MdPairEnergyCoefficients.h

#ifndef  SIMP_NOPAIR
#ifndef MCMD_MD_PAIR_ENERGY_COEFFICIENTS_H
#define MCMD_MD_PAIR_ENERGY_COEFFICIENTS_H

/*
* Simpatico - Simulation Package for Polymeric and Molecular Liquids
*
* Copyright 2010 - 2017, The Regents of the University of Minnesota
* Distributed under the terms of the GNU General Public License.
*/

#include <mcMd/analyzers/SystemAnalyzer.h>  // base class template
#include <mcMd/mdSimulation/MdSystem.h>         // base template parameter
#include <mcMd/analyzers/util/PairSelector.h>

#include <util/global.h> 
#include <util/containers/Pair.h>
#include <util/containers/DSArray.h>
#include <util/accumulators/Average.h>

namespace McMd
{

   using namespace Util;

   class MdPairPotential;
   class PairList;

   class MdPairEnergyCoefficients : public SystemAnalyzer<MdSystem>
   {

   public:
   
      MdPairEnergyCoefficients(MdSystem& system);

      ~MdPairEnergyCoefficients();

      virtual void readParameters(std::istream& in);
 
      virtual void loadParameters(Serializable::IArchive& ar);

      virtual void save(Serializable::OArchive& ar);

      template <class Archive>
      void serialize(Archive& ar, const unsigned int version);

      virtual void sample(long iStep);

      virtual void output();

   private:

      PairSelector  selector_;

      int nAtomType_;

      int nSpecies_;

      const PairList  *pairListPtr_;

      MdPairPotential* pairPotentialPtr_;

      Boundary *boundaryPtr_;

      int maxMoleculeNeighbors_;

      DArray< DArray< DSArray<  Pair< Atom *> > > > moleculeNeighbors_;

      DArray< DArray< double > > twoMoleculePairEnergy_;

      Average pairEnergyAccumulator_;

      Average moleculePESqAccumulator_;

      Average twoMoleculePESqAccumulator_;

      Average pESqAccumulator_;

      std::ofstream outputFile_;

      // Has readParam been called?
      bool isInitialized_;

      /*
      * Methods
      */

      // Reset the internal molecules' neighbor list arrays
      void clear();

   };

   /*
   * Serialize to/from an archive. 
   */
   template <class Archive>
   void MdPairEnergyCoefficients::serialize(Archive& ar, const unsigned int version)
   {
      ar & pairEnergyAccumulator_;
      ar & moleculePESqAccumulator_;
      ar & twoMoleculePESqAccumulator_;
      ar & pESqAccumulator_;
      //DArray< DArray< DSArray<  Pair< Atom *> > > > moleculeNeighbors_;
      //DArray< DArray< double > > twoMoleculePairEnergy_;

   }

}
#endif 
#endif