ReferenceCustomNonbondedIxn.h

/* Portions copyright (c) 2009-2016 Stanford University and Simbios.
 * Contributors: Peter Eastman
 *
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 * 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.
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 * OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
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#ifndef __ReferenceCustomNonbondedxIxn_H__
#define __ReferenceCustomNonbondedxIxn_H__

#include "ReferencePairIxn.h"
#include "ReferenceNeighborList.h"
#include "openmm/internal/CompiledExpressionSet.h"
#include <map>
#include <set>
#include <utility>
#include <vector>

namespace OpenMM {

class ReferenceCustomNonbondedIxn {

   private:

      bool cutoff;
      bool useSwitch;
      bool periodic;
      const OpenMM::NeighborList* neighborList;
      OpenMM::Vec3 periodicBoxVectors[3];
      double cutoffDistance, switchingDistance;
      Lepton::CompiledExpression energyExpression;
      Lepton::CompiledExpression forceExpression;
      std::vector<std::string> paramNames;
      std::vector<Lepton::CompiledExpression> energyParamDerivExpressions;
      CompiledExpressionSet expressionSet;
      std::vector<int> particleParamIndex;
      int rIndex;
      std::vector<std::pair<std::set<int>, std::set<int> > > interactionGroups;

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

         Calculate custom pair ixn between two atoms

         @param atom1            the index of the first atom
         @param atom2            the index of the second atom
         @param atomCoordinates  atom coordinates
         @param atomParameters   atomParameters[atomIndex][parameterIndex]
         @param forces           force array (forces added)
         @param energyByAtom     atom energy
         @param totalEnergy      total energy

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

      void calculateOneIxn(int atom1, int atom2, std::vector<OpenMM::Vec3>& atomCoordinates, std::vector<OpenMM::Vec3>& forces,
                           double* energyByAtom, double* totalEnergy, double* energyParamDerivs);


   public:

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

         Constructor

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

       ReferenceCustomNonbondedIxn(const Lepton::CompiledExpression& energyExpression, const Lepton::CompiledExpression& forceExpression,
                                   const std::vector<std::string>& parameterNames, const std::vector<Lepton::CompiledExpression> energyParamDerivExpressions);

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

         Destructor

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

       ~ReferenceCustomNonbondedIxn();

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

         Set the force to use a cutoff.

         @param distance            the cutoff distance
         @param neighbors           the neighbor list to use

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

      void setUseCutoff(double distance, const OpenMM::NeighborList& neighbors);

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

         Restrict the force to a list of interaction groups.

         @param distance            the cutoff distance
         @param neighbors           the neighbor list to use

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

      void setInteractionGroups(const std::vector<std::pair<std::set<int>, std::set<int> > >& groups);

      /**---------------------------------------------------------------------------------------
      
         Set the force to use a switching function.
      
         @param distance            the switching distance
      
         --------------------------------------------------------------------------------------- */
      
      void setUseSwitchingFunction(double distance);

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

         Set the force to use periodic boundary conditions.  This requires that a cutoff has
         already been set, and the smallest side of the periodic box is at least twice the cutoff
         distance.

         @param vectors    the vectors defining the periodic box

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

      void setPeriodic(OpenMM::Vec3* vectors);

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

         Calculate custom pair ixn

         @param numberOfAtoms    number of atoms
         @param atomCoordinates  atom coordinates
         @param atomParameters   atom parameters (charges, c6, c12, ...)     atomParameters[atomIndex][paramterIndex]
         @param exclusions       atom exclusion indices
                                 exclusions[atomIndex] contains the list of exclusions for that atom
         @param fixedParameters  non atom parameters (not currently used)
         @param globalParameters the values of global parameters
         @param forces           force array (forces added)
         @param energyByAtom     atom energy
         @param totalEnergy      total energy

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

      void calculatePairIxn(int numberOfAtoms, std::vector<OpenMM::Vec3>& atomCoordinates,
                            double** atomParameters, std::vector<std::set<int> >& exclusions,
                            double* fixedParameters, const std::map<std::string, double>& globalParameters,
                            std::vector<OpenMM::Vec3>& forces, double* energyByAtom, double* totalEnergy,
                            double* energyParamDerivs);

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

};

} // namespace OpenMM

#endif // __ReferenceCustomNonbondedxIxn_H__