ReferenceCMAPTorsionIxn.h

/* Portions copyright (c) 2010-2016 Stanford University and Simbios.
 * Contributors: Peter Eastman
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#ifndef __ReferenceCMAPTorsionIxn_H__
#define __ReferenceCMAPTorsionIxn_H__

#include "SimTKOpenMMUtilities.h"
#include "ReferenceBondIxn.h"
#include <vector>

namespace OpenMM {

class ReferenceCMAPTorsionIxn : public ReferenceBondIxn {

private:

    std::vector<std::vector<std::vector<double> > > coeff;
    std::vector<int> torsionMaps;
    std::vector<std::vector<int> > torsionIndices;
    bool usePeriodic;
    Vec3 boxVectors[3];

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

       Calculate the interaction due to a single torsion pair

       @param index            the index of the torsion
       @param atomCoordinates  atom coordinates
       @param forces           force array (forces added)
       @param totalEnergy      total energy

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

    void calculateOneIxn(int index, std::vector<OpenMM::Vec3>& atomCoordinates, std::vector<OpenMM::Vec3>& forces,
                         double* totalEnergy) const;

public:

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

       Constructor

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

    ReferenceCMAPTorsionIxn(const std::vector<std::vector<std::vector<double> > >& coeff,
                            const std::vector<int>& torsionMaps,
                            const std::vector<std::vector<int> >& torsionIndices);

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

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

       Calculate torsion interaction

       @param atomCoordinates    atom coordinates
       @param forces             force array (forces added)
       @param totalEnergy        total energy

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

    void calculateIxn(std::vector<OpenMM::Vec3>& atomCoordinates, std::vector<OpenMM::Vec3>& forces, double* totalEnergy) const;

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

       This is present only because we must define it to subclass ReferenceBondIxn.  It is never called.

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

    void calculateBondIxn(std::vector<int>& atomIndices, std::vector<OpenMM::Vec3>& atomCoordinates,
                         std::vector<double>& parameters, std::vector<OpenMM::Vec3>& forces,
                         double* totalEnergy, double* energyParamDerivs);

// ---------------------------------------------------------------------------------------

};

} // namespace OpenMM

#endif // __ReferenceCMAPTorsionIxn_H__