ReferenceVariableVerletDynamics.h

/* Portions copyright (c) 2006-2012 Stanford University and Simbios.
 * Contributors: Peter Eastman, Pande Group
 *
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 * permit persons to whom the Software is furnished to do so, subject
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 *
 * The above copyright notice and this permission notice shall be included
 * in all copies or substantial portions of the Software.
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 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
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#ifndef __ReferenceVariableVerletDynamics_H__
#define __ReferenceVariableVerletDynamics_H__

#include "ReferenceDynamics.h"

namespace OpenMM {

class ReferenceVariableVerletDynamics : public ReferenceDynamics {

   private:

      std::vector<OpenMM::RealVec> xPrime;
      std::vector<RealOpenMM> inverseMasses;
      RealOpenMM _accuracy;

   public:

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

         Constructor

         @param numberOfAtoms  number of atoms
         @param accuracy       required accuracy

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

       ReferenceVariableVerletDynamics( int numberOfAtoms, RealOpenMM accuracy );

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

         Destructor

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

       ~ReferenceVariableVerletDynamics( );

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

         Get the required accuracy

         @return accuracy

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

      RealOpenMM getAccuracy( void ) const;

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

         Set the required accuracy

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

      void setAccuracy( RealOpenMM 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

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

      void update(const OpenMM::System& system, std::vector<OpenMM::RealVec>& atomCoordinates,
                  std::vector<OpenMM::RealVec>& velocities, std::vector<OpenMM::RealVec>& forces, std::vector<RealOpenMM>& masses, RealOpenMM maxStepSize, RealOpenMM tolerance);

};

} // namespace OpenMM

#endif // __ReferenceVariableVerletDynamics_H__