ReferenceAngleBondIxn.h

/* Portions copyright (c) 2006 Stanford University and Simbios.
 * Contributors: Pande Group
 *
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 * permit persons to whom the Software is furnished to do so, subject
 * to the following conditions:
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 * The above copyright notice and this permission notice shall be included
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 * OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
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#ifndef __ReferenceAngleBondIxn_H__
#define __ReferenceAngleBondIxn_H__

#include "ReferenceBondIxn.h"

namespace OpenMM {

class OPENMM_EXPORT ReferenceAngleBondIxn : public ReferenceBondIxn {

   private:

        bool usePeriodic;
        RealVec boxVectors[3];

   public:

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

       ReferenceAngleBondIxn();

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

       ~ReferenceAngleBondIxn();

       /**---------------------------------------------------------------------------------------
      
         Set the force to use periodic boundary conditions.
      
         @param vectors    the vectors defining the periodic box
      
         --------------------------------------------------------------------------------------- */
      
      void setPeriodic(OpenMM::RealVec* vectors);

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

         Get dEdR and energy term for angle bond
      
         @param  cosine               cosine of angle
         @param  angleParameters      angleParameters: angleParameters[0] = angle in radians
                                                       angleParameters[1] = k (force constant)
         @param  dEdR                 output dEdR
         @param  energyTerm           output energyTerm
      
         --------------------------------------------------------------------------------------- */
      
      void getPrefactorsGivenAngleCosine(RealOpenMM cosine, RealOpenMM* angleParameters,
                                         RealOpenMM* dEdR, RealOpenMM* energyTerm) const;
      
      /**---------------------------------------------------------------------------------------

         Calculate Angle Bond ixn
      
         @param atomIndices      two bond indices
         @param atomCoordinates  atom coordinates
         @param parameters       parameters: parameters[0] = ideal bond length
                                             parameters[1] = bond k (includes factor of 2)
         @param forces           force array (forces added)
         @param totalEnergy      if not null, the energy will be added to this
      
         --------------------------------------------------------------------------------------- */
      
      void calculateBondIxn(int* atomIndices, std::vector<OpenMM::RealVec>& atomCoordinates,
                            RealOpenMM* parameters, std::vector<OpenMM::RealVec>& forces,
                            RealOpenMM* totalEnergy) const;
      

};

} // namespace OpenMM

#endif // __ReferenceAngleBondIxn_H__