McMuExchange.h

#ifndef MCMD_MC_MU_EXCHANGE_H
#define MCMD_MC_MU_EXCHANGE_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/mcSimulation/McSystem.h>     // base template parameter
#include <util/accumulators/Average.h>      // member
#include <util/containers/DArray.h>         // member template
#include <util/containers/DSArray.h>        // member template
#include <util/archives/Serializable.h>     // typedef

#include <cstdio>

namespace McMd
{

   using namespace Util;

   class Atom;

   class McMuExchange : public SystemAnalyzer<McSystem>
   {

   public:

      McMuExchange(McSystem& system);

      virtual void readParameters(std::istream& in);

      virtual void setup();
   
      virtual void sample(long iStep);
   
      virtual void output();

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

      virtual void loadParameters(Serializable::IArchive& ar);

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

   private:

      Simulation& simulation();

      Boundary& boundary();

      Simulation  *simulationPtr_;

      Boundary  *boundaryPtr_;

      std::ofstream outputFile_;

      DArray<Average> accumulators_;

      DArray<int> newTypeIds_;

      DArray<int> isAtomFlipped_;

      DSArray<int> flipAtomIds_;

      CellList::NeighborArray neighbors_;

      int  speciesId_; 

      int  nMolecule_; 

      int  nAtom_; 

      bool isInitialized_;

   };

   // Inline methods

   /*
   * Get Simulation object of parent McSystem.
   */
   inline Simulation& McMuExchange::simulation()
   {  return *simulationPtr_; }

   /*
   * Get Boundary object of parent McSystem.
   */
   inline Boundary& McMuExchange::boundary()
   {  return *boundaryPtr_; }

   /*
   * Serialize to/from an archive. 
   */
   template <class Archive>
   void McMuExchange::serialize(Archive& ar, 
                                const unsigned int version)
   {
      ar & interval_;
      ar & outputFileName_;
      ar & speciesId_;
      ar & nAtom_;
      ar & newTypeIds_;
      ar & nMolecule_;
      for (int i = 0; i < nMolecule_; ++i) {
         ar & accumulators_[i];
      }
   }

}
#endif