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<h1>Source code for MMTK.Minimization</h1><div class="highlight"><pre>
<span class="c"># This module implements energy minimizers.</span>
<span class="c">#</span>
<span class="c"># Written by Konrad Hinsen</span>
<span class="c">#</span>
<span class="sd">"""</span>
<span class="sd">Energy minimizers</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">Features</span><span class="p">,</span> <span class="n">Trajectory</span><span class="p">,</span> <span class="n">Units</span>
<span class="kn">from</span> <span class="nn">MMTK_minimization</span> <span class="kn">import</span> <span class="n">conjugateGradient</span><span class="p">,</span> <span class="n">steepestDescent</span>
<span class="c">#</span>
<span class="c"># Minimizer base class</span>
<span class="c">#</span>
<span class="k">class</span> <span class="nc">Minimizer</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">'steps'</span><span class="p">:</span> <span class="mi">100</span><span class="p">,</span> <span class="s">'step_size'</span><span class="p">:</span> <span class="mf">0.02</span><span class="o">*</span><span class="n">Units</span><span class="o">.</span><span class="n">Ang</span><span class="p">,</span>
<span class="s">'convergence'</span><span class="p">:</span> <span class="mf">0.01</span><span class="o">*</span><span class="n">Units</span><span class="o">.</span><span class="n">kJ</span><span class="o">/</span><span class="p">(</span><span class="n">Units</span><span class="o">.</span><span class="n">mol</span><span class="o">*</span><span class="n">Units</span><span class="o">.</span><span class="n">nm</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">'energy'</span><span class="p">,</span> <span class="s">'configuration'</span><span class="p">,</span> <span class="s">'gradients'</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">'energy'</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"># Steepest descent minimizer</span>
<span class="c">#</span>
<div class="viewcode-block" id="SteepestDescentMinimizer"><a class="viewcode-back" href="../../modules.html#MMTK.Minimization.SteepestDescentMinimizer">[docs]</a><span class="k">class</span> <span class="nc">SteepestDescentMinimizer</span><span class="p">(</span><span class="n">Minimizer</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Steepest-descent minimizer</span>
<span class="sd"> The minimizer can handle fixed atoms, but no distance constraints.</span>
<span class="sd"> It is fully thread-safe.</span>
<span class="sd"> The minimization is started by calling the minimizer object.</span>
<span class="sd"> All the keyword options (see documnentation of __init__) can be</span>
<span class="sd"> specified either when creating the minimizer 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 "configuration": configuration and box size (for</span>
<span class="sd"> periodic universes)</span>
<span class="sd"> - category "gradients": energy gradients for each atom</span>
<span class="sd"> - category "energy": potential energy and</span>
<span class="sd"> norm of the potential energy gradient</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 minimization steps (default is 100)</span>
<span class="sd"> :type steps: int</span>
<span class="sd"> :keyword step_size: the initial size of a minimization step</span>
<span class="sd"> (default is 0.002 nm)</span>
<span class="sd"> :type step_size: float</span>
<span class="sd"> :keyword convergence: the root-mean-square gradient length at which</span>
<span class="sd"> minimization stops (default is 0.01 kJ/mol/nm)</span>
<span class="sd"> :type convergence: 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">Minimizer</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="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 minimizer. 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">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">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">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">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="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">getOption</span><span class="p">(</span><span class="s">'step_size'</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">'convergence'</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="s">'Steepest descent minimization 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">'convergence'</span><span class="p">,</span> <span class="s">'step_size'</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">steepestDescent</span><span class="p">,</span> <span class="n">args</span><span class="p">)</span>
<span class="c">#</span>
<span class="c"># Conjugate gradient minimizer</span>
<span class="c">#</span></div>
<div class="viewcode-block" id="ConjugateGradientMinimizer"><a class="viewcode-back" href="../../modules.html#MMTK.Minimization.ConjugateGradientMinimizer">[docs]</a><span class="k">class</span> <span class="nc">ConjugateGradientMinimizer</span><span class="p">(</span><span class="n">Minimizer</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Conjugate gradient minimizer</span>
<span class="sd"> The minimizer can handle fixed atoms, but no distance constraints.</span>
<span class="sd"> It is fully thread-safe.</span>
<span class="sd"> The minimization is started by calling the minimizer object.</span>
<span class="sd"> All the keyword options can be specified either when</span>
<span class="sd"> creating the minimizer 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 "configuration": configuration and box size (for</span>
<span class="sd"> periodic universes)</span>
<span class="sd"> - category "gradients": energy gradients for each atom</span>
<span class="sd"> - category "energy": potential energy and</span>
<span class="sd"> norm of the potential energy gradient</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 minimization steps (default is 100)</span>
<span class="sd"> :type steps: int</span>
<span class="sd"> :keyword step_size: the initial size of a minimization step</span>
<span class="sd"> (default is 0.002 nm)</span>
<span class="sd"> :type step_size: float</span>
<span class="sd"> :keyword convergence: the root-mean-square gradient length at which</span>
<span class="sd"> minimization stops (default is 0.01 kJ/mol/nm)</span>
<span class="sd"> :type convergence: 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"> """</span>
<span class="n">Minimizer</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="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 minimizer. 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">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">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">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="o">.</span><span class="n">CEvaluator</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">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="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">getOption</span><span class="p">(</span><span class="s">'step_size'</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">'convergence'</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="s">'Conjugate gradient minimization 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">'convergence'</span><span class="p">,</span> <span class="s">'step_size'</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">conjugateGradient</span><span class="p">,</span> <span class="n">args</span><span class="p">)</span></div>
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