ReferenceVelocityVerletDynamics.h

/* Portions copyright (c) 2006-2012 Stanford University and Simbios.
 * Contributors: Pande Group
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#ifndef __ReferenceVelocityVerletDynamics_H__
#define __ReferenceVelocityVerletDynamics_H__

#include "ReferenceDynamics.h"

namespace OpenMM {

class ContextImpl;

class ReferenceVelocityVerletDynamics : public ReferenceDynamics {

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

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

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

       ReferenceVelocityVerletDynamics(int numberOfAtoms, double deltaT);

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

       ~ReferenceVelocityVerletDynamics();

      /**---------------------------------------------------------------------------------------
      
         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
         @param forcesAreValid      whether the forces are valid (duh!)
      
         --------------------------------------------------------------------------------------- */
     
      void update(OpenMM::ContextImpl &context, 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, bool &forcesAreValid);
      
};

} // namespace OpenMM

#endif // __ReferenceVelocityVerletDynamics_H__