n">conf_var</span> <span class="o">=</span> <span class="nb">file</span><span class="o">.</span><span class="n">variables</span><span class="p">[</span><span class="s">'configuration'</span><span class="p">]</span>
<span class="n">conf</span> <span class="o">=</span> <span class="n">conf_var</span><span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="p">:,</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">try</span><span class="p">:</span>
<span class="n">cell</span> <span class="o">=</span> <span class="nb">file</span><span class="o">.</span><span class="n">variables</span><span class="p">[</span><span class="s">'box_size'</span><span class="p">][</span><span class="mi">0</span><span class="p">,</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">conf_var</span> <span class="o">=</span> <span class="nb">file</span><span class="o">.</span><span class="n">variables</span><span class="p">[</span><span class="s">'configuration'</span><span class="p">]</span>
<span class="n">conf</span> <span class="o">=</span> <span class="n">conf_var</span><span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="p">:,</span> <span class="p">:,</span> <span class="mi">0</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">try</span><span class="p">:</span>
<span class="n">cell</span> <span class="o">=</span> <span class="nb">file</span><span class="o">.</span><span class="n">variables</span><span class="p">[</span><span class="s">'box_size'</span><span class="p">][</span><span class="mi">0</span><span class="p">,</span> <span class="p">:,</span> <span class="mi">0</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="nb">file</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
<span class="kn">import</span> <span class="nn">Skeleton</span>
<span class="n">local</span> <span class="o">=</span> <span class="p">{}</span>
<span class="n">skeleton</span> <span class="o">=</span> <span class="nb">eval</span><span class="p">(</span><span class="n">description</span><span class="p">,</span> <span class="nb">vars</span><span class="p">(</span><span class="n">Skeleton</span><span class="p">),</span> <span class="n">local</span><span class="p">)</span>
<span class="n">universe</span> <span class="o">=</span> <span class="n">skeleton</span><span class="o">.</span><span class="n">make</span><span class="p">({},</span> <span class="n">conf</span><span class="p">)</span>
<span class="n">universe</span><span class="o">.</span><span class="n">setCellParameters</span><span class="p">(</span><span class="n">cell</span><span class="p">)</span>
<span class="nb">object</span> <span class="o">=</span> <span class="n">universe</span>
<span class="n">initialize</span> <span class="o">=</span> <span class="mi">1</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">universe</span> <span class="o">=</span> <span class="nb">object</span><span class="o">.</span><span class="n">universe</span><span class="p">()</span>
<span class="k">if</span> <span class="n">universe</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">"objects not in the same universe"</span><span class="p">)</span>
<span class="n">description</span> <span class="o">=</span> <span class="bp">None</span>
<span class="n">initialize</span> <span class="o">=</span> <span class="mi">0</span>
<span class="n">universe</span><span class="o">.</span><span class="n">configuration</span><span class="p">()</span>
<span class="k">if</span> <span class="nb">object</span> <span class="ow">is</span> <span class="n">universe</span><span class="p">:</span>
<span class="n">index_map</span> <span class="o">=</span> <span class="bp">None</span>
<span class="n">inverse_map</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="n">mode</span> <span class="o">==</span> <span class="s">'r'</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s">"can't read trajectory for a non-universe"</span><span class="p">)</span>
<span class="n">index_map</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">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="nb">object</span><span class="o">.</span><span class="n">atomList</span><span class="p">()])</span>
<span class="n">inverse_map</span> <span class="o">=</span> <span class="n">universe</span><span class="o">.</span><span class="n">numberOfPoints</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">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">index_map</span><span class="p">)):</span>
<span class="n">inverse_map</span><span class="p">[</span><span class="n">index_map</span><span class="p">[</span><span class="n">i</span><span class="p">]]</span> <span class="o">=</span> <span class="n">i</span>
<span class="n">toplevel</span> <span class="o">=</span> <span class="nb">set</span><span class="p">()</span>
<span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">Collections</span><span class="o">.</span><span class="n">Collection</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
<span class="n">toplevel</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">o</span><span class="o">.</span><span class="n">topLevelChemicalObject</span><span class="p">())</span>
<span class="nb">object</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="nb">list</span><span class="p">(</span><span class="n">toplevel</span><span class="p">))</span>
<span class="k">if</span> <span class="n">description</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">description</span> <span class="o">=</span> <span class="n">universe</span><span class="o">.</span><span class="n">description</span><span class="p">(</span><span class="nb">object</span><span class="p">,</span> <span class="n">inverse_map</span><span class="p">)</span>
<span class="kn">import</span> <span class="nn">MMTK_trajectory</span>
<span class="bp">self</span><span class="o">.</span><span class="n">trajectory</span> <span class="o">=</span> <span class="n">MMTK_trajectory</span><span class="o">.</span><span class="n">Trajectory</span><span class="p">(</span><span class="n">universe</span><span class="p">,</span> <span class="n">description</span><span class="p">,</span>
<span class="n">index_map</span><span class="p">,</span> <span class="n">filename</span><span class="p">,</span>
<span class="n">mode</span> <span class="o">+</span> <span class="s">'s'</span><span class="p">,</span>
<span class="n">double_precision</span><span class="p">,</span> <span class="n">cycle</span><span class="p">,</span>
<span class="n">block_size</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">universe</span> <span class="o">=</span> <span class="n">universe</span>
<span class="bp">self</span><span class="o">.</span><span class="n">index_map</span> <span class="o">=</span> <span class="n">index_map</span>
<span class="k">try</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">block_size</span> <span class="o">=</span> \
<span class="bp">self</span><span class="o">.</span><span class="n">trajectory</span><span class="o">.</span><span class="n">file</span><span class="o">.</span><span class="n">dimensions</span><span class="p">[</span><span class="s">'minor_step_number'</span><span class="p">]</span>
<span class="k">except</span> <span class="ne">KeyError</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">block_size</span> <span class="o">=</span> <span class="mi">1</span>
<span class="k">if</span> <span class="n">comment</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">mode</span> <span class="o">==</span> <span class="s">'r'</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">IOError</span><span class="p">(</span><span class="s">'cannot add comment in read-only mode'</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">trajectory</span><span class="o">.</span><span class="n">file</span><span class="o">.</span><span class="n">comment</span> <span class="o">=</span> <span class="n">comment</span>
<span class="k">if</span> <span class="n">initialize</span> <span class="ow">and</span> <span class="n">conf</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">universe</span><span class="o">.</span><span class="n">setFromTrajectory</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">particle_trajectory_reader</span> <span class="o">=</span> <span class="n">ParticleTrajectoryReader</span><span class="p">(</span><span class="bp">self</span><span class="p">)</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="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">mode</span> <span class="o">!=</span> <span class="s">'r'</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s">"Cannot copy or pickle write-mode trajectories"</span><span class="p">)</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">filename</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="bp">self</span><span class="o">.</span><span class="n">__init__</span><span class="p">(</span><span class="bp">None</span><span class="p">,</span> <span class="n">state</span><span class="p">)</span>
<div class="viewcode-block" id="Trajectory.flush"><a class="viewcode-back" href="../../modules.html#MMTK.Trajectory.Trajectory.flush">[docs]</a> <span class="k">def</span> <span class="nf">flush</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Make sure that all data that has been written to the trajectory</span>
<span class="sd"> is also written to the file.</span>
<span class="sd"> """</span>
<span class="bp">self</span><span class="o">.</span><span class="n">trajectory</span><span class="o">.</span><span class="n">flush</span><span class="p">()</span>
</div>
<div class="viewcode-block" id="Trajectory.close"><a class="viewcode-back" href="../../modules.html#MMTK.Trajectory.Trajectory.close">[docs]</a> <span class="k">def</span> <span class="nf">close</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Close the trajectory file. Must be called after writing to</span>
<span class="sd"> ensure that all buffered data is written to the file. No data</span>
<span class="sd"> access is possible after closing a file.</span>
<span class="sd"> """</span>
<span class="bp">self</span><span class="o">.</span><span class="n">trajectory</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
</div>
<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="bp">self</span><span class="o">.</span><span class="n">trajectory</span><span class="o">.</span><span class="n">nsteps</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">if</span> <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">item</span><span class="p">,</span> <span class="nb">int</span><span class="p">):</span>
<span class="k">return</span> <span class="n">SubTrajectory</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">N</span><span class="o">.</span><span class="n">arange</span><span class="p">(</span><span class="nb">len</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">if</span> <span class="n">item</span> <span class="o"><</span> <span class="mi">0</span><span class="p">:</span>
<span class="n">item</span> <span class="o">+=</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
<span class="k">if</span> <span class="n">item</span> <span class="o">>=</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">raise</span> <span class="ne">IndexError</span>
<span class="n">data</span> <span class="o">=</span> <span class="p">{}</span>
<span class="k">for</span> <span class="n">name</span><span class="p">,</span> <span class="n">var</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">trajectory</span><span class="o">.</span><span class="n">file</span><span class="o">.</span><span class="n">variables</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
<span class="k">if</span> <span class="s">'step_number'</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">var</span><span class="o">.</span><span class="n">dimensions</span><span class="p">:</span>
<span class="k">continue</span>
<span class="k">if</span> <span class="s">'atom_number'</span> <span class="ow">in</span> <span class="n">var</span><span class="o">.</span><span class="n">dimensions</span><span class="p">:</span>
<span class="k">if</span> <span class="s">'xyz'</span> <span class="ow">in</span> <span class="n">var</span><span class="o">.</span><span class="n">dimensions</span><span class="p">:</span>
<span class="n">array</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="o">.</span><span class="n">universe</span><span class="p">,</span>
<span class="bp">self</span><span class="o">.</span><span class="n">trajectory</span><span class="o">.</span><span class="n">readParticleVector</span><span class="p">(</span><span class="n">name</span><span class="p">,</span> <span class="n">item</span><span class="p">))</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">array</span> <span class="o">=</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="o">.</span><span class="n">universe</span><span class="p">,</span>
<span class="bp">self</span><span class="o">.</span><span class="n">trajectory</span><span class="o">.</span><span class="n">readParticleScalar</span><span class="p">(</span><span class="n">name</span><span class="p">,</span> <span class="n">item</span><span class="p">))</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">bs</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">block_size</span>
<span class="k">if</span> <span class="n">bs</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
<span class="n">array</span> <span class="o">=</span> <span class="n">var</span><span class="p">[</span><span class="n">item</span><span class="p">]</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">var</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="n">array</span> <span class="o">=</span> <span class="n">var</span><span class="p">[</span><span class="n">item</span><span class="o">/</span><span class="n">bs</span><span class="p">,</span> <span class="n">item</span><span class="o">%</span><span class="n">bs</span><span class="p">]</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">array</span> <span class="o">=</span> <span class="n">var</span><span class="p">[</span><span class="n">item</span><span class="o">/</span><span class="n">bs</span><span class="p">,</span> <span class="o">...</span><span class="p">,</span> <span class="n">item</span><span class="o">%</span><span class="n">bs</span><span class="p">]</span>
<span class="n">data</span><span class="p">[</span><span class="n">name</span><span class="p">]</span> <span class="o">=</span> <span class="mf">0.</span><span class="o">+</span><span class="n">array</span>
<span class="k">if</span> <span class="n">data</span><span class="o">.</span><span class="n">has_key</span><span class="p">(</span><span class="s">'configuration'</span><span class="p">):</span>
<span class="n">box</span> <span class="o">=</span> <span class="n">data</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s">'box_size'</span><span class="p">,</span> <span class="bp">None</span><span class="p">)</span>
<span class="k">if</span> <span class="n">box</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">box</span> <span class="o">=</span> <span class="n">box</span><span class="o">.</span><span class="n">astype</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">conf</span> <span class="o">=</span> <span class="n">data</span><span class="p">[</span><span class="s">'configuration'</span><span class="p">]</span>
<span class="n">data</span><span class="p">[</span><span class="s">'configuration'</span><span class="p">]</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="n">conf</span><span class="o">.</span><span class="n">universe</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">box</span><span class="p">)</span>
<span class="k">return</span> <span class="n">data</span>
<span class="k">def</span> <span class="nf">__getslice__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">first</span><span class="p">,</span> <span class="n">last</span><span class="p">):</span>
<span class="k">return</span> <span class="bp">self</span><span class="p">[(</span><span class="nb">slice</span><span class="p">(</span><span class="n">first</span><span class="p">,</span> <span class="n">last</span><span class="p">),)]</span>
<span class="k">def</span> <span class="nf">__getattr__</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="k">try</span><span class="p">:</span>
<span class="n">var</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">trajectory</span><span class="o">.</span><span class="n">file</span><span class="o">.</span><span class="n">variables</span><span class="p">[</span><span class="n">name</span><span class="p">]</span>
<span class="k">except</span> <span class="ne">KeyError</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">AttributeError</span><span class="p">(</span><span class="s">"no variable named "</span> <span class="o">+</span> <span class="n">name</span><span class="p">)</span>
<span class="k">if</span> <span class="s">'atom_number'</span> <span class="ow">in</span> <span class="n">var</span><span class="o">.</span><span class="n">dimensions</span><span class="p">:</span>
<span class="k">return</span> <span class="n">TrajectoryVariable</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">universe</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="k">elif</span> <span class="s">'box_size_length'</span> <span class="ow">in</span> <span class="n">var</span><span class="o">.</span><span class="n">dimensions</span><span class="p">:</span>
<span class="k">if</span> <span class="s">'minor_step_number'</span> <span class="ow">in</span> <span class="n">var</span><span class="o">.</span><span class="n">dimensions</span><span class="p">:</span>
<span class="n">bs</span> <span class="o">=</span> <span class="n">N</span><span class="o">.</span><span class="n">transpose</span><span class="p">(</span><span class="n">var</span><span class="p">[:],</span> <span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">2</span><span class="p">,</span> <span class="mi">1</span><span class="p">])</span>
<span class="n">bs</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">bs</span><span class="p">,</span> <span class="p">(</span><span class="n">bs</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">*</span><span class="n">bs</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="n">bs</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">2</span><span class="p">]))</span>
<span class="k">return</span> <span class="n">bs</span><span class="p">[:</span><span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="p">)]</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">return</span> <span class="n">var</span><span class="p">[:]</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">return</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">array</span><span class="p">(</span><span class="n">var</span><span class="p">))[:</span><span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="p">)]</span>
<span class="k">def</span> <span class="nf">defaultStep</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">try</span><span class="p">:</span>
<span class="n">step</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">trajectory</span><span class="o">.</span><span class="n">file</span><span class="o">.</span><span class="n">last_step</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
<span class="k">except</span> <span class="ne">AttributeError</span><span class="p">:</span>
<span class="n">step</span> <span class="o">=</span> <span class="mi">0</span>
<span class="k">return</span> <span class="n">step</span>
<div class="viewcode-block" id="Trajectory.readParticleTrajectory"><a class="viewcode-back" href="../../modules.html#MMTK.Trajectory.Trajectory.readParticleTrajectory">[docs]</a> <span class="k">def</span> <span class="nf">readParticleTrajectory</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="n">first</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="n">last</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">skip</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span>
<span class="n">variable</span> <span class="o">=</span> <span class="s">"configuration"</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Read trajectory information for a single atom but for multiple</span>
<span class="sd"> time steps.</span>
<span class="sd"> :param atom: the atom whose trajectory is requested</span>
<span class="sd"> :type atom: :class:`~MMTK.ChemicalObjects.Atom`</span>
<span class="sd"> :param first: the number of the first step to be read</span>
<span class="sd"> :type first: int</span>
<span class="sd"> :param last: the number of the first step not to be read.</span>
<span class="sd"> A value of None indicates that the</span>
<span class="sd"> whole trajectory should be read.</span>
<span class="sd"> :type last: int</span>
<span class="sd"> :param skip: the number of steps to skip between two steps read</span>
<span class="sd"> :type skip: int</span>
<span class="sd"> :param variable: the name of the trajectory variable to be read.</span>
<span class="sd"> If the variable is "configuration", the resulting</span>
<span class="sd"> trajectory is made continuous by eliminating all</span>
<span class="sd"> jumps caused by periodic boundary conditions.</span>
<span class="sd"> The pseudo-variable "box_coordinates" can be read</span>
<span class="sd"> to obtain the values of the variable "configuration"</span>
<span class="sd"> scaled to box coordinates. For non-periodic universes</span>
<span class="sd"> there is no difference between box coordinates</span>
<span class="sd"> and real coordinates.</span>
<span class="sd"> :type variable: str</span>
<span class="sd"> :returns: the trajectory for a single atom</span>
<span class="sd"> :rtype: :class:`~MMTK.Trajectory.ParticleTrajectory`</span>
<span class="sd"> """</span>
<span class="k">return</span> <span class="n">ParticleTrajectory</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="n">first</span><span class="p">,</span> <span class="n">last</span><span class="p">,</span> <span class="n">skip</span><span class="p">,</span> <span class="n">variable</span><span class="p">)</span>
</div>
<div class="viewcode-block" id="Trajectory.readRigidBodyTrajectory"><a class="viewcode-back" href="../../modules.html#MMTK.Trajectory.Trajectory.readRigidBodyTrajectory">[docs]</a> <span class="k">def</span> <span class="nf">readRigidBodyTrajectory</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">first</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="n">last</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">skip</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span>
<span class="n">reference</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Read the positions for an object at multiple time steps</span>
<span class="sd"> and extract the rigid-body motion (center-of-mass position plus</span>
<span class="sd"> orientation as a quaternion) by an optimal-transformation fit.</span>
<span class="sd"> :param object: the object whose rigid-body trajectory is requested</span>
<span class="sd"> :type object: :class:`~MMTK.Collections.GroupOfAtoms`</span>
<span class="sd"> :param first: the number of the first step to be read</span>
<span class="sd"> :type first: int</span>
<span class="sd"> :param last: the number of the first step not to be read.</span>
<span class="sd"> A value of None indicates that the</span>
<span class="sd"> whole trajectory should be read.</span>
<span class="sd"> :type last: int</span>
<span class="sd"> :param skip: the number of steps to skip between two steps read</span>
<span class="sd"> :type skip: int</span>
<span class="sd"> :param reference: the reference configuration for the fit</span>
<span class="sd"> :type reference: :class:`~MMTK.ParticleProperties.Configuration`</span>
<span class="sd"> :returns: the trajectory for a single rigid body</span>
<span class="sd"> :rtype: :class:`~MMTK.Trajectory.RigidBodyTrajectory`</span>
<span class="sd"> """</span>
<span class="k">return</span> <span class="n">RigidBodyTrajectory</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">first</span><span class="p">,</span> <span class="n">last</span><span class="p">,</span> <span class="n">skip</span><span class="p">,</span> <span class="n">reference</span><span class="p">)</span>
</div>
<div class="viewcode-block" id="Trajectory.variables"><a class="viewcode-back" href="../../modules.html#MMTK.Trajectory.Trajectory.variables">[docs]</a> <span class="k">def</span> <span class="nf">variables</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 the names of all variables that are stored</span>
<span class="sd"> in the trajectory</span>
<span class="sd"> :rtype: list of str</span>
<span class="sd"> """</span>
<span class="nb">vars</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">trajectory</span><span class="o">.</span><span class="n">file</span><span class="o">.</span><span class="n">variables</span><span class="o">.</span><span class="n">keys</span><span class="p">())</span>
<span class="nb">vars</span><span class="o">.</span><span class="n">remove</span><span class="p">(</span><span class="s">'step'</span><span class="p">)</span>
<span class="k">try</span><span class="p">:</span>
<span class="nb">vars</span><span class="o">.</span><span class="n">remove</span><span class="p">(</span><span class="s">'description'</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">return</span> <span class="nb">vars</span>
</div>
<div class="viewcode-block" id="Trajectory.view"><a class="viewcode-back" href="../../modules.html#MMTK.Trajectory.Trajectory.view">[docs]</a> <span class="k">def</span> <span class="nf">view</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">first</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="n">last</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">skip</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="nb">object</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Show an animation of the trajectory using an external visualization</span>
<span class="sd"> program.</span>
<span class="sd"> :param first: the number of the first step in the animation</span>
<span class="sd"> :type first: int</span>
<span class="sd"> :param last: the number of the first step not to include in the</span>
<span class="sd"> animation. A value of None indicates that the</span>
<span class="sd"> whole trajectory should be used.</span>
<span class="sd"> :type last: int</span>
<span class="sd"> :param skip: the number of steps to skip between two steps read</span>
<span class="sd"> :type skip: int</span>
<span class="sd"> :param object: the object to be animated, which must be in the</span>
<span class="sd"> universe stored in the trajectory. None</span>
<span class="sd"> stands for the whole universe.</span>
<span class="sd"> :type object: :class:`~MMTK.Collections.GroupOfAtoms`</span>
<span class="sd"> """</span>
<span class="n">Visualization</span><span class="o">.</span><span class="n">viewTrajectory</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">first</span><span class="p">,</span> <span class="n">last</span><span class="p">,</span> <span class="n">skip</span><span class="p">,</span> <span class="nb">object</span><span class="p">)</span>
</div>
<span class="k">def</span> <span class="nf">_boxTransformation</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">pt_in</span><span class="p">,</span> <span class="n">pt_out</span><span class="p">,</span> <span class="n">to_box</span><span class="o">=</span><span class="mi">0</span><span class="p">):</span>
<span class="kn">from</span> <span class="nn">MMTK_trajectory</span> <span class="kn">import</span> <span class="n">boxTransformation</span>
<span class="k">try</span><span class="p">:</span>
<span class="n">box_size</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">trajectory</span><span class="o">.</span><span class="n">recently_read_box_size</span>
<span class="k">except</span> <span class="ne">AttributeError</span><span class="p">:</span>
<span class="k">return</span>
<span class="n">boxTransformation</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">universe</span><span class="o">.</span><span class="n">_spec</span><span class="p">,</span>
<span class="n">pt_in</span><span class="p">,</span> <span class="n">pt_out</span><span class="p">,</span> <span class="n">box_size</span><span class="p">,</span> <span class="n">to_box</span><span class="p">)</span>
</div>
<div class="viewcode-block" id="SubTrajectory"><a class="viewcode-back" href="../../modules.html#MMTK.Trajectory.SubTrajectory">[docs]</a><span class="k">class</span> <span class="nc">SubTrajectory</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Reference to a subset of a trajectory</span>
<span class="sd"> A SubTrajectory object is created by slicing a Trajectory object</span>
<span class="sd"> or another SubTrajectory object. It provides all the operations</span>
<span class="sd"> defined on Trajectory objects.</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">trajectory</span><span class="p">,</span> <span class="n">indices</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">trajectory</span> <span class="o">=</span> <span class="n">trajectory</span>
<span class="bp">self</span><span class="o">.</span><span class="n">indices</span> <span class="o">=</span> <span class="n">indices</span>
<span class="bp">self</span><span class="o">.</span><span class="n">universe</span> <span class="o">=</span> <span class="n">trajectory</span><span class="o">.</span><span class="n">universe</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">indices</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">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">item</span><span class="p">,</span> <span class="nb">int</span><span class="p">):</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">trajectory</span><span class="p">[</span><span class="nb">int</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">indices</span><span class="p">[</span><span class="n">item</span><span class="p">])]</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">return</span> <span class="n">SubTrajectory</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">trajectory</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">indices</span><span class="p">[</span><span class="n">item</span><span class="p">])</span>
<span class="k">def</span> <span class="nf">__getslice__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">first</span><span class="p">,</span> <span class="n">last</span><span class="p">):</span>
<span class="k">return</span> <span class="bp">self</span><span class="p">[(</span><span class="nb">slice</span><span class="p">(</span><span class="n">first</span><span class="p">,</span> <span class="n">last</span><span class="p">),)]</span>
<span class="k">def</span> <span class="nf">__getattr__</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="k">return</span> <span class="n">SubVariable</span><span class="p">(</span><span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">trajectory</span><span class="p">,</span> <span class="n">name</span><span class="p">),</span> <span class="bp">self</span><span class="o">.</span><span class="n">indices</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">readParticleTrajectory</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="n">first</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="n">last</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">skip</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span>
<span class="n">variable</span> <span class="o">=</span> <span class="s">"configuration"</span><span class="p">):</span>
<span class="k">if</span> <span class="n">last</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">last</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">indices</span><span class="p">)</span>
<span class="n">indices</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">indices</span><span class="p">[</span><span class="n">first</span><span class="p">:</span><span class="n">last</span><span class="p">:</span><span class="n">skip</span><span class="p">]</span>
<span class="n">first</span> <span class="o">=</span> <span class="n">indices</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
<span class="n">last</span> <span class="o">=</span> <span class="n">indices</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span><span class="o">+</span><span class="mi">1</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">indices</span><span class="p">)</span> <span class="o">></span> <span class="mi">1</span><span class="p">:</span>
<span class="n">skip</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">indices</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">-</span><span class="bp">self</span><span class="o">.</span><span class="n">indices</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">skip</span> <span class="o">=</span> <span class="mi">1</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">trajectory</span><span class="o">.</span><span class="n">readParticleTrajectory</span><span class="p">(</span><span class="n">atom</span><span class="p">,</span> <span class="n">first</span><span class="p">,</span> <span class="n">last</span><span class="p">,</span>
<span class="n">skip</span><span class="p">,</span> <span class="n">variable</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">readRigidBodyTrajectory</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">first</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="n">last</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">skip</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span>
<span class="n">reference</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
<span class="k">if</span> <span class="n">last</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">last</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">indices</span><span class="p">)</span>
<span class="n">indices</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">indices</span><span class="p">[</span><span class="n">first</span><span class="p">:</span><span class="n">last</span><span class="p">:</span><span class="n">skip</span><span class="p">]</span>
<span class="n">first</span> <span class="o">=</span> <span class="n">indices</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
<span class="n">last</span> <span class="o">=</span> <span class="n">indices</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span><span class="o">+</span><span class="mi">1</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">indices</span><span class="p">)</span> <span class="o">></span> <span class="mi">1</span><span class="p">:</span>
<span class="n">skip</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">indices</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">-</span><span class="bp">self</span><span class="o">.</span><span class="n">indices</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">skip</span> <span class="o">=</span> <span class="mi">1</span>
<span class="k">return</span> <span class="n">RigidBodyTrajectory</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">trajectory</span><span class="p">,</span> <span class="nb">object</span><span class="p">,</span>
<span class="n">first</span><span class="p">,</span> <span class="n">last</span><span class="p">,</span> <span class="n">skip</span><span class="p">,</span> <span class="n">reference</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">variables</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">trajectory</span><span class="o">.</span><span class="n">variables</span><span class="p">()</span>
<span class="k">def</span> <span class="nf">view</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">first</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="n">last</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">step</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="n">subset</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
<span class="n">Visualization</span><span class="o">.</span><span class="n">viewTrajectory</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">first</span><span class="p">,</span> <span class="n">last</span><span class="p">,</span> <span class="n">step</span><span class="p">,</span> <span class="n">subset</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">close</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">del</span> <span class="bp">self</span><span class="o">.</span><span class="n">trajectory</span>
<span class="k">def</span> <span class="nf">_boxTransformation</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">pt_in</span><span class="p">,</span> <span class="n">pt_out</span><span class="p">,</span> <span class="n">to_box</span><span class="o">=</span><span class="mi">0</span><span class="p">):</span>
<span class="n">Trajectory</span><span class="o">.</span><span class="n">_boxTransformation</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">trajectory</span><span class="p">,</span> <span class="n">pt_in</span><span class="p">,</span> <span class="n">pt_out</span><span class="p">,</span> <span class="n">to_box</span><span class="p">)</span>
<span class="c">#</span>
<span class="c"># Trajectory variables</span>
<span class="c">#</span></div>
<div class="viewcode-block" id="TrajectoryVariable"><a class="viewcode-back" href="../../modules.html#MMTK.Trajectory.TrajectoryVariable">[docs]</a><span class="k">class</span> <span class="nc">TrajectoryVariable</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Variable in a trajectory</span>
<span class="sd"> A TrajectoryVariable object is created by extracting a variable from</span>
<span class="sd"> a Trajectory object if that variable contains data for each atom and</span>
<span class="sd"> is thus potentially large. No data is read from the trajectory file</span>
<span class="sd"> when a TrajectoryVariable object is created; the read operation</span>
<span class="sd"> takes place when the TrajectoryVariable is indexed with a specific</span>
<span class="sd"> step number.</span>
<span class="sd"> If t is a TrajectoryVariable object, then:</span>
<span class="sd"> * len(t) is the number of steps</span>
<span class="sd"> * t[i] is the data for step i, in the form of a ParticleScalar,</span>
<span class="sd"> a ParticleVector, or a Configuration object, depending on the</span>
<span class="sd"> variable</span>
<span class="sd"> * t[i:j] and t[i:j:n] return a SubVariable object that refers</span>
<span class="sd"> to a subset of the total number of steps</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">universe</span><span class="p">,</span> <span class="n">trajectory</span><span class="p">,</span> <span class="n">name</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">universe</span> <span class="o">=</span> <span class="n">universe</span>
<span class="bp">self</span><span class="o">.</span><span class="n">trajectory</span> <span class="o">=</span> <span class="n">trajectory</span>
<span class="bp">self</span><span class="o">.</span><span class="n">name</span> <span class="o">=</span> <span class="n">name</span>
<span class="bp">self</span><span class="o">.</span><span class="n">var</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">trajectory</span><span class="o">.</span><span class="n">trajectory</span><span class="o">.</span><span class="n">file</span><span class="o">.</span><span class="n">variables</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">]</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span> <span class="o">==</span> <span class="s">'configuration'</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">box_size</span> <span class="o">=</span> \
<span class="bp">self</span><span class="o">.</span><span class="n">trajectory</span><span class="o">.</span><span class="n">trajectory</span><span class="o">.</span><span class="n">file</span><span class="o">.</span><span class="n">variables</span><span class="p">[</span><span class="s">'box_size'</span><span class="p">]</span>
<span class="k">except</span> <span class="ne">KeyError</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">box_size</span> <span class="o">=</span> <span class="bp">None</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">trajectory</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">if</span> <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">item</span><span class="p">,</span> <span class="nb">int</span><span class="p">):</span>
<span class="k">return</span> <span class="n">SubVariable</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">N</span><span class="o">.</span><span class="n">arange</span><span class="p">(</span><span class="nb">len</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="n">item</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">item</span><span class="p">)</span> <span class="c"># gets rid of numpy.intXX objects</span>
<span class="k">if</span> <span class="n">item</span> <span class="o"><</span> <span class="mi">0</span><span class="p">:</span>
<span class="n">item</span> <span class="o">=</span> <span class="n">item</span> <span class="o">+</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">trajectory</span><span class="p">)</span>
<span class="k">if</span> <span class="n">item</span> <span class="o">>=</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">trajectory</span><span class="p">):</span>
<span class="k">raise</span> <span class="ne">IndexError</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span> <span class="o">==</span> <span class="s">'configuration'</span><span class="p">:</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">box_size</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">box</span> <span class="o">=</span> <span class="bp">None</span>
<span class="k">elif</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">box_size</span><span class="o">.</span><span class="n">shape</span><span class="p">)</span> <span class="o">==</span> <span class="mi">3</span><span class="p">:</span>
<span class="n">bs</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">trajectory</span><span class="o">.</span><span class="n">block_size</span>
<span class="n">box</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">box_size</span><span class="p">[</span><span class="n">item</span><span class="o">/</span><span class="n">bs</span><span class="p">,</span> <span class="p">:,</span> <span class="n">item</span><span class="o">%</span><span class="n">bs</span><span class="p">]</span><span class="o">.</span><span class="n">astype</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">else</span><span class="p">:</span>
<span class="n">box</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">box_size</span><span class="p">[</span><span class="n">item</span><span class="p">]</span><span class="o">.</span><span class="n">astype</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">array</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="o">.</span><span class="n">universe</span><span class="p">,</span>
<span class="bp">self</span><span class="o">.</span><span class="n">trajectory</span><span class="o">.</span><span class="n">trajectory</span><span class="o">.</span><span class="n">readParticleVector</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span> <span class="n">item</span><span class="p">),</span>
<span class="n">box</span><span class="p">)</span>
<span class="k">elif</span> <span class="s">'xyz'</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">var</span><span class="o">.</span><span class="n">dimensions</span><span class="p">:</span>
<span class="n">array</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="o">.</span><span class="n">universe</span><span class="p">,</span>
<span class="bp">self</span><span class="o">.</span><span class="n">trajectory</span><span class="o">.</span><span class="n">trajectory</span><span class="o">.</span><span class="n">readParticleVector</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span> <span class="n">item</span><span class="p">))</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">array</span> <span class="o">=</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="o">.</span><span class="n">universe</span><span class="p">,</span>
<span class="bp">self</span><span class="o">.</span><span class="n">trajectory</span><span class="o">.</span><span class="n">trajectory</span><span class="o">.</span><span class="n">readParticleScalar</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span> <span class="n">item</span><span class="p">))</span>
<span class="k">return</span> <span class="n">array</span>
<span class="k">def</span> <span class="nf">__getslice__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">first</span><span class="p">,</span> <span class="n">last</span><span class="p">):</span>
<span class="k">return</span> <span class="bp">self</span><span class="p">[(</span><span class="nb">slice</span><span class="p">(</span><span class="n">first</span><span class="p">,</span> <span class="n">last</span><span class="p">),)]</span>
<span class="k">def</span> <span class="nf">average</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="nb">sum</span> <span class="o">=</span> <span class="bp">self</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
<span class="k">for</span> <span class="n">value</span> <span class="ow">in</span> <span class="bp">self</span><span class="p">[</span><span class="mi">1</span><span class="p">:]:</span>
<span class="nb">sum</span> <span class="o">=</span> <span class="nb">sum</span> <span class="o">+</span> <span class="n">value</span>
<span class="k">return</span> <span class="nb">sum</span><span class="o">/</span><span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
</div>
<div class="viewcode-block" id="SubVariable"><a class="viewcode-back" href="../../modules.html#MMTK.Trajectory.SubVariable">[docs]</a><span class="k">class</span> <span class="nc">SubVariable</span><span class="p">(</span><span class="n">TrajectoryVariable</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Reference to a subset of a :class:`~MMTK.Trajectory.TrajectoryVariable`</span>
<span class="sd"> A SubVariable object is created by slicing a TrajectoryVariable</span>
<span class="sd"> object or another SubVariable object. It provides all the operations</span>
<span class="sd"> defined on TrajectoryVariable objects.</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">variable</span><span class="p">,</span> <span class="n">indices</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">variable</span> <span class="o">=</span> <span class="n">variable</span>
<span class="bp">self</span><span class="o">.</span><span class="n">indices</span> <span class="o">=</span> <span class="n">indices</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">indices</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">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">item</span><span class="p">,</span> <span class="nb">int</span><span class="p">):</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">variable</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">indices</span><span class="p">[</span><span class="n">item</span><span class="p">]]</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">return</span> <span class="n">SubVariable</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">variable</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">indices</span><span class="p">[</span><span class="n">item</span><span class="p">])</span>
<span class="k">def</span> <span class="nf">__getslice__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">first</span><span class="p">,</span> <span class="n">last</span><span class="p">):</span>
<span class="k">return</span> <span class="bp">self</span><span class="p">[(</span><span class="nb">slice</span><span class="p">(</span><span class="n">first</span><span class="p">,</span> <span class="n">last</span><span class="p">),)]</span>
<span class="c">#</span>
<span class="c"># Trajectory consisting of multiple files</span>
<span class="c">#</span></div>
<div class="viewcode-block" id="TrajectorySet"><a class="viewcode-back" href="../../modules.html#MMTK.Trajectory.TrajectorySet">[docs]</a><span class="k">class</span> <span class="nc">TrajectorySet</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Trajectory file set</span>
<span class="sd"> A TrajectorySet permits to treat a sequence of trajectory files</span>
<span class="sd"> like a single trajectory for reading data. It behaves exactly like a</span>
<span class="sd"> :class:`~MMTK.Trajectory.Trajectory` object. The trajectory files must all contain data</span>
<span class="sd"> for the same system. The variables stored in the individual files</span>
<span class="sd"> need not be the same, but only variables common to all files</span>
<span class="sd"> can be accessed.</span>
<span class="sd"> Note: depending on how the sequence of trajectories was constructed,</span>
<span class="sd"> the first configuration of each trajectory might be the same as the</span>
<span class="sd"> last one in the preceding trajectory. To avoid counting it twice,</span>
<span class="sd"> specify (filename, 1, None, 1) for all but the first trajectory in</span>
<span class="sd"> the set.</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="nb">object</span><span class="p">,</span> <span class="n">filenames</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :param object: the object whose data is stored in the trajectory files.</span>
<span class="sd"> This can be (and usually is) None;</span>
<span class="sd"> in that case, a universe object is constructed from the</span>
<span class="sd"> description stored in the first trajectory file.</span>
<span class="sd"> This universe object can be accessed via the attribute</span>
<span class="sd"> universe of the trajectory set object.</span>
<span class="sd"> :param filenames: a list of trajectory file names or</span>
<span class="sd"> (filename, first_step, last_step, increment)</span>
<span class="sd"> tuples.</span>
<span class="sd"> """</span>
<span class="n">first</span> <span class="o">=</span> <span class="n">filenames</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
<span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">first</span><span class="p">,</span> <span class="nb">tuple</span><span class="p">):</span>
<span class="n">first</span> <span class="o">=</span> <span class="n">Trajectory</span><span class="p">(</span><span class="nb">object</span><span class="p">,</span> <span class="n">first</span><span class="p">[</span><span class="mi">0</span><span class="p">])[</span><span class="n">first</span><span class="p">[</span><span class="mi">1</span><span class="p">]:</span><span class="n">first</span><span class="p">[</span><span class="mi">2</span><span class="p">]:</span><span class="n">first</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">first</span> <span class="o">=</span> <span class="n">Trajectory</span><span class="p">(</span><span class="nb">object</span><span class="p">,</span> <span class="n">first</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">universe</span> <span class="o">=</span> <span class="n">first</span><span class="o">.</span><span class="n">universe</span>
<span class="bp">self</span><span class="o">.</span><span class="n">trajectories</span> <span class="o">=</span> <span class="p">[</span><span class="n">first</span><span class="p">]</span>
<span class="bp">self</span><span class="o">.</span><span class="n">nsteps</span> <span class="o">=</span> <span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="n">first</span><span class="p">)]</span>
<span class="bp">self</span><span class="o">.</span><span class="n">cell_parameters</span> <span class="o">=</span> <span class="p">[]</span>
<span class="k">for</span> <span class="nb">file</span> <span class="ow">in</span> <span class="n">filenames</span><span class="p">[</span><span class="mi">1</span><span class="p">:]:</span>
<span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="nb">file</span><span class="p">,</span> <span class="nb">tuple</span><span class="p">):</span>
<span class="n">t</span> <span class="o">=</span> <span class="n">Trajectory</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">universe</span><span class="p">,</span> <span class="nb">file</span><span class="p">[</span><span class="mi">0</span><span class="p">])[</span><span class="nb">file</span><span class="p">[</span><span class="mi">1</span><span class="p">]:</span><span class="nb">file</span><span class="p">[</span><span class="mi">2</span><span class="p">]:</span><span class="nb">file</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">t</span> <span class="o">=</span> <span class="n">Trajectory</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">universe</span><span class="p">,</span> <span class="nb">file</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">trajectories</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">t</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">nsteps</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">nsteps</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span><span class="o">+</span><span class="nb">len</span><span class="p">(</span><span class="n">t</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">cell_parameters</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">t</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="s">'box_size'</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="nb">vars</span> <span class="o">=</span> <span class="p">{}</span>
<span class="k">for</span> <span class="n">t</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">trajectories</span><span class="p">:</span>
<span class="k">for</span> <span class="n">v</span> <span class="ow">in</span> <span class="n">t</span><span class="o">.</span><span class="n">variables</span><span class="p">():</span>
<span class="nb">vars</span><span class="p">[</span><span class="n">v</span><span class="p">]</span> <span class="o">=</span> <span class="nb">vars</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">v</span><span class="p">,</span> <span class="mi">0</span><span class="p">)</span> <span class="o">+</span> <span class="mi">1</span>
<span class="bp">self</span><span class="o">.</span><span class="n">vars</span> <span class="o">=</span> <span class="p">[]</span>
<span class="k">for</span> <span class="n">v</span><span class="p">,</span> <span class="n">count</span> <span class="ow">in</span> <span class="nb">vars</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
<span class="k">if</span> <span class="n">count</span> <span class="o">==</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">trajectories</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">vars</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">v</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">close</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">for</span> <span class="n">t</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">trajectories</span><span class="p">:</span>
<span class="n">t</span><span class="o">.</span><span class="n">close</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="bp">self</span><span class="o">.</span><span class="n">nsteps</span><span class="p">[</span><span class="o">-</span><span class="mi">1</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">if</span> <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">item</span><span class="p">,</span> <span class="nb">int</span><span class="p">):</span>
<span class="k">return</span> <span class="n">SubTrajectory</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">N</span><span class="o">.</span><span class="n">arange</span><span class="p">(</span><span class="nb">len</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">if</span> <span class="n">item</span> <span class="o">>=</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">raise</span> <span class="ne">IndexError</span>
<span class="n">tindex</span> <span class="o">=</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">N</span><span class="o">.</span><span class="n">greater_equal</span><span class="p">(</span><span class="n">item</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">nsteps</span><span class="p">))</span><span class="o">-</span><span class="mi">1</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">trajectories</span><span class="p">[</span><span class="n">tindex</span><span class="p">][</span><span class="n">item</span><span class="o">-</span><span class="bp">self</span><span class="o">.</span><span class="n">nsteps</span><span class="p">[</span><span class="n">tindex</span><span class="p">]]</span>
<span class="k">def</span> <span class="nf">__getslice__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">first</span><span class="p">,</span> <span class="n">last</span><span class="p">):</span>
<span class="k">return</span> <span class="bp">self</span><span class="p">[(</span><span class="nb">slice</span><span class="p">(</span><span class="n">first</span><span class="p">,</span> <span class="n">last</span><span class="p">),)]</span>
<span class="k">def</span> <span class="nf">__getattr__</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="k">if</span> <span class="n">name</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">vars</span><span class="o">+</span><span class="p">[</span><span class="s">'step'</span><span class="p">]:</span>
<span class="k">raise</span> <span class="ne">AttributeError</span><span class="p">(</span><span class="s">"no variable named "</span> <span class="o">+</span> <span class="n">name</span><span class="p">)</span>
<span class="n">var</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">trajectories</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">trajectory</span><span class="o">.</span><span class="n">file</span><span class="o">.</span><span class="n">variables</span><span class="p">[</span><span class="n">name</span><span class="p">]</span>
<span class="k">if</span> <span class="s">'atom_number'</span> <span class="ow">in</span> <span class="n">var</span><span class="o">.</span><span class="n">dimensions</span><span class="p">:</span>
<span class="k">return</span> <span class="n">TrajectorySetVariable</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">universe</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="k">else</span><span class="p">:</span>
<span class="n">data</span> <span class="o">=</span> <span class="p">[]</span>
<span class="k">for</span> <span class="n">t</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">trajectories</span><span class="p">:</span>
<span class="n">var</span> <span class="o">=</span> <span class="n">t</span><span class="o">.</span><span class="n">trajectory</span><span class="o">.</span><span class="n">file</span><span class="o">.</span><span class="n">variables</span><span class="p">[</span><span class="n">name</span><span class="p">]</span>
<span class="n">data</span><span class="o">.</span><span class="n">append</span><span class="p">(</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">array</span><span class="p">(</span><span class="n">var</span><span class="p">))[:</span><span class="nb">len</span><span class="p">(</span><span class="n">t</span><span class="p">)])</span>
<span class="k">return</span> <span class="n">N</span><span class="o">.</span><span class="n">concatenate</span><span class="p">(</span><span class="n">data</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">readParticleTrajectory</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="n">first</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="n">last</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">skip</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span>
<span class="n">variable</span> <span class="o">=</span> <span class="s">"configuration"</span><span class="p">):</span>
<span class="n">total</span> <span class="o">=</span> <span class="bp">None</span>
<span class="bp">self</span><span class="o">.</span><span class="n">steps_read</span> <span class="o">=</span> <span class="p">[]</span>
<span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">trajectories</span><span class="p">)):</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">nsteps</span><span class="p">[</span><span class="n">i</span><span class="o">+</span><span class="mi">1</span><span class="p">]</span> <span class="o"><=</span> <span class="n">first</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">steps_read</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span>
<span class="k">continue</span>
<span class="k">if</span> <span class="n">last</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span> <span class="ow">and</span> <span class="bp">self</span><span class="o">.</span><span class="n">nsteps</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">>=</span> <span class="n">last</span><span class="p">:</span>
<span class="k">break</span>
<span class="n">n</span> <span class="o">=</span> <span class="nb">max</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">nsteps</span><span class="p">[</span><span class="n">i</span><span class="p">]</span><span class="o">-</span><span class="n">first</span><span class="o">+</span><span class="n">skip</span><span class="o">-</span><span class="mi">1</span><span class="p">)</span><span class="o">/</span><span class="n">skip</span><span class="p">)</span>
<span class="n">start</span> <span class="o">=</span> <span class="n">first</span><span class="o">+</span><span class="n">skip</span><span class="o">*</span><span class="n">n</span><span class="o">-</span><span class="bp">self</span><span class="o">.</span><span class="n">nsteps</span><span class="p">[</span><span class="n">i</span><span class="p">]</span>
<span class="n">n</span> <span class="o">=</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">nsteps</span><span class="p">[</span><span class="n">i</span><span class="o">+</span><span class="mi">1</span><span class="p">]</span><span class="o">-</span><span class="n">first</span><span class="o">+</span><span class="n">skip</span><span class="o">-</span><span class="mi">1</span><span class="p">)</span><span class="o">/</span><span class="n">skip</span>
<span class="n">stop</span> <span class="o">=</span> <span class="n">first</span><span class="o">+</span><span class="n">skip</span><span class="o">*</span><span class="n">n</span>
<span class="k">if</span> <span class="n">last</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">stop</span> <span class="o">=</span> <span class="nb">min</span><span class="p">(</span><span class="n">stop</span><span class="p">,</span> <span class="n">last</span><span class="p">)</span>
<span class="n">stop</span> <span class="o">=</span> <span class="n">stop</span><span class="o">-</span><span class="bp">self</span><span class="o">.</span><span class="n">nsteps</span><span class="p">[</span><span class="n">i</span><span class="p">]</span>
<span class="k">if</span> <span class="n">start</span> <span class="o">>=</span> <span class="mi">0</span> <span class="ow">and</span> <span class="n">start</span> <span class="o"><</span> <span class="bp">self</span><span class="o">.</span><span class="n">nsteps</span><span class="p">[</span><span class="n">i</span><span class="o">+</span><span class="mi">1</span><span class="p">]</span><span class="o">-</span><span class="bp">self</span><span class="o">.</span><span class="n">nsteps</span><span class="p">[</span><span class="n">i</span><span class="p">]:</span>
<span class="n">t</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">trajectories</span><span class="p">[</span><span class="n">i</span><span class="p">]</span>
<span class="n">pt</span> <span class="o">=</span> <span class="n">t</span><span class="o">.</span><span class="n">readParticleTrajectory</span><span class="p">(</span><span class="n">atom</span><span class="p">,</span> <span class="n">start</span><span class="p">,</span> <span class="n">stop</span><span class="p">,</span> <span class="n">skip</span><span class="p">,</span>
<span class="n">variable</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">steps_read</span><span class="o">.</span><span class="n">append</span><span class="p">((</span><span class="n">stop</span><span class="o">-</span><span class="n">start</span><span class="p">)</span><span class="o">/</span><span class="n">skip</span><span class="p">)</span>
<span class="k">if</span> <span class="n">total</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">total</span> <span class="o">=</span> <span class="n">pt</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">if</span> <span class="n">variable</span> <span class="o">==</span> <span class="s">"configuration"</span> \
<span class="ow">and</span> <span class="bp">self</span><span class="o">.</span><span class="n">cell_parameters</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">jump</span> <span class="o">=</span> <span class="n">pt</span><span class="o">.</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">total</span><span class="o">.</span><span class="n">array</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span>
<span class="n">mult</span> <span class="o">=</span> <span class="o">-</span><span class="p">(</span><span class="n">jump</span><span class="o">/</span><span class="bp">self</span><span class="o">.</span><span class="n">cell_parameters</span><span class="p">[</span><span class="n">i</span><span class="o">-</span><span class="mi">1</span><span class="p">])</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="s">'i'</span><span class="p">)</span>
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">N</span><span class="o">.</span><span class="n">nonzero</span><span class="p">(</span><span class="n">mult</span><span class="p">))</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
<span class="n">t</span><span class="o">.</span><span class="n">_boxTransformation</span><span class="p">(</span><span class="n">pt</span><span class="o">.</span><span class="n">array</span><span class="p">,</span> <span class="n">pt</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="n">N</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">pt</span><span class="o">.</span><span class="n">array</span><span class="p">,</span> <span class="n">mult</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="p">],</span>
<span class="n">pt</span><span class="o">.</span><span class="n">array</span><span class="p">)</span>
<span class="n">t</span><span class="o">.</span><span class="n">_boxTransformation</span><span class="p">(</span><span class="n">pt</span><span class="o">.</span><span class="n">array</span><span class="p">,</span> <span class="n">pt</span><span class="o">.</span><span class="n">array</span><span class="p">,</span> <span class="mi">0</span><span class="p">)</span>
<span class="n">jump</span> <span class="o">=</span> <span class="n">pt</span><span class="o">.</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">total</span><span class="o">.</span><span class="n">array</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span>
<span class="n">mask</span> <span class="o">=</span> <span class="n">N</span><span class="o">.</span><span class="n">less</span><span class="p">(</span><span class="n">jump</span><span class="p">,</span>
<span class="o">-</span><span class="mf">0.5</span><span class="o">*</span><span class="bp">self</span><span class="o">.</span><span class="n">cell_parameters</span><span class="p">[</span><span class="n">i</span><span class="o">-</span><span class="mi">1</span><span class="p">])</span><span class="o">-</span> \
<span class="n">N</span><span class="o">.</span><span class="n">greater</span><span class="p">(</span><span class="n">jump</span><span class="p">,</span>
<span class="mf">0.5</span><span class="o">*</span><span class="bp">self</span><span class="o">.</span><span class="n">cell_parameters</span><span class="p">[</span><span class="n">i</span><span class="o">-</span><span class="mi">1</span><span class="p">])</span>
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">N</span><span class="o">.</span><span class="n">nonzero</span><span class="p">(</span><span class="n">mask</span><span class="p">))</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
<span class="n">t</span><span class="o">.</span><span class="n">_boxTransformation</span><span class="p">(</span><span class="n">pt</span><span class="o">.</span><span class="n">array</span><span class="p">,</span> <span class="n">pt</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="n">N</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">pt</span><span class="o">.</span><span class="n">array</span><span class="p">,</span> <span class="n">mask</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">pt</span><span class="o">.</span><span class="n">array</span><span class="p">)</span>
<span class="n">t</span><span class="o">.</span><span class="n">_boxTransformation</span><span class="p">(</span><span class="n">pt</span><span class="o">.</span><span class="n">array</span><span class="p">,</span> <span class="n">pt</span><span class="o">.</span><span class="n">array</span><span class="p">,</span> <span class="mi">0</span><span class="p">)</span>
<span class="k">elif</span> <span class="n">variable</span> <span class="o">==</span> <span class="s">"box_coordinates"</span> \
<span class="ow">and</span> <span class="bp">self</span><span class="o">.</span><span class="n">cell_parameters</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">jump</span> <span class="o">=</span> <span class="n">pt</span><span class="o">.</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">total</span><span class="o">.</span><span class="n">array</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span>
<span class="n">mult</span> <span class="o">=</span> <span class="o">-</span><span class="n">jump</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="s">'i'</span><span class="p">)</span>
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">N</span><span class="o">.</span><span class="n">nonzero</span><span class="p">(</span><span class="n">mult</span><span class="p">))</span> <span class="o">></span> <span class="mi">0</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">pt</span><span class="o">.</span><span class="n">array</span><span class="p">,</span> <span class="n">mult</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="p">],</span>
<span class="n">pt</span><span class="o">.</span><span class="n">array</span><span class="p">)</span>
<span class="n">jump</span> <span class="o">=</span> <span class="n">pt</span><span class="o">.</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">total</span><span class="o">.</span><span class="n">array</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span>
<span class="n">mask</span> <span class="o">=</span> <span class="n">N</span><span class="o">.</span><span class="n">less</span><span class="p">(</span><span class="n">jump</span><span class="p">,</span> <span class="o">-</span><span class="mf">0.5</span><span class="p">)</span><span class="o">-</span> \
<span class="n">N</span><span class="o">.</span><span class="n">greater</span><span class="p">(</span><span class="n">jump</span><span class="p">,</span> <span class="mf">0.5</span><span class="p">)</span>
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">N</span><span class="o">.</span><span class="n">nonzero</span><span class="p">(</span><span class="n">mask</span><span class="p">))</span> <span class="o">></span> <span class="mi">0</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">pt</span><span class="o">.</span><span class="n">array</span><span class="p">,</span> <span class="n">mask</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">pt</span><span class="o">.</span><span class="n">array</span><span class="p">)</span>
<span class="n">total</span><span class="o">.</span><span class="n">array</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">total</span><span class="o">.</span><span class="n">array</span><span class="p">,</span> <span class="n">pt</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="bp">self</span><span class="o">.</span><span class="n">steps_read</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span>
<span class="k">return</span> <span class="n">total</span>
<span class="k">def</span> <span class="nf">readRigidBodyTrajectory</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">first</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="n">last</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">skip</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span>
<span class="n">reference</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
<span class="k">return</span> <span class="n">RigidBodyTrajectory</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">first</span><span class="p">,</span> <span class="n">last</span><span class="p">,</span> <span class="n">skip</span><span class="p">,</span> <span class="n">reference</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">_boxTransformation</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">pt_in</span><span class="p">,</span> <span class="n">pt_out</span><span class="p">,</span> <span class="n">to_box</span><span class="o">=</span><span class="mi">0</span><span class="p">):</span>
<span class="n">n</span> <span class="o">=</span> <span class="mi">0</span>
<span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">steps_read</span><span class="p">)):</span>
<span class="n">t</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">trajectories</span><span class="p">[</span><span class="n">i</span><span class="p">]</span>
<span class="n">steps</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">steps_read</span><span class="p">[</span><span class="n">i</span><span class="p">]</span>
<span class="k">if</span> <span class="n">steps</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
<span class="n">t</span><span class="o">.</span><span class="n">_boxTransformation</span><span class="p">(</span><span class="n">pt_in</span><span class="p">[</span><span class="n">n</span><span class="p">:</span><span class="n">n</span><span class="o">+</span><span class="n">steps</span><span class="p">],</span> <span class="n">pt_out</span><span class="p">[</span><span class="n">n</span><span class="p">:</span><span class="n">n</span><span class="o">+</span><span class="n">steps</span><span class="p">],</span>
<span class="n">to_box</span><span class="p">)</span>
<span class="n">n</span> <span class="o">=</span> <span class="n">n</span> <span class="o">+</span> <span class="n">steps</span>
<span class="k">def</span> <span class="nf">variables</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">vars</span>
<span class="k">def</span> <span class="nf">view</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">first</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="n">last</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">step</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="nb">object</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
<span class="n">Visualization</span><span class="o">.</span><span class="n">viewTrajectory</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">first</span><span class="p">,</span> <span class="n">last</span><span class="p">,</span> <span class="n">step</span><span class="p">,</span> <span class="nb">object</span><span class="p">)</span>
</div>
<div class="viewcode-block" id="TrajectorySetVariable"><a class="viewcode-back" href="../../modules.html#MMTK.Trajectory.TrajectorySetVariable">[docs]</a><span class="k">class</span> <span class="nc">TrajectorySetVariable</span><span class="p">(</span><span class="n">TrajectoryVariable</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Variable in a trajectory set</span>
<span class="sd"> A TrajectorySetVariable object is created by extracting a variable from</span>
<span class="sd"> a TrajectorySet object if that variable contains data for each atom and</span>
<span class="sd"> is thus potentially large. It behaves exactly like a TrajectoryVariable</span>
<span class="sd"> object.</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">universe</span><span class="p">,</span> <span class="n">trajectory_set</span><span class="p">,</span> <span class="n">name</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">universe</span> <span class="o">=</span> <span class="n">universe</span>
<span class="bp">self</span><span class="o">.</span><span class="n">trajectory_set</span> <span class="o">=</span> <span class="n">trajectory_set</span>
<span class="bp">self</span><span class="o">.</span><span class="n">name</span> <span class="o">=</span> <span class="n">name</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">trajectory_set</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">if</span> <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">item</span><span class="p">,</span> <span class="nb">int</span><span class="p">):</span>
<span class="k">return</span> <span class="n">SubVariable</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">N</span><span class="o">.</span><span class="n">arange</span><span class="p">(</span><span class="nb">len</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">if</span> <span class="n">item</span> <span class="o">>=</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">trajectory_set</span><span class="p">):</span>
<span class="k">raise</span> <span class="ne">IndexError</span>
<span class="n">tindex</span> <span class="o">=</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">N</span><span class="o">.</span><span class="n">greater_equal</span><span class="p">(</span><span class="n">item</span><span class="p">,</span>
<span class="bp">self</span><span class="o">.</span><span class="n">trajectory_set</span><span class="o">.</span><span class="n">nsteps</span><span class="p">))</span><span class="o">-</span><span class="mi">1</span>
<span class="n">step</span> <span class="o">=</span> <span class="n">item</span><span class="o">-</span><span class="bp">self</span><span class="o">.</span><span class="n">trajectory_set</span><span class="o">.</span><span class="n">nsteps</span><span class="p">[</span><span class="n">tindex</span><span class="p">]</span>
<span class="n">t</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">trajectory_set</span><span class="o">.</span><span class="n">trajectories</span><span class="p">[</span><span class="n">tindex</span><span class="p">]</span>
<span class="k">return</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">t</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">)[</span><span class="n">step</span><span class="p">]</span>
<span class="c">#</span>
<span class="c"># Cache for atom trajectories</span>
<span class="c">#</span></div>
<span class="k">class</span> <span class="nc">ParticleTrajectoryReader</span><span class="p">(</span><span class="nb">object</span><span class="p">):</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">trajectory</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">trajectory</span> <span class="o">=</span> <span class="n">trajectory</span>
<span class="bp">self</span><span class="o">.</span><span class="n">natoms</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">trajectory</span><span class="o">.</span><span class="n">universe</span><span class="o">.</span><span class="n">numberOfAtoms</span><span class="p">()</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_trajectory</span> <span class="o">=</span> <span class="n">trajectory</span><span class="o">.</span><span class="n">trajectory</span>
<span class="bp">self</span><span class="o">.</span><span class="n">cache</span> <span class="o">=</span> <span class="p">{}</span>
<span class="bp">self</span><span class="o">.</span><span class="n">cache_lifetime</span> <span class="o">=</span> <span class="mi">2</span>
<span class="k">def</span> <span class="nf">__call__</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="n">variable</span><span class="p">,</span> <span class="n">first</span><span class="p">,</span> <span class="n">last</span><span class="p">,</span> <span class="n">skip</span><span class="p">,</span> <span class="n">correct</span><span class="p">,</span> <span class="n">box</span><span class="p">):</span>
<span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">atom</span><span class="p">,</span> <span class="nb">int</span><span class="p">):</span>
<span class="n">index</span> <span class="o">=</span> <span class="n">atom</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">index</span> <span class="o">=</span> <span class="n">atom</span><span class="o">.</span><span class="n">index</span>
<span class="k">if</span> <span class="n">atom</span><span class="o">.</span><span class="n">universe</span><span class="p">()</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">trajectory</span><span class="o">.</span><span class="n">universe</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s">"objects not in the same universe"</span><span class="p">)</span>
<span class="n">key</span> <span class="o">=</span> <span class="p">(</span><span class="n">index</span><span class="p">,</span> <span class="n">variable</span><span class="p">,</span> <span class="n">first</span><span class="p">,</span> <span class="n">last</span><span class="p">,</span> <span class="n">skip</span><span class="p">,</span> <span class="n">correct</span><span class="p">,</span> <span class="n">box</span><span class="p">)</span>
<span class="n">data</span><span class="p">,</span> <span class="n">count</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">cache</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">key</span><span class="p">,</span> <span class="p">(</span><span class="bp">None</span><span class="p">,</span> <span class="mi">0</span><span class="p">))</span>
<span class="k">if</span> <span class="n">data</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">cache</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="p">(</span><span class="n">data</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">cache_lifetime</span><span class="p">)</span>
<span class="k">return</span> <span class="n">data</span>
<span class="n">delete</span> <span class="o">=</span> <span class="p">[]</span>
<span class="k">for</span> <span class="n">k</span><span class="p">,</span> <span class="n">value</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">cache</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
<span class="n">data</span><span class="p">,</span> <span class="n">count</span> <span class="o">=</span> <span class="n">value</span>
<span class="n">count</span> <span class="o">-=</span> <span class="mi">1</span>
<span class="k">if</span> <span class="n">count</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
<span class="n">delete</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">k</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">cache</span><span class="p">[</span><span class="n">k</span><span class="p">]</span> <span class="o">=</span> <span class="p">(</span><span class="n">data</span><span class="p">,</span> <span class="n">count</span><span class="p">)</span>
<span class="k">for</span> <span class="n">k</span> <span class="ow">in</span> <span class="n">delete</span><span class="p">:</span>
<span class="k">del</span> <span class="bp">self</span><span class="o">.</span><span class="n">cache</span><span class="p">[</span><span class="n">k</span><span class="p">]</span>
<span class="n">cache_size</span> <span class="o">=</span> <span class="nb">min</span><span class="p">(</span><span class="mi">10</span><span class="p">,</span> <span class="nb">max</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="mi">100000</span><span class="o">/</span><span class="nb">max</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">trajectory</span><span class="p">))))</span>
<span class="n">natoms</span> <span class="o">=</span> <span class="nb">min</span><span class="p">(</span><span class="n">cache_size</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">natoms</span><span class="o">-</span><span class="n">index</span><span class="p">)</span>
<span class="n">data</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_trajectory</span><span class="o">.</span><span class="n">readParticleTrajectories</span><span class="p">(</span><span class="n">index</span><span class="p">,</span> <span class="n">natoms</span><span class="p">,</span>
<span class="n">variable</span><span class="p">,</span>
<span class="n">first</span><span class="p">,</span> <span class="n">last</span><span class="p">,</span> <span class="n">skip</span><span class="p">,</span>
<span class="n">correct</span><span class="p">,</span> <span class="n">box</span><span class="p">)</span>
<span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">natoms</span><span class="p">):</span>
<span class="n">key</span> <span class="o">=</span> <span class="p">(</span><span class="n">index</span><span class="o">+</span><span class="n">i</span><span class="p">,</span> <span class="n">variable</span><span class="p">,</span> <span class="n">first</span><span class="p">,</span> <span class="n">last</span><span class="p">,</span> <span class="n">skip</span><span class="p">,</span> <span class="n">correct</span><span class="p">,</span> <span class="n">box</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">cache</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="p">(</span><span class="n">data</span><span class="p">[</span><span class="n">i</span><span class="p">],</span> <span class="bp">self</span><span class="o">.</span><span class="n">cache_lifetime</span><span class="p">)</span>
<span class="k">return</span> <span class="n">data</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
<span class="c">#</span>
<span class="c"># Single-atom trajectory</span>
<span class="c">#</span>
<div class="viewcode-block" id="ParticleTrajectory"><a class="viewcode-back" href="../../modules.html#MMTK.Trajectory.ParticleTrajectory">[docs]</a><span class="k">class</span> <span class="nc">ParticleTrajectory</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Trajectory data for a single particle</span>
<span class="sd"> A ParticleTrajectory object is created by calling the method</span>
<span class="sd"> :func:`~MMTK.Trajectory.Trajectory.readParticleTrajectory`</span>
<span class="sd"> on a :class:`~MMTK.Trajectory.Trajectory` object.</span>
<span class="sd"> If pt is a ParticleTrajectory object, then</span>
<span class="sd"> * len(pt) is the number of steps stored in it</span>
<span class="sd"> * pt[i] is the value at step i (a vector)</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">trajectory</span><span class="p">,</span> <span class="n">atom</span><span class="p">,</span> <span class="n">first</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="n">last</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">skip</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span>
<span class="n">variable</span> <span class="o">=</span> <span class="s">"configuration"</span><span class="p">):</span>
<span class="k">if</span> <span class="n">last</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">last</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">trajectory</span><span class="p">)</span>
<span class="k">if</span> <span class="n">variable</span> <span class="o">==</span> <span class="s">"box_coordinates"</span><span class="p">:</span>
<span class="n">variable</span> <span class="o">=</span> <span class="s">"configuration"</span>
<span class="n">box</span> <span class="o">=</span> <span class="mi">1</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">box</span> <span class="o">=</span> <span class="mi">0</span>
<span class="n">reader</span> <span class="o">=</span> <span class="n">trajectory</span><span class="o">.</span><span class="n">particle_trajectory_reader</span>
<span class="bp">self</span><span class="o">.</span><span class="n">array</span> <span class="o">=</span> <span class="n">reader</span><span class="p">(</span><span class="n">atom</span><span class="p">,</span> <span class="n">variable</span><span class="p">,</span> <span class="n">first</span><span class="p">,</span> <span class="n">last</span><span class="p">,</span> <span class="n">skip</span><span class="p">,</span>
<span class="n">variable</span> <span class="o">==</span> <span class="s">"configuration"</span><span class="p">,</span> <span class="n">box</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="bp">self</span><span class="o">.</span><span class="n">array</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">0</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">index</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">array</span><span class="p">[</span><span class="n">index</span><span class="p">])</span>
<div class="viewcode-block" id="ParticleTrajectory.translateBy"><a class="viewcode-back" href="../../modules.html#MMTK.Trajectory.ParticleTrajectory.translateBy">[docs]</a> <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="sd">"""</span>
<span class="sd"> Adds a vector to the values at all steps. This does B{not}</span>
<span class="sd"> change the data in the trajectory file.</span>
<span class="sd"> :param vector: the vector to be added</span>
<span class="sd"> :type vector: Scientific.Geometry.Vector</span>
<span class="sd"> """</span>
<span class="n">N</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">array</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="bp">self</span><span class="o">.</span><span class="n">array</span><span class="p">)</span>
<span class="c">#</span>
<span class="c"># Rigid-body trajectory</span>
<span class="c">#</span></div></div>
<div class="viewcode-block" id="RigidBodyTrajectory"><a class="viewcode-back" href="../../modules.html#MMTK.Trajectory.RigidBodyTrajectory">[docs]</a><span class="k">class</span> <span class="nc">RigidBodyTrajectory</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Rigid-body trajectory data</span>
<span class="sd"> A RigidBodyTrajectory object is created by calling the method</span>
<span class="sd"> :func:`~MMTK.Trajectory.Trajectory.readRigidBodyTrajectory`</span>
<span class="sd"> on a :class:`~MMTK.Trajectory.Trajectory` object.</span>
<span class="sd"> If rbt is a RigidBodyTrajectory object, then</span>
<span class="sd"> * len(rbt) is the number of steps stored in it</span>
<span class="sd"> * rbt[i] is the value at step i (a vector for the center of mass</span>
<span class="sd"> and a quaternion for the orientation)</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">trajectory</span><span class="p">,</span> <span class="nb">object</span><span class="p">,</span> <span class="n">first</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="n">last</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">skip</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span>
<span class="n">reference</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">trajectory</span> <span class="o">=</span> <span class="n">trajectory</span>
<span class="n">universe</span> <span class="o">=</span> <span class="n">trajectory</span><span class="o">.</span><span class="n">universe</span>
<span class="k">if</span> <span class="n">last</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span> <span class="n">last</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">trajectory</span><span class="p">)</span>
<span class="n">first_conf</span> <span class="o">=</span> <span class="n">trajectory</span><span class="o">.</span><span class="n">configuration</span><span class="p">[</span><span class="n">first</span><span class="p">]</span>
<span class="n">offset</span> <span class="o">=</span> <span class="n">universe</span><span class="o">.</span><span class="n">contiguousObjectOffset</span><span class="p">([</span><span class="nb">object</span><span class="p">],</span> <span class="n">first_conf</span><span class="p">,</span> <span class="bp">True</span><span class="p">)</span>
<span class="k">if</span> <span class="n">reference</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">reference</span> <span class="o">=</span> <span class="n">first_conf</span>
<span class="n">reference</span> <span class="o">=</span> <span class="n">universe</span><span class="o">.</span><span class="n">contiguousObjectConfiguration</span><span class="p">([</span><span class="nb">object</span><span class="p">],</span> <span class="n">reference</span><span class="p">)</span>
<span class="n">steps</span> <span class="o">=</span> <span class="p">(</span><span class="n">last</span><span class="o">-</span><span class="n">first</span><span class="o">+</span><span class="n">skip</span><span class="o">-</span><span class="mi">1</span><span class="p">)</span><span class="o">/</span><span class="n">skip</span>
<span class="n">mass</span> <span class="o">=</span> <span class="nb">object</span><span class="o">.</span><span class="n">mass</span><span class="p">()</span>
<span class="n">ref_cms</span> <span class="o">=</span> <span class="nb">object</span><span class="o">.</span><span class="n">centerOfMass</span><span class="p">(</span><span class="n">reference</span><span class="p">)</span>
<span class="n">atoms</span> <span class="o">=</span> <span class="nb">object</span><span class="o">.</span><span class="n">atomList</span><span class="p">()</span>
<span class="n">possq</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">steps</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">cross</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">steps</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="n">N</span><span class="o">.</span><span class="n">Float</span><span class="p">)</span>
<span class="n">rcms</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">steps</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="c"># cms of the CONTIGUOUS object made of CONTINUOUS atom trajectories </span>
<span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">atoms</span><span class="p">:</span>
<span class="n">r</span> <span class="o">=</span> <span class="n">trajectory</span><span class="o">.</span><span class="n">readParticleTrajectory</span><span class="p">(</span><span class="n">a</span><span class="p">,</span> <span class="n">first</span><span class="p">,</span> <span class="n">last</span><span class="p">,</span> <span class="n">skip</span><span class="p">,</span>
<span class="s">"box_coordinates"</span><span class="p">)</span><span class="o">.</span><span class="n">array</span>
<span class="n">w</span> <span class="o">=</span> <span class="n">a</span><span class="o">.</span><span class="n">_mass</span><span class="o">/</span><span class="n">mass</span>
<span class="n">N</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">rcms</span><span class="p">,</span> <span class="n">w</span><span class="o">*</span><span class="n">r</span><span class="p">,</span> <span class="n">rcms</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="n">N</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">rcms</span><span class="p">,</span> <span class="n">w</span><span class="o">*</span><span class="n">offset</span><span class="p">[</span><span class="n">a</span><span class="p">]</span><span class="o">.</span><span class="n">array</span><span class="p">,</span> <span class="n">rcms</span><span class="p">)</span>
<span class="c"># relative coords of the CONTIGUOUS reference</span>
<span class="n">r_ref</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">atoms</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">a</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">atoms</span><span class="p">)):</span>
<span class="n">r_ref</span><span class="p">[</span><span class="n">a</span><span class="p">]</span> <span class="o">=</span> <span class="n">atoms</span><span class="p">[</span><span class="n">a</span><span class="p">]</span><span class="o">.</span><span class="n">position</span><span class="p">(</span><span class="n">reference</span><span class="p">)</span><span class="o">.</span><span class="n">array</span> <span class="o">-</span> <span class="n">ref_cms</span><span class="o">.</span><span class="n">array</span>
<span class="c"># main loop: storing data needed to fill M matrix </span>
<span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">atoms</span><span class="p">)):</span>
<span class="n">r</span> <span class="o">=</span> <span class="n">trajectory</span><span class="o">.</span><span class="n">readParticleTrajectory</span><span class="p">(</span><span class="n">atoms</span><span class="p">[</span><span class="n">a</span><span class="p">],</span>
<span class="n">first</span><span class="p">,</span> <span class="n">last</span><span class="p">,</span> <span class="n">skip</span><span class="p">,</span>
<span class="s">"box_coordinates"</span><span class="p">)</span><span class="o">.</span><span class="n">array</span>
<span class="n">r</span> <span class="o">=</span> <span class="n">r</span> <span class="o">-</span> <span class="n">rcms</span> <span class="c"># (a-b)**2 != a**2 - b**2</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="n">N</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">r</span><span class="p">,</span> <span class="n">offset</span><span class="p">[</span><span class="n">atoms</span><span class="p">[</span><span class="n">a</span><span class="p">]]</span><span class="o">.</span><span class="n">array</span><span class="p">,</span><span class="n">r</span><span class="p">)</span>
<span class="n">trajectory</span><span class="o">.</span><span class="n">_boxTransformation</span><span class="p">(</span><span class="n">r</span><span class="p">,</span> <span class="n">r</span><span class="p">)</span>
<span class="n">w</span> <span class="o">=</span> <span class="n">atoms</span><span class="p">[</span><span class="n">a</span><span class="p">]</span><span class="o">.</span><span class="n">_mass</span><span class="o">/</span><span class="n">mass</span>
<span class="n">N</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">possq</span><span class="p">,</span> <span class="n">w</span><span class="o">*</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">r</span><span class="o">*</span><span class="n">r</span><span class="p">,</span> <span class="o">-</span><span class="mi">1</span><span class="p">),</span> <span class="n">possq</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">possq</span><span class="p">,</span> <span class="n">w</span><span class="o">*</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">r_ref</span><span class="p">[</span><span class="n">a</span><span class="p">]</span><span class="o">*</span><span class="n">r_ref</span><span class="p">[</span><span class="n">a</span><span class="p">],</span><span class="o">-</span><span class="mi">1</span><span class="p">),</span>
<span class="n">possq</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">cross</span><span class="p">,</span> <span class="n">w</span><span class="o">*</span><span class="n">r</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="o">*</span><span class="n">r_ref</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="n">a</span><span class="p">,:],</span><span class="n">cross</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">trajectory</span><span class="o">.</span><span class="n">_boxTransformation</span><span class="p">(</span><span class="n">rcms</span><span class="p">,</span> <span class="n">rcms</span><span class="p">)</span>
<span class="c"># filling matrix M (formula no 40)</span>
<span class="n">k</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">steps</span><span class="p">,</span> <span class="mi">4</span><span class="p">,</span> <span class="mi">4</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">k</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="o">=</span> <span class="o">-</span><span class="n">cross</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="o">-</span><span class="n">cross</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="o">-</span><span class="n">cross</span><span class="p">[:,</span> <span class="mi">2</span><span class="p">,</span> <span class="mi">2</span><span class="p">]</span>
<span class="n">k</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="o">=</span> <span class="n">cross</span><span class="p">[:,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">]</span><span class="o">-</span><span class="n">cross</span><span class="p">[:,</span> <span class="mi">2</span><span class="p">,</span> <span class="mi">1</span><span class="p">]</span>
<span class="n">k</span><span class="p">[:,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">2</span><span class="p">]</span> <span class="o">=</span> <span class="n">cross</span><span class="p">[:,</span> <span class="mi">2</span><span class="p">,</span> <span class="mi">0</span><span class="p">]</span><span class="o">-</span><span class="n">cross</span><span class="p">[:,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">2</span><span class="p">]</span>
<span class="n">k</span><span class="p">[:,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">3</span><span class="p">]</span> <span class="o">=</span> <span class="n">cross</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="o">-</span><span class="n">cross</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">k</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="o">=</span> <span class="o">-</span><span class="n">cross</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="o">+</span><span class="n">cross</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="o">+</span><span class="n">cross</span><span class="p">[:,</span> <span class="mi">2</span><span class="p">,</span> <span class="mi">2</span><span class="p">]</span>
<span class="n">k</span><span class="p">[:,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">]</span> <span class="o">=</span> <span class="o">-</span><span class="n">cross</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="o">-</span><span class="n">cross</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">k</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="o">=</span> <span class="o">-</span><span class="n">cross</span><span class="p">[:,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">2</span><span class="p">]</span><span class="o">-</span><span class="n">cross</span><span class="p">[:,</span> <span class="mi">2</span><span class="p">,</span> <span class="mi">0</span><span class="p">]</span>
<span class="n">k</span><span class="p">[:,</span> <span class="mi">2</span><span class="p">,</span> <span class="mi">2</span><span class="p">]</span> <span class="o">=</span> <span class="n">cross</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="o">-</span><span class="n">cross</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="o">+</span><span class="n">cross</span><span class="p">[:,</span> <span class="mi">2</span><span class="p">,</span> <span class="mi">2</span><span class="p">]</span>
<span class="n">k</span><span class="p">[:,</span> <span class="mi">2</span><span class="p">,</span> <span class="mi">3</span><span class="p">]</span> <span class="o">=</span> <span class="o">-</span><span class="n">cross</span><span class="p">[:,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">]</span><span class="o">-</span><span class="n">cross</span><span class="p">[:,</span> <span class="mi">2</span><span class="p">,</span> <span class="mi">1</span><span class="p">]</span>
<span class="n">k</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="o">=</span> <span class="n">cross</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="o">+</span><span class="n">cross</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="o">-</span><span class="n">cross</span><span class="p">[:,</span> <span class="mi">2</span><span class="p">,</span> <span class="mi">2</span><span class="p">]</span>
<span class="k">del</span> <span class="n">cross</span>
<span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="mi">4</span><span class="p">):</span>
<span class="k">for</span> <span class="n">j</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">i</span><span class="p">):</span>
<span class="n">k</span><span class="p">[:,</span> <span class="n">i</span><span class="p">,</span> <span class="n">j</span><span class="p">]</span> <span class="o">=</span> <span class="n">k</span><span class="p">[:,</span> <span class="n">j</span><span class="p">,</span> <span class="n">i</span><span class="p">]</span>
<span class="n">N</span><span class="o">.</span><span class="n">multiply</span><span class="p">(</span><span class="n">k</span><span class="p">,</span> <span class="mf">2.</span><span class="p">,</span> <span class="n">k</span><span class="p">)</span>
<span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">4</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">k</span><span class="p">[:,</span><span class="n">i</span><span class="p">,</span><span class="n">i</span><span class="p">],</span> <span class="n">possq</span><span class="p">,</span> <span class="n">k</span><span class="p">[:,</span><span class="n">i</span><span class="p">,</span><span class="n">i</span><span class="p">])</span>
<span class="k">del</span> <span class="n">possq</span>
<span class="n">quaternions</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">steps</span><span class="p">,</span> <span class="mi">4</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">fit</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">steps</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">Scientific.LA</span> <span class="kn">import</span> <span class="n">eigenvectors</span>
<span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">steps</span><span class="p">):</span>
<span class="n">e</span><span class="p">,</span> <span class="n">v</span> <span class="o">=</span> <span class="n">eigenvectors</span><span class="p">(</span><span class="n">k</span><span class="p">[</span><span class="n">i</span><span class="p">])</span>
<span class="n">j</span> <span class="o">=</span> <span class="n">N</span><span class="o">.</span><span class="n">argmin</span><span class="p">(</span><span class="n">e</span><span class="p">)</span>
<span class="k">if</span> <span class="n">e</span><span class="p">[</span><span class="n">j</span><span class="p">]</span> <span class="o"><</span> <span class="mf">0.</span><span class="p">:</span>
<span class="n">fit</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">=</span> <span class="mf">0.</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">fit</span><span class="p">[</span><span class="n">i</span><span class="p">]</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">e</span><span class="p">[</span><span class="n">j</span><span class="p">])</span>
<span class="k">if</span> <span class="n">v</span><span class="p">[</span><span class="n">j</span><span class="p">,</span><span class="mi">0</span><span class="p">]</span> <span class="o"><</span> <span class="mf">0.</span><span class="p">:</span> <span class="n">quaternions</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">=</span> <span class="o">-</span><span class="n">v</span><span class="p">[</span><span class="n">j</span><span class="p">]</span> <span class="c"># eliminate jumps</span>
<span class="k">else</span><span class="p">:</span> <span class="n">quaternions</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">=</span> <span class="n">v</span><span class="p">[</span><span class="n">j</span><span class="p">]</span>
<span class="bp">self</span><span class="o">.</span><span class="n">fit</span> <span class="o">=</span> <span class="n">fit</span>
<span class="bp">self</span><span class="o">.</span><span class="n">cms</span> <span class="o">=</span> <span class="n">rcms</span>
<span class="bp">self</span><span class="o">.</span><span class="n">quaternions</span> <span class="o">=</span> <span class="n">quaternions</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="bp">self</span><span class="o">.</span><span class="n">cms</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">0</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">index</span><span class="p">):</span>
<span class="kn">from</span> <span class="nn">Scientific.Geometry.Quaternion</span> <span class="kn">import</span> <span class="n">Quaternion</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">cms</span><span class="p">[</span><span class="n">index</span><span class="p">]),</span> <span class="n">Quaternion</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">quaternions</span><span class="p">[</span><span class="n">index</span><span class="p">])</span>
<span class="c">#</span>
<span class="c"># Type check for trajectory objects</span>
<span class="c">#</span></div>
<div class="viewcode-block" id="isTrajectory"><a class="viewcode-back" href="../../modules.html#MMTK.Trajectory.isTrajectory">[docs]</a><span class="k">def</span> <span class="nf">isTrajectory</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 trajectory</span>
<span class="sd"> """</span>
<span class="kn">import</span> <span class="nn">MMTK_trajectory</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="p">(</span><span class="n">Trajectory</span><span class="p">,</span> <span class="n">MMTK_trajectory</span><span class="o">.</span><span class="n">trajectory_type</span><span class="p">))</span>
<span class="c">#</span>
<span class="c"># Base class for all objects that generate trajectories</span>
<span class="c">#</span></div>
<div class="viewcode-block" id="TrajectoryGenerator"><a class="viewcode-back" href="../../modules.html#MMTK.Trajectory.TrajectoryGenerator">[docs]</a><span class="k">class</span> <span class="nc">TrajectoryGenerator</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Trajectory generator base class</span>
<span class="sd"> This base class implements the common aspects of everything that</span>
<span class="sd"> generates trajectories: integrators, minimizers, etc.</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">universe</span><span class="p">,</span> <span class="n">options</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">universe</span> <span class="o">=</span> <span class="n">universe</span>
<span class="bp">self</span><span class="o">.</span><span class="n">options</span> <span class="o">=</span> <span class="n">options</span>
<span class="k">def</span> <span class="nf">setCallOptions</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">options</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">call_options</span> <span class="o">=</span> <span class="n">options</span>
<span class="k">def</span> <span class="nf">getActions</span><span class="p">(</span><span class="bp">self</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">actions</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">getOption</span><span class="p">(</span><span class="s">'actions'</span><span class="p">)</span>
<span class="k">except</span> <span class="ne">ValueError</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">actions</span> <span class="o">=</span> <span class="p">[]</span>
<span class="k">try</span><span class="p">:</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">getOption</span><span class="p">(</span><span class="s">'background'</span><span class="p">):</span>
<span class="kn">import</span> <span class="nn">MMTK_state_accessor</span>
<span class="bp">self</span><span class="o">.</span><span class="n">state_accessor</span> <span class="o">=</span> <span class="n">MMTK_state_accessor</span><span class="o">.</span><span class="n">StateAccessor</span><span class="p">()</span>
<span class="bp">self</span><span class="o">.</span><span class="n">actions</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">state_accessor</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">try</span><span class="p">:</span>
<span class="n">steps</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">getOption</span><span class="p">(</span><span class="s">'steps'</span><span class="p">)</span>
<span class="k">except</span> <span class="ne">ValueError</span><span class="p">:</span>
<span class="n">steps</span> <span class="o">=</span> <span class="bp">None</span>
<span class="k">return</span> <span class="nb">map</span><span class="p">(</span><span class="k">lambda</span> <span class="n">a</span><span class="p">,</span> <span class="n">t</span><span class="o">=</span><span class="bp">self</span><span class="p">,</span> <span class="n">s</span><span class="o">=</span><span class="n">steps</span><span class="p">:</span> <span class="n">a</span><span class="o">.</span><span class="n">getSpecificationList</span><span class="p">(</span><span class="n">t</span><span class="p">,</span> <span class="n">s</span><span class="p">),</span>
<span class="bp">self</span><span class="o">.</span><span class="n">actions</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">cleanupActions</span><span class="p">(</span><span class="bp">self</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">actions</span><span class="p">:</span>
<span class="n">a</span><span class="o">.</span><span class="n">cleanup</span><span class="p">()</span>
<span class="k">def</span> <span class="nf">getOption</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">option</span><span class="p">):</span>
<span class="k">try</span><span class="p">:</span>
<span class="n">value</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">call_options</span><span class="p">[</span><span class="n">option</span><span class="p">]</span>
<span class="k">except</span> <span class="ne">KeyError</span><span class="p">:</span>
<span class="k">try</span><span class="p">:</span>
<span class="n">value</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">options</span><span class="p">[</span><span class="n">option</span><span class="p">]</span>
<span class="k">except</span> <span class="ne">KeyError</span><span class="p">:</span>
<span class="k">try</span><span class="p">:</span>
<span class="n">value</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">default_options</span><span class="p">[</span><span class="n">option</span><span class="p">]</span>
<span class="k">except</span> <span class="ne">KeyError</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s">'undefined option: '</span> <span class="o">+</span> <span class="n">option</span><span class="p">)</span>
<span class="k">return</span> <span class="n">value</span>
<span class="k">def</span> <span class="nf">optionString</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">options</span><span class="p">):</span>
<span class="n">s</span> <span class="o">=</span> <span class="s">''</span>
<span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">options</span><span class="p">:</span>
<span class="n">s</span> <span class="o">=</span> <span class="n">s</span> <span class="o">+</span> <span class="n">o</span> <span class="o">+</span> <span class="s">'='</span> <span class="o">+</span> <span class="sb">`self.getOption(o)`</span> <span class="o">+</span> <span class="s">', '</span>
<span class="k">return</span> <span class="n">s</span><span class="p">[:</span><span class="o">-</span><span class="mi">2</span><span class="p">]</span>
<span class="k">def</span> <span class="nf">run</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="n">args</span><span class="p">):</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">getOption</span><span class="p">(</span><span class="s">'background'</span><span class="p">):</span>
<span class="kn">import</span> <span class="nn">ThreadManager</span>
<span class="k">return</span> <span class="n">ThreadManager</span><span class="o">.</span><span class="n">TrajectoryGeneratorThread</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">universe</span><span class="p">,</span>
<span class="n">function</span><span class="p">,</span> <span class="n">args</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">state_accessor</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="nb">apply</span><span class="p">(</span><span class="n">function</span><span class="p">,</span> <span class="n">args</span><span class="p">)</span>
<span class="c">#</span>
<span class="c"># Trajectory action base class</span>
<span class="c">#</span></div>
<div class="viewcode-block" id="TrajectoryAction"><a class="viewcode-back" href="../../modules.html#MMTK.Trajectory.TrajectoryAction">[docs]</a><span class="k">class</span> <span class="nc">TrajectoryAction</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Trajectory action base class</span>
<span class="sd"> Subclasses of this base class implement the actions that can be</span>
<span class="sd"> inserted into trajectory generation at regular intervals.</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">first</span><span class="p">,</span> <span class="n">last</span><span class="p">,</span> <span class="n">skip</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">first</span> <span class="o">=</span> <span class="n">first</span>
<span class="bp">self</span><span class="o">.</span><span class="n">last</span> <span class="o">=</span> <span class="n">last</span>
<span class="bp">self</span><span class="o">.</span><span class="n">skip</span> <span class="o">=</span> <span class="n">skip</span>
<span class="n">spec_type</span> <span class="o">=</span> <span class="s">'function'</span>
<span class="k">def</span> <span class="nf">_getSpecificationList</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">trajectory_generator</span><span class="p">,</span> <span class="n">steps</span><span class="p">):</span>
<span class="n">first</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">first</span>
<span class="n">last</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">last</span>
<span class="k">if</span> <span class="n">first</span> <span class="o"><</span> <span class="mi">0</span><span class="p">:</span>
<span class="n">first</span> <span class="o">=</span> <span class="n">first</span> <span class="o">+</span> <span class="n">steps</span>
<span class="k">if</span> <span class="n">last</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="kn">import</span> <span class="nn">MMTK_trajectory</span>
<span class="n">last</span> <span class="o">=</span> <span class="n">MMTK_trajectory</span><span class="o">.</span><span class="n">maxint</span>
<span class="k">elif</span> <span class="n">last</span> <span class="o"><</span> <span class="mi">0</span><span class="p">:</span>
<span class="n">last</span> <span class="o">=</span> <span class="n">last</span> <span class="o">+</span> <span class="n">steps</span><span class="o">+</span><span class="mi">1</span>
<span class="k">return</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">spec_type</span><span class="p">,</span> <span class="n">first</span><span class="p">,</span> <span class="n">last</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">skip</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">getSpecificationList</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">trajectory_generator</span><span class="p">,</span> <span class="n">steps</span><span class="p">):</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_getSpecificationList</span><span class="p">(</span><span class="n">trajectory_generator</span><span class="p">,</span> <span class="n">steps</span><span class="p">)</span> \
<span class="o">+</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">Cfunction</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">parameters</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">cleanup</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">pass</span>
</div>
<div class="viewcode-block" id="TrajectoryOutput"><a class="viewcode-back" href="../../modules.html#MMTK.Trajectory.TrajectoryOutput">[docs]</a><span class="k">class</span> <span class="nc">TrajectoryOutput</span><span class="p">(</span><span class="n">TrajectoryAction</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Trajectory output action</span>
<span class="sd"> A TrajectoryOutput object can be used in the action list of any</span>
<span class="sd"> trajectory-generating operation. It writes any of the available</span>
<span class="sd"> data to a trajectory file. It is possible to use several</span>
<span class="sd"> TrajectoryOutput objects at the same time in order to produce</span>
<span class="sd"> multiple trajectories from a single run.</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">trajectory</span><span class="p">,</span> <span class="n">data</span> <span class="o">=</span> <span class="bp">None</span><span class="p">,</span>
<span class="n">first</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="n">last</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">skip</span><span class="o">=</span><span class="mi">1</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :param trajectory: a trajectory object or a string, which is</span>
<span class="sd"> interpreted as the name of a file that is opened</span>
<span class="sd"> as a trajectory in append mode</span>
<span class="sd"> :param data: a list of data categories. All variables provided by the</span>
<span class="sd"> trajectory generator that fall in any of the listed</span>
<span class="sd"> categories are written to the trajectory file. See the</span>
<span class="sd"> descriptions of the trajectory generators for a list</span>
<span class="sd"> of variables and categories. By default (data = None)</span>
<span class="sd"> the categories "configuration", "energy",</span>
<span class="sd"> "thermodynamic", and "time" are written.</span>
<span class="sd"> :param first: the number of the first step at which the action is run</span>
<span class="sd"> :type first: int</span>
<span class="sd"> :param last: the number of the step at which the action is suspended.</span>
<span class="sd"> A value of None indicates that the action should</span>
<span class="sd"> be applied indefinitely.</span>
<span class="sd"> :type last: int</span>
<span class="sd"> :param skip: the number of steps to skip between two action runs</span>
<span class="sd"> :type skip: int</span>
<span class="sd"> """</span>
<span class="n">TrajectoryAction</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">first</span><span class="p">,</span> <span class="n">last</span><span class="p">,</span> <span class="n">skip</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">destination</span> <span class="o">=</span> <span class="n">trajectory</span>
<span class="bp">self</span><span class="o">.</span><span class="n">categories</span> <span class="o">=</span> <span class="n">data</span>
<span class="bp">self</span><span class="o">.</span><span class="n">must_be_closed</span> <span class="o">=</span> <span class="bp">None</span>
<span class="n">spec_type</span> <span class="o">=</span> <span class="s">'trajectory'</span>
<span class="k">def</span> <span class="nf">getSpecificationList</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">trajectory_generator</span><span class="p">,</span> <span class="n">steps</span><span class="p">):</span>
<span class="k">if</span> <span class="nb">type</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">destination</span><span class="p">)</span> <span class="o">==</span> <span class="nb">type</span><span class="p">(</span><span class="s">''</span><span class="p">):</span>
<span class="n">destination</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_setupDestination</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">destination</span><span class="p">,</span>
<span class="n">trajectory_generator</span><span class="o">.</span><span class="n">universe</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">destination</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">destination</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">categories</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">categories</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_defaultCategories</span><span class="p">(</span><span class="n">trajectory_generator</span><span class="p">)</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">categories</span> <span class="o">==</span> <span class="s">'all'</span> <span class="ow">or</span> <span class="bp">self</span><span class="o">.</span><span class="n">categories</span> <span class="o">==</span> <span class="p">[</span><span class="s">'all'</span><span class="p">]:</span>
<span class="n">categories</span> <span class="o">=</span> <span class="n">trajectory_generator</span><span class="o">.</span><span class="n">available_data</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">categories</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">categories</span>
<span class="k">for</span> <span class="n">item</span> <span class="ow">in</span> <span class="n">categories</span><span class="p">:</span>
<span class="k">if</span> <span class="n">item</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">trajectory_generator</span><span class="o">.</span><span class="n">available_data</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s">'data item </span><span class="si">%s</span><span class="s"> is not available'</span> <span class="o">%</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">_getSpecificationList</span><span class="p">(</span><span class="n">trajectory_generator</span><span class="p">,</span> <span class="n">steps</span><span class="p">)</span> \
<span class="o">+</span> <span class="p">(</span><span class="n">destination</span><span class="p">,</span> <span class="n">categories</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">_setupDestination</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">destination</span><span class="p">,</span> <span class="n">universe</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">must_be_closed</span> <span class="o">=</span> <span class="n">Trajectory</span><span class="p">(</span><span class="n">universe</span><span class="p">,</span> <span class="n">destination</span><span class="p">,</span> <span class="s">'a'</span><span class="p">)</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">must_be_closed</span>
<span class="k">def</span> <span class="nf">cleanup</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">must_be_closed</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">must_be_closed</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
<span class="k">def</span> <span class="nf">_defaultCategories</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">trajectory_generator</span><span class="p">):</span>
<span class="n">available</span> <span class="o">=</span> <span class="n">trajectory_generator</span><span class="o">.</span><span class="n">available_data</span>
<span class="k">return</span> <span class="nb">tuple</span><span class="p">(</span><span class="nb">filter</span><span class="p">(</span><span class="k">lambda</span> <span class="n">x</span><span class="p">,</span> <span class="n">a</span><span class="o">=</span><span class="n">available</span><span class="p">:</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">a</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">default_data</span><span class="p">))</span>
<span class="n">default_data</span> <span class="o">=</span> <span class="p">[</span><span class="s">'configuration'</span><span class="p">,</span> <span class="s">'energy'</span><span class="p">,</span> <span class="s">'thermodynamic'</span><span class="p">,</span> <span class="s">'time'</span><span class="p">]</span>
</div>
<div class="viewcode-block" id="RestartTrajectoryOutput"><a class="viewcode-back" href="../../modules.html#MMTK.Trajectory.RestartTrajectoryOutput">[docs]</a><span class="k">class</span> <span class="nc">RestartTrajectoryOutput</span><span class="p">(</span><span class="n">TrajectoryOutput</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Restart trajectory output action</span>
<span class="sd"> A RestartTrajectoryOutput object is used in the action list of any</span>
<span class="sd"> trajectory-generating operation. It writes those variables to a</span>
<span class="sd"> trajectory that the trajectory generator declares as necessary</span>
<span class="sd"> for restarting.</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">trajectory</span><span class="p">,</span> <span class="n">skip</span><span class="o">=</span><span class="mi">100</span><span class="p">,</span> <span class="n">length</span><span class="o">=</span><span class="mi">3</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :param trajectory: a trajectory object or a string, which is interpreted</span>
<span class="sd"> as the name of a file that is opened as a trajectory</span>
<span class="sd"> in append mode with a cycle length of length and</span>
<span class="sd"> double-precision variables</span>
<span class="sd"> :param skip: the number of steps between two write operations to the</span>
<span class="sd"> restart trajectory</span>
<span class="sd"> :type skip: int</span>
<span class="sd"> :param length: the number of steps stored in the restart trajectory;</span>
<span class="sd"> used only if trajectory is a string</span>
<span class="sd"> """</span>
<span class="n">TrajectoryAction</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="mi">0</span><span class="p">,</span> <span class="bp">None</span><span class="p">,</span> <span class="n">skip</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">destination</span> <span class="o">=</span> <span class="n">trajectory</span>
<span class="bp">self</span><span class="o">.</span><span class="n">categories</span> <span class="o">=</span> <span class="bp">None</span>
<span class="bp">self</span><span class="o">.</span><span class="n">length</span> <span class="o">=</span> <span class="n">length</span>
<span class="k">def</span> <span class="nf">_setupDestination</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">destination</span><span class="p">,</span> <span class="n">universe</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">must_be_closed</span> <span class="o">=</span> <span class="n">Trajectory</span><span class="p">(</span><span class="n">universe</span><span class="p">,</span> <span class="n">destination</span><span class="p">,</span> <span class="s">'a'</span><span class="p">,</span>
<span class="s">'Restart trajectory'</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">length</span><span class="p">)</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">must_be_closed</span>
<span class="k">def</span> <span class="nf">_defaultCategories</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">trajectory_generator</span><span class="p">):</span>
<span class="k">if</span> <span class="n">trajectory_generator</span><span class="o">.</span><span class="n">restart_data</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">"Trajectory generator does not permit restart"</span><span class="p">)</span>
<span class="k">return</span> <span class="n">trajectory_generator</span><span class="o">.</span><span class="n">restart_data</span>
</div>
<div class="viewcode-block" id="LogOutput"><a class="viewcode-back" href="../../modules.html#MMTK.Trajectory.LogOutput">[docs]</a><span class="k">class</span> <span class="nc">LogOutput</span><span class="p">(</span><span class="n">TrajectoryOutput</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Protocol file output action</span>
<span class="sd"> A LogOutput object can be used in the action list of any</span>
<span class="sd"> trajectory-generating operation. It writes any of the available</span>
<span class="sd"> data to a text file.</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="nb">file</span><span class="p">,</span> <span class="n">data</span> <span class="o">=</span> <span class="bp">None</span><span class="p">,</span> <span class="n">first</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="n">last</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">skip</span><span class="o">=</span><span class="mi">1</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :param file: a file object or a string, which is interpreted as the</span>
<span class="sd"> name of a file that is opened in write mode</span>
<span class="sd"> :param data: a list of data categories. All variables provided by the</span>
<span class="sd"> trajectory generator that fall in any of the listed</span>
<span class="sd"> categories are written to the trajectory file. See the</span>
<span class="sd"> descriptions of the trajectory generators for a list</span>
<span class="sd"> of variables and categories. By default (data = None)</span>
<span class="sd"> the categories "configuration", "energy",</span>
<span class="sd"> "thermodynamic", and "time" are written.</span>
<span class="sd"> :param first: the number of the first step at which the action is run</span>
<span class="sd"> :type first: int</span>
<span class="sd"> :param last: the number of the step at which the action is suspended.</span>
<span class="sd"> A value of None indicates that the action should</span>
<span class="sd"> be applied indefinitely.</span>
<span class="sd"> :type last: int</span>
<span class="sd"> :param skip: the number of steps to skip between two action runs</span>
<span class="sd"> :type skip: int</span>
<span class="sd"> """</span>
<span class="n">TrajectoryOutput</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="nb">file</span><span class="p">,</span> <span class="n">data</span><span class="p">,</span> <span class="n">first</span><span class="p">,</span> <span class="n">last</span><span class="p">,</span> <span class="n">skip</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">_setupDestination</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">destination</span><span class="p">,</span> <span class="n">universe</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">must_be_closed</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">destination</span><span class="p">,</span> <span class="s">'w'</span><span class="p">)</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">must_be_closed</span>
<span class="n">spec_type</span> <span class="o">=</span> <span class="s">'print'</span>
<span class="n">default_data</span> <span class="o">=</span> <span class="p">[</span><span class="s">'energy'</span><span class="p">,</span> <span class="s">'time'</span><span class="p">]</span>
</div>
<div class="viewcode-block" id="StandardLogOutput"><a class="viewcode-back" href="../../modules.html#MMTK.Trajectory.StandardLogOutput">[docs]</a><span class="k">class</span> <span class="nc">StandardLogOutput</span><span class="p">(</span><span class="n">LogOutput</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Standard protocol output action</span>
<span class="sd"> A StandardLogOutput object can be used in the action list of any</span>
<span class="sd"> trajectory-generating operation. It is a specialization of</span>
<span class="sd"> LogOutput to the most common case and writes data in the categories</span>
<span class="sd"> "time" and "energy" to the standard output stream.</span>
<span class="sd"> :param skip: the number of steps to skip between two action runs</span>
<span class="sd"> :type skip: int</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">skip</span><span class="o">=</span><span class="mi">50</span><span class="p">):</span>
<span class="n">LogOutput</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">sys</span><span class="o">.</span><span class="n">stdout</span><span class="p">,</span> <span class="bp">None</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="bp">None</span><span class="p">,</span> <span class="n">skip</span><span class="p">)</span>
<span class="c">#</span>
<span class="c"># Snapshot generator</span>
<span class="c">#</span></div>
<div class="viewcode-block" id="SnapshotGenerator"><a class="viewcode-back" href="../../modules.html#MMTK.Trajectory.SnapshotGenerator">[docs]</a><span class="k">class</span> <span class="nc">SnapshotGenerator</span><span class="p">(</span><span class="n">TrajectoryGenerator</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Trajectory generator for single steps</span>
<span class="sd"> A SnapshotGenerator is used for manual assembly of trajectory</span>
<span class="sd"> files. At each call it writes one step to the trajectory,</span>
<span class="sd"> using the current state of the universe (configuration, velocities, etc.)</span>
<span class="sd"> and data provided explicitly with the call.</span>
<span class="sd"> Each call to the SnapshotGenerator object produces one step.</span>
<span class="sd"> All the keyword options can be specified either when</span>
<span class="sd"> creating the generator or when calling it.</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">universe</span><span class="p">,</span> <span class="o">**</span><span class="n">options</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :param universe: the universe on which the generator acts</span>
<span class="sd"> :keyword data: a dictionary that supplies values for variables</span>
<span class="sd"> that are not part of the universe state</span>
<span class="sd"> (e.g. potential energy)</span>
<span class="sd"> :keyword actions: a list of actions to be executed periodically</span>
<span class="sd"> (default is none)</span>
<span class="sd"> """</span>
<span class="n">TrajectoryGenerator</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">universe</span><span class="p">,</span> <span class="n">options</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">available_data</span> <span class="o">=</span> <span class="p">[]</span>
<span class="k">try</span><span class="p">:</span>
<span class="n">e</span><span class="p">,</span> <span class="n">g</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">universe</span><span class="o">.</span><span class="n">energyAndGradients</span><span class="p">()</span>
<span class="k">except</span><span class="p">:</span> <span class="k">pass</span>
<span class="k">else</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">available_data</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s">'energy'</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">available_data</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s">'gradients'</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">universe</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">available_data</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s">'configuration'</span><span class="p">)</span>
<span class="k">except</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">universe</span><span class="o">.</span><span class="n">cellVolume</span><span class="p">()</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">available_data</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s">'thermodynamic'</span><span class="p">)</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">universe</span><span class="o">.</span><span class="n">velocities</span><span class="p">()</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">available_data</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s">'velocities'</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">available_data</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s">'energy'</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">available_data</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s">'thermodynamic'</span><span class="p">)</span>
<span class="n">default_options</span> <span class="o">=</span> <span class="p">{</span><span class="s">'steps'</span><span class="p">:</span> <span class="mi">0</span><span class="p">,</span> <span class="s">'actions'</span><span class="p">:</span> <span class="p">[]}</span>
<span class="k">def</span> <span class="nf">__call__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">options</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">setCallOptions</span><span class="p">(</span><span class="n">options</span><span class="p">)</span>
<span class="kn">from</span> <span class="nn">MMTK_trajectory</span> <span class="kn">import</span> <span class="n">snapshot</span>
<span class="n">data</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="n">options</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s">'data'</span><span class="p">,</span> <span class="p">{}))</span>
<span class="n">energy_terms</span> <span class="o">=</span> <span class="mi">0</span>
<span class="k">for</span> <span class="n">name</span> <span class="ow">in</span> <span class="n">data</span><span class="o">.</span><span class="n">keys</span><span class="p">():</span>
<span class="k">if</span> <span class="n">name</span> <span class="o">==</span> <span class="s">'time'</span> <span class="ow">and</span> <span class="s">'time'</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">available_data</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">available_data</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s">'time'</span><span class="p">)</span>
<span class="k">if</span> <span class="n">name</span><span class="p">[</span><span class="o">-</span><span class="mi">7</span><span class="p">:]</span> <span class="o">==</span> <span class="s">'_energy'</span><span class="p">:</span>
<span class="n">energy_terms</span> <span class="o">=</span> <span class="n">energy_terms</span> <span class="o">+</span> <span class="mi">1</span>
<span class="k">if</span> <span class="s">'energy'</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">available_data</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">available_data</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s">'energy'</span><span class="p">)</span>
<span class="k">if</span> <span class="p">(</span><span class="n">name</span> <span class="o">==</span> <span class="s">'temperature'</span> <span class="ow">or</span> <span class="n">name</span> <span class="o">==</span> <span class="s">'pressure'</span><span class="p">)</span> \
<span class="ow">and</span> <span class="s">'thermodynamic'</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">available_data</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">available_data</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s">'thermodynamic'</span><span class="p">)</span>
<span class="k">if</span> <span class="n">name</span> <span class="o">==</span> <span class="s">'gradients'</span> <span class="ow">and</span> <span class="s">'gradients'</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">available_data</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">available_data</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s">'gradients'</span><span class="p">)</span>
<span class="n">actions</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">getActions</span><span class="p">()</span>
<span class="k">for</span> <span class="n">action</span> <span class="ow">in</span> <span class="n">actions</span><span class="p">:</span>
<span class="n">categories</span> <span class="o">=</span> <span class="n">action</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span>
<span class="k">for</span> <span class="n">c</span> <span class="ow">in</span> <span class="n">categories</span><span class="p">:</span>
<span class="k">if</span> <span class="n">c</span> <span class="o">==</span> <span class="s">'energy'</span> <span class="ow">and</span> <span class="ow">not</span> <span class="n">data</span><span class="o">.</span><span class="n">has_key</span><span class="p">(</span><span class="s">'kinetic_energy'</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">universe</span><span class="o">.</span><span class="n">velocities</span><span class="p">()</span>
<span class="k">if</span> <span class="n">v</span> <span class="ow">is</span> <span class="ow">not</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">universe</span><span class="o">.</span><span class="n">masses</span><span class="p">()</span>
<span class="n">e</span> <span class="o">=</span> <span class="p">(</span><span class="n">v</span><span class="o">*</span><span class="n">v</span><span class="o">*</span><span class="n">m</span><span class="o">*</span><span class="mf">0.5</span><span class="p">)</span><span class="o">.</span><span class="n">sumOverParticles</span><span class="p">()</span>
<span class="n">data</span><span class="p">[</span><span class="s">'kinetic_energy'</span><span class="p">]</span> <span class="o">=</span> <span class="n">e</span>
<span class="n">df</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">universe</span><span class="o">.</span><span class="n">degreesOfFreedom</span><span class="p">()</span>
<span class="n">data</span><span class="p">[</span><span class="s">'temperature'</span><span class="p">]</span> <span class="o">=</span> <span class="mf">2.</span><span class="o">*</span><span class="n">e</span><span class="o">/</span><span class="n">df</span><span class="o">/</span><span class="n">Units</span><span class="o">.</span><span class="n">k_B</span><span class="o">/</span><span class="n">Units</span><span class="o">.</span><span class="n">K</span>
<span class="k">if</span> <span class="n">c</span> <span class="o">==</span> <span class="s">'configuration'</span><span class="p">:</span>
<span class="k">if</span> <span class="n">data</span><span class="o">.</span><span class="n">has_key</span><span class="p">(</span><span class="s">'configuration'</span><span class="p">):</span>
<span class="n">data</span><span class="p">[</span><span class="s">'configuration'</span><span class="p">]</span> <span class="o">=</span> <span class="n">data</span><span class="p">[</span><span class="s">'configuration'</span><span class="p">]</span><span class="o">.</span><span class="n">array</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">data</span><span class="p">[</span><span class="s">'configuration'</span><span class="p">]</span> <span class="o">=</span> \
<span class="bp">self</span><span class="o">.</span><span class="n">universe</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="k">if</span> <span class="n">c</span> <span class="o">==</span> <span class="s">'velocities'</span><span class="p">:</span>
<span class="k">if</span> <span class="n">data</span><span class="o">.</span><span class="n">has_key</span><span class="p">(</span><span class="s">'velocities'</span><span class="p">):</span>
<span class="n">data</span><span class="p">[</span><span class="s">'velocities'</span><span class="p">]</span> <span class="o">=</span> <span class="n">data</span><span class="p">[</span><span class="s">'velocities'</span><span class="p">]</span><span class="o">.</span><span class="n">array</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">data</span><span class="p">[</span><span class="s">'velocities'</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">universe</span><span class="o">.</span><span class="n">velocities</span><span class="p">()</span><span class="o">.</span><span class="n">array</span>
<span class="k">if</span> <span class="n">c</span> <span class="o">==</span> <span class="s">'gradients'</span><span class="p">:</span>
<span class="k">if</span> <span class="n">data</span><span class="o">.</span><span class="n">has_key</span><span class="p">(</span><span class="s">'gradients'</span><span class="p">):</span>
<span class="n">data</span><span class="p">[</span><span class="s">'gradients'</span><span class="p">]</span> <span class="o">=</span> <span class="n">data</span><span class="p">[</span><span class="s">'gradients'</span><span class="p">]</span><span class="o">.</span><span class="n">array</span>
<span class="n">p</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">universe</span><span class="o">.</span><span class="n">cellParameters</span><span class="p">()</span>
<span class="k">if</span> <span class="n">p</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">data</span><span class="p">[</span><span class="s">'box_size'</span><span class="p">]</span> <span class="o">=</span> <span class="n">p</span>
<span class="n">volume</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">universe</span><span class="o">.</span><span class="n">cellVolume</span><span class="p">()</span>
<span class="k">if</span> <span class="n">volume</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">data</span><span class="p">[</span><span class="s">'volume'</span><span class="p">]</span> <span class="o">=</span> <span class="n">volume</span>
<span class="k">try</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">universe</span><span class="o">.</span><span class="n">masses</span><span class="p">()</span>
<span class="n">data</span><span class="p">[</span><span class="s">'masses'</span><span class="p">]</span> <span class="o">=</span> <span class="n">m</span><span class="o">.</span><span class="n">array</span>
<span class="k">except</span><span class="p">:</span> <span class="k">pass</span>
<span class="n">snapshot</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">universe</span><span class="p">,</span> <span class="n">data</span><span class="p">,</span> <span class="n">actions</span><span class="p">,</span> <span class="n">energy_terms</span><span class="p">)</span>
<span class="c">#</span>
<span class="c"># Trajectory reader (not yet functional...)</span>
<span class="c">#</span></div>
<span class="k">if</span> <span class="bp">False</span><span class="p">:</span>
<span class="k">class</span> <span class="nc">TrajectoryReader</span><span class="p">(</span><span class="n">TrajectoryGenerator</span><span class="p">):</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">trajectory</span><span class="p">,</span> <span class="n">options</span><span class="p">):</span>
<span class="n">TrajectoryGenerator</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">trajectory</span><span class="o">.</span><span class="n">universe</span><span class="p">,</span> <span class="n">options</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">input</span> <span class="o">=</span> <span class="n">trajectory</span>
<span class="bp">self</span><span class="o">.</span><span class="n">available_data</span> <span class="o">=</span> <span class="n">trajectory</span><span class="o">.</span><span class="n">variables</span><span class="p">()</span>
<span class="n">default_options</span> <span class="o">=</span> <span class="p">{</span><span class="s">'trajectory'</span><span class="p">:</span> <span class="bp">None</span><span class="p">,</span> <span class="s">'log'</span><span class="p">:</span> <span class="bp">None</span><span class="p">,</span> <span class="s">'options'</span><span class="p">:</span> <span class="p">[]}</span>
<span class="k">def</span> <span class="nf">__call__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">options</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">setCallOptions</span><span class="p">(</span><span class="n">options</span><span class="p">)</span>
<span class="kn">from</span> <span class="nn">MMTK_trajectory</span> <span class="kn">import</span> <span class="n">readTrajectory</span>
<span class="n">readTrajectory</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">universe</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">input</span><span class="o">.</span><span class="n">trajectory</span><span class="p">,</span>
<span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">getOption</span><span class="p">(</span><span class="s">'trajectory'</span><span class="p">),</span>
<span class="bp">self</span><span class="o">.</span><span class="n">getOption</span><span class="p">(</span><span class="s">'log'</span><span class="p">)]</span> <span class="o">+</span>
<span class="bp">self</span><span class="o">.</span><span class="n">getOption</span><span class="p">(</span><span class="s">'options'</span><span class="p">))</span>
<span class="c">#</span>
<span class="c"># Print information about trajectory file</span>
<span class="c">#</span>
<div class="viewcode-block" id="trajectoryInfo"><a class="viewcode-back" href="../../modules.html#MMTK.Trajectory.trajectoryInfo">[docs]</a><span class="k">def</span> <span class="nf">trajectoryInfo</span><span class="p">(</span><span class="n">filename</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> :param filename: the name of a trajectory file</span>
<span class="sd"> :type filename: str</span>
<span class="sd"> :returns: a string with summarial information about the trajectory</span>
<span class="sd"> """</span>
<span class="kn">from</span> <span class="nn">Scientific.IO</span> <span class="kn">import</span> <span class="n">NetCDF</span>
<span class="nb">file</span> <span class="o">=</span> <span class="n">NetCDF</span><span class="o">.</span><span class="n">NetCDFFile</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="s">'r'</span><span class="p">)</span>
<span class="n">nsteps</span> <span class="o">=</span> <span class="nb">file</span><span class="o">.</span><span class="n">variables</span><span class="p">[</span><span class="s">'step'</span><span class="p">]</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
<span class="k">if</span> <span class="s">'minor_step_number'</span> <span class="ow">in</span> <span class="nb">file</span><span class="o">.</span><span class="n">dimensions</span><span class="o">.</span><span class="n">keys</span><span class="p">():</span>
<span class="n">nsteps</span> <span class="o">=</span> <span class="n">nsteps</span><span class="o">*</span><span class="nb">file</span><span class="o">.</span><span class="n">variables</span><span class="p">[</span><span class="s">'step'</span><span class="p">]</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
<span class="n">s</span> <span class="o">=</span> <span class="s">'Information about trajectory file '</span> <span class="o">+</span> <span class="n">filename</span> <span class="o">+</span> <span class="s">':</span><span class="se">\n</span><span class="s">'</span>
<span class="k">try</span><span class="p">:</span>
<span class="n">s</span> <span class="o">+=</span> <span class="nb">file</span><span class="o">.</span><span class="n">comment</span> <span class="o">+</span> <span class="s">'</span><span class="se">\n</span><span class="s">'</span>
<span class="k">except</span> <span class="ne">AttributeError</span><span class="p">:</span>
<span class="k">pass</span>
<span class="n">s</span> <span class="o">+=</span> <span class="sb">`file.dimensions['atom_number']`</span> <span class="o">+</span> <span class="s">' atoms</span><span class="se">\n</span><span class="s">'</span>
<span class="n">s</span> <span class="o">+=</span> <span class="sb">`nsteps`</span> <span class="o">+</span> <span class="s">' steps</span><span class="se">\n</span><span class="s">'</span>
<span class="n">s</span> <span class="o">+=</span> <span class="nb">file</span><span class="o">.</span><span class="n">history</span>
<span class="nb">file</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
<span class="k">return</span> <span class="n">s</span></div>
</pre></div>
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