ReferenceBondForce.h

/* Portions copyright (c) 2006 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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 * 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
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 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
 * OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
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#ifndef __ReferenceBondForce_H__
#define __ReferenceBondForce_H__

#include "ReferenceForce.h"
#include "ReferenceBondIxn.h"

namespace OpenMM {

class OPENMM_EXPORT ReferenceBondForce : public ReferenceForce {

   private:

   public:

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

       ReferenceBondForce();

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

       ~ReferenceBondForce();

      /**---------------------------------------------------------------------------------------
      
         Calculate forces/energy for bonds
      
         @param numberOfBonds    number of bonds
         @param atomIndices      indices of atoms participating in bond ixn: atomIndices[bondIndex][indices]
         @param atomCoordinates  atom coordinates: atomCoordinates[atomIndex][3]
         @param parameters       parameters: parameters[bondIndex][*]; contents of array 
                                 depend on ixn
         @param forces           force array (forces added to current values): forces[atomIndex][3]
         @param totalEnergy      if not null, the energy will be added to this
         @param ReferenceBondIxn ixn to be calculated
      
         --------------------------------------------------------------------------------------- */
      
       void calculateForce(int numberOfBonds, int** atomIndices,
                           std::vector<OpenMM::Vec3>& atomCoordinates,
                           double** parameters, std::vector<OpenMM::Vec3>& forces, 
                           double* totalEnergy, ReferenceBondIxn& referenceBondIxn);

};

} // namespace OpenMM

#endif // __ReferenceBondForce_H__