ReferenceBrownianDynamics.h

/* Portions copyright (c) 2006-2012 Stanford University and Simbios.
 * Contributors: Pande Group
 *
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 * a copy of this software and associated documentation files (the
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 * distribute, sublicense, and/or sell copies of the Software, and to
 * permit persons to whom the Software is furnished to do so, subject
 * to the following conditions:
 *
 * The above copyright notice and this permission notice shall be included
 * in all copies or substantial portions of the Software.
 *
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
 * OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
 * MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
 * IN NO EVENT SHALL THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE
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 */

#ifndef __ReferenceBrownianDynamics_H__
#define __ReferenceBrownianDynamics_H__

#include "ReferenceDynamics.h"

namespace OpenMM {

class ReferenceBrownianDynamics : public ReferenceDynamics {

   private:

      std::vector<OpenMM::Vec3> xPrime;
      std::vector<double> inverseMasses;
      double friction;
      
   public:

      /**---------------------------------------------------------------------------------------
      
         Constructor

         @param numberOfAtoms  number of atoms
         @param deltaT         delta t for dynamics
         @param friction       friction coefficient
         @param temperature    temperature
      
         --------------------------------------------------------------------------------------- */

       ReferenceBrownianDynamics(int numberOfAtoms, double deltaT, double friction, double temperature);

      /**---------------------------------------------------------------------------------------
      
         Destructor
      
         --------------------------------------------------------------------------------------- */

       ~ReferenceBrownianDynamics();

      /**---------------------------------------------------------------------------------------
      
         Get the friction coefficient
      
         @return friction
      
         --------------------------------------------------------------------------------------- */
      
      double getFriction() const;
      
      /**---------------------------------------------------------------------------------------
      
         Update
      
         @param system              the System to be integrated
         @param atomCoordinates     atom coordinates
         @param velocities          velocities
         @param forces              forces
         @param masses              atom masses
         @param tolerance           the constraint tolerance
      
         --------------------------------------------------------------------------------------- */
     
      void update(const OpenMM::System& system, std::vector<OpenMM::Vec3>& atomCoordinates,
                  std::vector<OpenMM::Vec3>& velocities, std::vector<OpenMM::Vec3>& forces, std::vector<double>& masses, double tolerance);
      
};

} // namespace OpenMM

#endif // __ReferenceBrownianDynamics_H__