ReferenceCustomBondIxn.h

/* Portions copyright (c) 2009-2016 Stanford University and Simbios.
 * Contributors: Peter Eastman
 *
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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
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 *
 * The above copyright notice and this permission notice shall be included
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#ifndef __ReferenceCustomBondIxn_H__
#define __ReferenceCustomBondIxn_H__

#include "ReferenceBondIxn.h"
#include "openmm/internal/CompiledExpressionSet.h"

namespace OpenMM {

class ReferenceCustomBondIxn : public ReferenceBondIxn {

   private:
      Lepton::CompiledExpression energyExpression;
      Lepton::CompiledExpression forceExpression;
      std::vector<Lepton::CompiledExpression> energyParamDerivExpressions;
      CompiledExpressionSet expressionSet;
      std::vector<int> bondParamIndex;
      int rIndex;
      int numParameters;
      bool usePeriodic;
      Vec3 boxVectors[3];

   public:

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

         Constructor

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

       ReferenceCustomBondIxn(const Lepton::CompiledExpression& energyExpression, const Lepton::CompiledExpression& forceExpression,
                              const std::vector<std::string>& parameterNames, std::map<std::string, double> globalParameters,
                              const std::vector<Lepton::CompiledExpression> energyParamDerivExpressions);

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

         Destructor

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

       ~ReferenceCustomBondIxn();

       /**---------------------------------------------------------------------------------------
      
         Set the force to use periodic boundary conditions.
      
         @param vectors    the vectors defining the periodic box
      
         --------------------------------------------------------------------------------------- */
      
      void setPeriodic(OpenMM::Vec3* vectors);

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

         Calculate Custom Bond Ixn

         @param atomIndices      two bond indices
         @param atomCoordinates  atom coordinates
         @param parameters       parameter values
         @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 // _ReferenceCustomBondIxn___