ReferenceVariableStochasticDynamics.h

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 * Contributors: Pande Group
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#ifndef __ReferenceVariableStochasticDynamics_H__
#define __ReferenceVariableStochasticDynamics_H__

#include "ReferenceDynamics.h"

namespace OpenMM {

class ReferenceVariableStochasticDynamics : public ReferenceDynamics {

   private:

      std::vector<OpenMM::Vec3> xPrime, oldx;
      std::vector<double> inverseMasses;
      double friction, _accuracy;

   public:

      /**---------------------------------------------------------------------------------------

         Constructor

         @param numberOfAtoms  number of atoms
         @param friction       friction coefficient
         @param temperature    temperature
         @param accuracy       required accuracy

         --------------------------------------------------------------------------------------- */

       ReferenceVariableStochasticDynamics(int numberOfAtoms, double friction, double temperature, double accuracy);

      /**---------------------------------------------------------------------------------------

         Destructor

         --------------------------------------------------------------------------------------- */

       ~ReferenceVariableStochasticDynamics();

      /**---------------------------------------------------------------------------------------

         Get friction coefficient

         --------------------------------------------------------------------------------------- */

      double getFriction() const;
      
      /**---------------------------------------------------------------------------------------

         Get the required accuracy

         @return accuracy

         --------------------------------------------------------------------------------------- */

      double getAccuracy() const;

      /**---------------------------------------------------------------------------------------

         Set the required accuracy

         --------------------------------------------------------------------------------------- */

      void setAccuracy(double accuracy);

      /**---------------------------------------------------------------------------------------

         Update

         @param system              the System to be integrated
         @param atomCoordinates     atom coordinates
         @param velocities          velocities
         @param forces              forces
         @param masses              atom masses
         @param maxStepSize         maximum time step
         @param tolerance           the constraint tolerance
         @param boxVectors          the current periodic box vectors

         --------------------------------------------------------------------------------------- */

      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 maxStepSize, double tolerance, const Vec3* boxVectors);

      /**---------------------------------------------------------------------------------------
            
         @param numberOfAtoms       number of atoms
         @param velocities          velocities
         @param forces              forces
         @param inverseMasses       inverse atom masses
         @param maxStepSize         maximum time step
      
         --------------------------------------------------------------------------------------- */
      
      void updatePart1(int numberOfAtoms, std::vector<OpenMM::Vec3>& velocities,  std::vector<OpenMM::Vec3>& forces, std::vector<double>& inverseMasses, double maxStepSize);

      /**---------------------------------------------------------------------------------------
      
         Second update
      
         @param numberOfAtoms       number of atoms
         @param atomCoordinates     atom coordinates
         @param velocities          velocities
         @param inverseMasses       inverse atom masses
         @param xPrime              xPrime
      
         --------------------------------------------------------------------------------------- */
      
      void updatePart2(int numberOfAtoms, std::vector<OpenMM::Vec3>& atomCoordinates, std::vector<OpenMM::Vec3>& velocities,
                               std::vector<double>& inverseMasses, std::vector<OpenMM::Vec3>& xPrime);
      
};

} // namespace OpenMM

#endif // __ReferenceVariableStochasticDynamics_H__