ReferenceBondIxn.h

/* Portions copyright (c) 2006-2016 Stanford University and Simbios.
 * Contributors: Pande Group
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#ifndef __ReferenceBondIxn_H__
#define __ReferenceBondIxn_H__

#include "openmm/Vec3.h"
#include "openmm/internal/windowsExport.h"
#include <vector>

namespace OpenMM {

class OPENMM_EXPORT ReferenceBondIxn {

   private:

   public:

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

       ReferenceBondIxn();

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

       ~ReferenceBondIxn();

      /**---------------------------------------------------------------------------------------
      
         Calculate Bond Ixn -- virtual method
      
         @param atomIndices      bond indices
         @param atomCoordinates  atom coordinates
         @param parameters       parameters
         @param forces           force array (forces added)
         @param totalEnergy      if not null, the energy will be added to this
      
         --------------------------------------------------------------------------------------- */
      
      virtual void calculateBondIxn(int* atomIndices, std::vector<OpenMM::Vec3>& atomCoordinates,
                                    double* parameters, std::vector<OpenMM::Vec3>& forces,
                                    double* totalEnergy, double* energyParamDerivs);
      
      /**---------------------------------------------------------------------------------------
      
         Get normed dot product between two vectors
      
         @param  vector1            first vector
         @param  vector2            second vector
         @param  hasREntry          if set, then vector1[ReferenceForce::RIndex] = norm of vector;
                                    defaults to 0
      
         @return dot product
      
         --------------------------------------------------------------------------------------- */
      
      static double getNormedDotProduct(double* vector1, double* vector2, int hasREntry);
      
      /**---------------------------------------------------------------------------------------
      
         Get angle between two vectors
      
         @param  vector1            first vector
         @param  vector2            second vector
         @param  outputDotProduct   cosine of angle between two vectors (optional)
         @param  hasREntry          if set, then vector1[ReferenceForce::R2Index] = square norm of vector;
                                    defaults to 0
      
         @return cosine of angles in radians
      
         --------------------------------------------------------------------------------------- */
      
      static double getAngleBetweenTwoVectors(double* vector1, double* vector2, 
                                              double* outputDotProduct, int hasREntry);
      
      /**---------------------------------------------------------------------------------------
      
         Get dihedral angle between two vectors
      
         @param  vector1            first vector
         @param  vector2            second vector
         @param  vector3            third vector
         @param  outputCrossProduct output cross product vectors
         @param  cosineOfAngle      cosine of angle (output)
         @param  signVector         vector to test sign (optional)
         @param  signOfAngle        sign of angle (output) (optional)
         @param  hasREntry          if set, then vector1[ReferenceForce::R2Index] = square norm of vector
                                    defaults to 0
      
         @return cosine of angles in radians
      
         --------------------------------------------------------------------------------------- */
      
      static double getDihedralAngleBetweenThreeVectors(double* vector1, double* vector2, 
                                                        double* vector3, double** outputCrossProduct, 
                                                        double* cosineOfAngle, double* signVector, 
                                                        double* signOfAngle, int hasREntry);
      
};

} // namespace OpenMM

#endif // __ReferenceBondIxn_H__