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<h1>Source code for MMTK.Dynamics</h1><div class="highlight"><pre>
<span class="c"># This module implements MD integrators</span>
<span class="c">#</span>
<span class="c"># Written by Konrad Hinsen</span>
<span class="c">#</span>
<span class="sd">"""</span>
<span class="sd">Molecular Dynamics integrators</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">Environment</span><span class="p">,</span> <span class="n">Features</span><span class="p">,</span> <span class="n">Trajectory</span><span class="p">,</span> <span class="n">Units</span>
<span class="kn">import</span> <span class="nn">MMTK_dynamics</span>
<span class="kn">from</span> <span class="nn">Scientific</span> <span class="kn">import</span> <span class="n">N</span>
<span class="c">#</span>
<span class="c"># Integrator base class</span>
<span class="c">#</span>
<span class="k">class</span> <span class="nc">Integrator</span><span class="p">(</span><span class="n">Trajectory</span><span class="o">.</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">universe</span><span class="p">,</span> <span class="n">options</span><span class="p">):</span>
<span class="n">Trajectory</span><span class="o">.</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="n">default_options</span> <span class="o">=</span> <span class="p">{</span><span class="s">'first_step'</span><span class="p">:</span> <span class="mi">0</span><span class="p">,</span> <span class="s">'steps'</span><span class="p">:</span> <span class="mi">100</span><span class="p">,</span> <span class="s">'delta_t'</span><span class="p">:</span> <span class="mf">1.</span><span class="o">*</span><span class="n">Units</span><span class="o">.</span><span class="n">fs</span><span class="p">,</span>
<span class="s">'background'</span><span class="p">:</span> <span class="bp">False</span><span class="p">,</span> <span class="s">'threads'</span><span class="p">:</span> <span class="bp">None</span><span class="p">,</span>
<span class="s">'mpi_communicator'</span><span class="p">:</span> <span class="bp">None</span><span class="p">,</span> <span class="s">'actions'</span><span class="p">:</span> <span class="p">[]}</span>
<span class="n">available_data</span> <span class="o">=</span> <span class="p">[</span><span class="s">'configuration'</span><span class="p">,</span> <span class="s">'velocities'</span><span class="p">,</span> <span class="s">'gradients'</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> <span class="s">'auxiliary'</span><span class="p">]</span>
<span class="n">restart_data</span> <span class="o">=</span> <span class="p">[</span><span class="s">'configuration'</span><span class="p">,</span> <span class="s">'velocities'</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">'auxiliary'</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="n">options</span><span class="p">):</span>
<span class="k">raise</span> <span class="ne">AttributeError</span>
<span class="c">#</span>
<span class="c"># Velocity-Verlet integrator</span>
<span class="c">#</span>
<div class="viewcode-block" id="VelocityVerletIntegrator"><a class="viewcode-back" href="../../modules.html#MMTK.Dynamics.VelocityVerletIntegrator">[docs]</a><span class="k">class</span> <span class="nc">VelocityVerletIntegrator</span><span class="p">(</span><span class="n">Integrator</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Velocity-Verlet molecular dynamics integrator</span>
<span class="sd"> The integrator can handle fixed atoms, distance constraints,</span>
<span class="sd"> a thermostat, and a barostat, as well as any combination.</span>
<span class="sd"> It is fully thread-safe.</span>
<span class="sd"> The integration is started by calling the integrator object.</span>
<span class="sd"> All the keyword options (see documnentation of __init__) can be</span>
<span class="sd"> specified either when creating the integrator or when calling it.</span>
<span class="sd"> The following data categories and variables are available for</span>
<span class="sd"> output:</span>
<span class="sd"> - category "time": time</span>
<span class="sd"> - category "configuration": configuration and box size (for</span>
<span class="sd"> periodic universes)</span>
<span class="sd"> - category "velocities": atomic velocities</span>
<span class="sd"> - category "gradients": energy gradients for each atom</span>
<span class="sd"> - category "energy": potential and kinetic energy, plus</span>
<span class="sd"> extended-system energy terms if a thermostat and/or barostat</span>
<span class="sd"> are used</span>
<span class="sd"> - category "thermodynamic": temperature, volume (if a barostat</span>
<span class="sd"> is used) and pressure</span>
<span class="sd"> - category "auxiliary": extended-system coordinates if a thermostat</span>
<span class="sd"> and/or barostat are used</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 integrator acts</span>
<span class="sd"> :type universe: :class:`~MMTK.Universe.Universe`</span>
<span class="sd"> :keyword steps: the number of integration steps (default is 100)</span>
<span class="sd"> :type steps: int</span>
<span class="sd"> :keyword delta_t: the time step (default is 1 fs)</span>
<span class="sd"> :type delta_t: float</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"> :type actions: list</span>
<span class="sd"> :keyword threads: the number of threads to use in energy evaluation</span>
<span class="sd"> (default set by MMTK_ENERGY_THREADS)</span>
<span class="sd"> :type threads: int</span>
<span class="sd"> :keyword background: if True, the integration is executed as a</span>
<span class="sd"> separate thread (default: False)</span>
<span class="sd"> :type background: bool</span>
<span class="sd"> :keyword mpi_communicator: an MPI communicator object, or None,</span>
<span class="sd"> meaning no parallelization (default: None)</span>
<span class="sd"> :type mpi_communicator: Scientific.MPI.MPICommunicator</span>
<span class="sd"> """</span>
<span class="n">Integrator</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">features</span> <span class="o">=</span> <span class="p">[</span><span class="n">Features</span><span class="o">.</span><span class="n">FixedParticleFeature</span><span class="p">,</span>
<span class="n">Features</span><span class="o">.</span><span class="n">NoseThermostatFeature</span><span class="p">,</span>
<span class="n">Features</span><span class="o">.</span><span class="n">AndersenBarostatFeature</span><span class="p">,</span>
<span class="n">Features</span><span class="o">.</span><span class="n">DistanceConstraintsFeature</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="sd">"""</span>
<span class="sd"> Run the integrator. The keyword options are the same as described</span>
<span class="sd"> under __init__.</span>
<span class="sd"> """</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="n">used_features</span> <span class="o">=</span> <span class="n">Features</span><span class="o">.</span><span class="n">checkFeatures</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">universe</span><span class="p">)</span>
<span class="n">configuration</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="n">velocities</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">velocities</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s">"no velocities"</span><span class="p">)</span>
<span class="n">masses</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">universe</span><span class="o">.</span><span class="n">masses</span><span class="p">()</span>
<span class="n">fixed</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">universe</span><span class="o">.</span><span class="n">getAtomBooleanArray</span><span class="p">(</span><span class="s">'fixed'</span><span class="p">)</span>
<span class="n">nt</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">'threads'</span><span class="p">)</span>
<span class="n">comm</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">'mpi_communicator'</span><span class="p">)</span>
<span class="n">evaluator</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">energyEvaluator</span><span class="p">(</span><span class="n">threads</span><span class="o">=</span><span class="n">nt</span><span class="p">,</span>
<span class="n">mpi_communicator</span><span class="o">=</span><span class="n">comm</span><span class="p">)</span>
<span class="n">evaluator</span> <span class="o">=</span> <span class="n">evaluator</span><span class="o">.</span><span class="n">CEvaluator</span><span class="p">()</span>
<span class="n">constraints</span><span class="p">,</span> <span class="n">const_distances_sq</span><span class="p">,</span> <span class="n">c_blocks</span> <span class="o">=</span> \
<span class="n">_constraintArrays</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">type</span> <span class="o">=</span> <span class="s">'NVE'</span>
<span class="k">if</span> <span class="n">Features</span><span class="o">.</span><span class="n">NoseThermostatFeature</span> <span class="ow">in</span> <span class="n">used_features</span><span class="p">:</span>
<span class="nb">type</span> <span class="o">=</span> <span class="s">'NVT'</span>
<span class="n">thermostat</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">environmentObjectList</span><span class="p">(</span>
<span class="n">Environment</span><span class="o">.</span><span class="n">NoseThermostat</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
<span class="n">t_parameters</span> <span class="o">=</span> <span class="n">thermostat</span><span class="o">.</span><span class="n">parameters</span>
<span class="n">t_coordinates</span> <span class="o">=</span> <span class="n">thermostat</span><span class="o">.</span><span class="n">coordinates</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">t_parameters</span> <span class="o">=</span> <span class="n">N</span><span class="o">.</span><span class="n">zeros</span><span class="p">((</span><span class="mi">0</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">t_coordinates</span> <span class="o">=</span> <span class="n">N</span><span class="o">.</span><span class="n">zeros</span><span class="p">((</span><span class="mi">2</span><span class="p">,),</span> <span class="n">N</span><span class="o">.</span><span class="n">Float</span><span class="p">)</span>
<span class="k">if</span> <span class="n">Features</span><span class="o">.</span><span class="n">AndersenBarostatFeature</span> <span class="ow">in</span> <span class="n">used_features</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">cellVolume</span><span class="p">()</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">"Barostat requires finite volume universe"</span><span class="p">)</span>
<span class="k">if</span> <span class="nb">type</span> <span class="o">==</span> <span class="s">'NVE'</span><span class="p">:</span>
<span class="nb">type</span> <span class="o">=</span> <span class="s">'NPH'</span>
<span class="k">else</span><span class="p">:</span>
<span class="nb">type</span> <span class="o">=</span> <span class="s">'NPT'</span>
<span class="n">barostat</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">environmentObjectList</span><span class="p">(</span>
<span class="n">Environment</span><span class="o">.</span><span class="n">AndersenBarostat</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
<span class="n">b_parameters</span> <span class="o">=</span> <span class="n">barostat</span><span class="o">.</span><span class="n">parameters</span>
<span class="n">b_coordinates</span> <span class="o">=</span> <span class="n">barostat</span><span class="o">.</span><span class="n">coordinates</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">b_parameters</span> <span class="o">=</span> <span class="n">N</span><span class="o">.</span><span class="n">zeros</span><span class="p">((</span><span class="mi">0</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">b_coordinates</span> <span class="o">=</span> <span class="n">N</span><span class="o">.</span><span class="n">zeros</span><span class="p">((</span><span class="mi">1</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">args</span> <span class="o">=</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">configuration</span><span class="o">.</span><span class="n">array</span><span class="p">,</span> <span class="n">velocities</span><span class="o">.</span><span class="n">array</span><span class="p">,</span>
<span class="n">masses</span><span class="o">.</span><span class="n">array</span><span class="p">,</span> <span class="n">fixed</span><span class="o">.</span><span class="n">array</span><span class="p">,</span> <span class="n">evaluator</span><span class="p">,</span>
<span class="n">constraints</span><span class="p">,</span> <span class="n">const_distances_sq</span><span class="p">,</span> <span class="n">c_blocks</span><span class="p">,</span>
<span class="n">t_parameters</span><span class="p">,</span> <span class="n">t_coordinates</span><span class="p">,</span>
<span class="n">b_parameters</span><span class="p">,</span> <span class="n">b_coordinates</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">'delta_t'</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">'first_step'</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">'steps'</span><span class="p">),</span> <span class="bp">self</span><span class="o">.</span><span class="n">getActions</span><span class="p">(),</span>
<span class="nb">type</span> <span class="o">+</span> <span class="s">' dynamics trajectory with '</span> <span class="o">+</span>
<span class="bp">self</span><span class="o">.</span><span class="n">optionString</span><span class="p">([</span><span class="s">'delta_t'</span><span class="p">,</span> <span class="s">'steps'</span><span class="p">]))</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">run</span><span class="p">(</span><span class="n">MMTK_dynamics</span><span class="o">.</span><span class="n">integrateVV</span><span class="p">,</span> <span class="n">args</span><span class="p">)</span>
<span class="c">#</span>
<span class="c"># Velocity scaling, removal of global translation/rotation</span>
<span class="c">#</span></div>
<div class="viewcode-block" id="VelocityScaler"><a class="viewcode-back" href="../../modules.html#MMTK.Dynamics.VelocityScaler">[docs]</a><span class="k">class</span> <span class="nc">VelocityScaler</span><span class="p">(</span><span class="n">Trajectory</span><span class="o">.</span><span class="n">TrajectoryAction</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Periodic velocity scaling action</span>
<span class="sd"> A VelocityScaler object is used in the action list of</span>
<span class="sd"> a VelocityVerletIntegrator. It rescales all atomic velocities</span>
<span class="sd"> by a common factor to make the temperature of the system equal</span>
<span class="sd"> to a predefined value.</span>
<span class="sd"> """</span>
<span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">temperature</span><span class="p">,</span> <span class="n">window</span><span class="o">=</span><span class="mf">0.</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 temperature: the temperature value to which the velocities</span>
<span class="sd"> should be scaled</span>
<span class="sd"> :type temperature: float</span>
<span class="sd"> :param window: the deviation from the ideal temperature that</span>
<span class="sd"> is tolerated in either direction before rescaling</span>
<span class="sd"> takes place</span>
<span class="sd"> :type window: float</span>
<span class="sd"> :param first: the number of the first step at which the action</span>
<span class="sd"> is executed</span>
<span class="sd"> :type first: int</span>
<span class="sd"> :param last: the number of the first step at which the action</span>
<span class="sd"> is no longer executed. A value of None indicates</span>
<span class="sd"> that the action should be executed indefinitely.</span>
<span class="sd"> :type last: int</span>
<span class="sd"> :param skip: the number of steps to skip between two applications</span>
<span class="sd"> of the action</span>
<span class="sd"> :type skip: int</span>
<span class="sd"> """</span>
<span class="n">Trajectory</span><span class="o">.</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">parameters</span> <span class="o">=</span> <span class="n">N</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="n">temperature</span><span class="p">,</span> <span class="n">window</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="bp">self</span><span class="o">.</span><span class="n">Cfunction</span> <span class="o">=</span> <span class="n">MMTK_dynamics</span><span class="o">.</span><span class="n">scaleVelocities</span>
</div>
<div class="viewcode-block" id="Heater"><a class="viewcode-back" href="../../modules.html#MMTK.Dynamics.Heater">[docs]</a><span class="k">class</span> <span class="nc">Heater</span><span class="p">(</span><span class="n">Trajectory</span><span class="o">.</span><span class="n">TrajectoryAction</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Periodic heating action</span>
<span class="sd"> A Heater object us used in the action list of a VelocityVerletIntegrator.</span>
<span class="sd"> It scales the velocities to a temperature that increases over time.</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">temp1</span><span class="p">,</span> <span class="n">temp2</span><span class="p">,</span> <span class="n">gradient</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 temp1: the temperature value to which the velocities</span>
<span class="sd"> should be scaled initially</span>
<span class="sd"> :type temp1: float</span>
<span class="sd"> :param temp2: the final temperature value to which the velocities</span>
<span class="sd"> should be scaled</span>
<span class="sd"> :type temp2: float</span>
<span class="sd"> :param gradient: the temperature gradient (in K/ps)</span>
<span class="sd"> :type gradient: float</span>
<span class="sd"> :param first: the number of the first step at which the action</span>
<span class="sd"> is executed</span>
<span class="sd"> :type first: int</span>
<span class="sd"> :param last: the number of the first step at which the action</span>
<span class="sd"> is no longer executed. A value of None indicates</span>
<span class="sd"> that the action should be executed indefinitely.</span>
<span class="sd"> :type last: int</span>
<span class="sd"> :param skip: the number of steps to skip between two applications</span>
<span class="sd"> of the action</span>
<span class="sd"> :type skip: int</span>
<span class="sd"> """</span>
<span class="n">Trajectory</span><span class="o">.</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">parameters</span> <span class="o">=</span> <span class="n">N</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="n">temp1</span><span class="p">,</span> <span class="n">temp2</span><span class="p">,</span> <span class="n">gradient</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="bp">self</span><span class="o">.</span><span class="n">Cfunction</span> <span class="o">=</span> <span class="n">MMTK_dynamics</span><span class="o">.</span><span class="n">heat</span>
</div>
<div class="viewcode-block" id="BarostatReset"><a class="viewcode-back" href="../../modules.html#MMTK.Dynamics.BarostatReset">[docs]</a><span class="k">class</span> <span class="nc">BarostatReset</span><span class="p">(</span><span class="n">Trajectory</span><span class="o">.</span><span class="n">TrajectoryAction</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Barostat reset action</span>
<span class="sd"> A BarostatReset object is used in the action list of a</span>
<span class="sd"> VelocityVerletIntegrator. It resets the barostat coordinate</span>
<span class="sd"> to zero.</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="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 first: the number of the first step at which the action</span>
<span class="sd"> is executed</span>
<span class="sd"> :type first: int</span>
<span class="sd"> :param last: the number of the first step at which the action</span>
<span class="sd"> is no longer executed. A value of None indicates</span>
<span class="sd"> that the action should be executed indefinitely.</span>
<span class="sd"> :type last: int</span>
<span class="sd"> :param skip: the number of steps to skip between two applications</span>
<span class="sd"> of the action</span>
<span class="sd"> :type skip: int</span>
<span class="sd"> """</span>
<span class="n">Trajectory</span><span class="o">.</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">parameters</span> <span class="o">=</span> <span class="n">N</span><span class="o">.</span><span class="n">zeros</span><span class="p">((</span><span class="mi">0</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="bp">self</span><span class="o">.</span><span class="n">Cfunction</span> <span class="o">=</span> <span class="n">MMTK_dynamics</span><span class="o">.</span><span class="n">resetBarostat</span>
</div>
<div class="viewcode-block" id="TranslationRemover"><a class="viewcode-back" href="../../modules.html#MMTK.Dynamics.TranslationRemover">[docs]</a><span class="k">class</span> <span class="nc">TranslationRemover</span><span class="p">(</span><span class="n">Trajectory</span><span class="o">.</span><span class="n">TrajectoryAction</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Action that eliminates global translation</span>
<span class="sd"> A TranslationRemover object is used in the action list of a</span>
<span class="sd"> VelocityVerletIntegrator. It subtracts the total velocity</span>
<span class="sd"> of the system from each atomic velocity.</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="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 first: the number of the first step at which the action</span>
<span class="sd"> is executed</span>
<span class="sd"> :type first: int</span>
<span class="sd"> :param last: the number of the first step at which the action</span>
<span class="sd"> is no longer executed. A value of None indicates</span>
<span class="sd"> that the action should be executed indefinitely.</span>
<span class="sd"> :type last: int</span>
<span class="sd"> :param skip: the number of steps to skip between two applications</span>
<span class="sd"> of the action</span>
<span class="sd"> :type skip: int</span>
<span class="sd"> """</span>
<span class="n">Trajectory</span><span class="o">.</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">parameters</span> <span class="o">=</span> <span class="bp">None</span>
<span class="bp">self</span><span class="o">.</span><span class="n">Cfunction</span> <span class="o">=</span> <span class="n">MMTK_dynamics</span><span class="o">.</span><span class="n">removeTranslation</span>
</div>
<div class="viewcode-block" id="RotationRemover"><a class="viewcode-back" href="../../modules.html#MMTK.Dynamics.RotationRemover">[docs]</a><span class="k">class</span> <span class="nc">RotationRemover</span><span class="p">(</span><span class="n">Trajectory</span><span class="o">.</span><span class="n">TrajectoryAction</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Action that eliminates global rotation</span>
<span class="sd"> A RotationRemover object is used in the action list of a</span>
<span class="sd"> VelocityVerletIntegrator. It adjusts the atomic velocities</span>
<span class="sd"> such that the total angular momentum is zero.</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="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 first: the number of the first step at which the action</span>
<span class="sd"> is executed</span>
<span class="sd"> :type first: int</span>
<span class="sd"> :param last: the number of the first step at which the action</span>
<span class="sd"> is no longer executed. A value of None indicates</span>
<span class="sd"> that the action should be executed indefinitely.</span>
<span class="sd"> :type last: int</span>
<span class="sd"> :param skip: the number of steps to skip between two applications</span>
<span class="sd"> of the action</span>
<span class="sd"> :type skip: int</span>
<span class="sd"> """</span>
<span class="n">Trajectory</span><span class="o">.</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">parameters</span> <span class="o">=</span> <span class="bp">None</span>
<span class="bp">self</span><span class="o">.</span><span class="n">Cfunction</span> <span class="o">=</span> <span class="n">MMTK_dynamics</span><span class="o">.</span><span class="n">removeRotation</span>
<span class="c">#</span>
<span class="c"># Construct constraint arrays</span>
<span class="c">#</span></div>
<span class="k">def</span> <span class="nf">_constraintArrays</span><span class="p">(</span><span class="n">universe</span><span class="p">):</span>
<span class="n">nc</span> <span class="o">=</span> <span class="n">universe</span><span class="o">.</span><span class="n">numberOfDistanceConstraints</span><span class="p">()</span>
<span class="n">constraints</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">nc</span><span class="p">,</span> <span class="mi">2</span><span class="p">),</span> <span class="n">N</span><span class="o">.</span><span class="n">Int</span><span class="p">)</span>
<span class="n">const_distances_sq</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">nc</span><span class="p">,</span> <span class="p">),</span> <span class="n">N</span><span class="o">.</span><span class="n">Float</span><span class="p">)</span>
<span class="k">if</span> <span class="n">nc</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
<span class="n">i</span> <span class="o">=</span> <span class="mi">0</span>
<span class="n">c_blocks</span> <span class="o">=</span> <span class="p">[</span><span class="mi">0</span><span class="p">]</span>
<span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">universe</span><span class="o">.</span><span class="n">objectList</span><span class="p">():</span>
<span class="k">for</span> <span class="n">c</span> <span class="ow">in</span> <span class="n">o</span><span class="o">.</span><span class="n">distanceConstraintList</span><span class="p">():</span>
<span class="n">constraints</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="mi">0</span><span class="p">]</span> <span class="o">=</span> <span class="n">c</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">index</span>
<span class="n">constraints</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="mi">1</span><span class="p">]</span> <span class="o">=</span> <span class="n">c</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">index</span>
<span class="n">const_distances_sq</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">=</span> <span class="n">c</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span><span class="o">*</span><span class="n">c</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span>
<span class="n">i</span> <span class="o">=</span> <span class="n">i</span> <span class="o">+</span> <span class="mi">1</span>
<span class="n">c_blocks</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">i</span><span class="p">)</span>
<span class="n">c_blocks</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">c_blocks</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">c_blocks</span> <span class="o">=</span> <span class="n">N</span><span class="o">.</span><span class="n">zeros</span><span class="p">((</span><span class="mi">1</span><span class="p">,),</span> <span class="n">N</span><span class="o">.</span><span class="n">Int</span><span class="p">)</span>
<span class="k">return</span> <span class="n">constraints</span><span class="p">,</span> <span class="n">const_distances_sq</span><span class="p">,</span> <span class="n">c_blocks</span>
<span class="c">#</span>
<span class="c"># Enforce distance constraints for current configuration</span>
<span class="c">#</span>
<span class="k">def</span> <span class="nf">enforceConstraints</span><span class="p">(</span><span class="n">universe</span><span class="p">,</span> <span class="n">configuration</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span>
<span class="n">constraints</span><span class="p">,</span> <span class="n">const_distances_sq</span><span class="p">,</span> <span class="n">c_blocks</span> <span class="o">=</span> <span class="n">_constraintArrays</span><span class="p">(</span><span class="n">universe</span><span class="p">)</span>
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">constraints</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
<span class="k">return</span>
<span class="k">if</span> <span class="n">configuration</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">configuration</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="n">MMTK_dynamics</span><span class="o">.</span><span class="n">enforceConstraints</span><span class="p">(</span><span class="n">universe</span><span class="o">.</span><span class="n">_spec</span><span class="p">,</span> <span class="n">configuration</span><span class="o">.</span><span class="n">array</span><span class="p">,</span>
<span class="n">universe</span><span class="o">.</span><span class="n">masses</span><span class="p">()</span><span class="o">.</span><span class="n">array</span><span class="p">,</span>
<span class="n">constraints</span><span class="p">,</span> <span class="n">const_distances_sq</span><span class="p">,</span> <span class="n">c_blocks</span><span class="p">)</span>
<span class="c">#</span>
<span class="c"># Project velocity vector onto the constraint surface</span>
<span class="c">#</span>
<span class="k">def</span> <span class="nf">projectVelocities</span><span class="p">(</span><span class="n">universe</span><span class="p">,</span> <span class="n">velocities</span><span class="p">):</span>
<span class="n">constraints</span><span class="p">,</span> <span class="n">const_distances_sq</span><span class="p">,</span> <span class="n">c_blocks</span> <span class="o">=</span> <span class="n">_constraintArrays</span><span class="p">(</span><span class="n">universe</span><span class="p">)</span>
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">constraints</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
<span class="k">return</span>
<span class="n">MMTK_dynamics</span><span class="o">.</span><span class="n">projectVelocities</span><span class="p">(</span><span class="n">universe</span><span class="o">.</span><span class="n">_spec</span><span class="p">,</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="p">,</span>
<span class="n">velocities</span><span class="o">.</span><span class="n">array</span><span class="p">,</span> <span class="n">universe</span><span class="o">.</span><span class="n">masses</span><span class="p">()</span><span class="o">.</span><span class="n">array</span><span class="p">,</span>
<span class="n">constraints</span><span class="p">,</span> <span class="n">const_distances_sq</span><span class="p">,</span> <span class="n">c_blocks</span><span class="p">)</span>
</pre></div>
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