ReferenceAngleBondIxn.h

/* Portions copyright (c) 2006-2016 Stanford University and Simbios.
 * Contributors: Pande Group
 *
 * Permission is hereby granted, free of charge, to any person obtaining
 * a copy of this software and associated documentation files (the
 * "Software"), to deal in the Software without restriction, including
 * without limitation the rights to use, copy, modify, merge, publish,
 * distribute, sublicense, and/or sell copies of the Software, and to
 * 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
 * in all copies or substantial portions of the Software.
 *
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
 * OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
 * MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
 * IN NO EVENT SHALL THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE
 * LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
 * OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
 * WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */

#ifndef __ReferenceAngleBondIxn_H__
#define __ReferenceAngleBondIxn_H__

#include "ReferenceBondIxn.h"
#include "openmm/Vec3.h"

namespace OpenMM {

class OPENMM_EXPORT ReferenceAngleBondIxn : public ReferenceBondIxn {

   private:

        bool usePeriodic;
        Vec3 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::Vec3* 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(double cosine, double* angleParameters,
                                         double* dEdR, double* 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::Vec3>& atomCoordinates,
                            double* parameters, std::vector<OpenMM::Vec3>& forces,
                            double* totalEnergy, double* energyParamDerivs);
      

};

} // namespace OpenMM

#endif // __ReferenceAngleBondIxn_H__