IntraPairAutoCorr.h

#ifndef MCMD_INTRA_PAIR_AUTO_CORR_H
#define MCMD_INTRA_PAIR_AUTO_CORR_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/simulation/System.h>              // base class template parameter
#include <util/accumulators/AutoCorrArray.h>     // base class template parameter
#include <util/space/Vector.h>                   // template parameter
#include <util/containers/DArray.h>              // member template

namespace Simp {
   class Species;
}

namespace McMd
{

   using namespace Util;
   using namespace Simp;

   class IntraPairAutoCorr 
    : public SystemAnalyzer<System>
   {
   
   public:
  
      IntraPairAutoCorr(System &system);
  
      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 setup();
   
      virtual void sample(long iStep);
   
      virtual void output();

   private:
   
      std::ofstream outputFile_;

      AutoCorrArray<Vector, double> accumulator_;

      DArray<Vector> data_;
   
      Species *speciesPtr_;
   
      int     speciesId_;
   
      int     nMolecule_;
   
      int     atom1Id_;
   
      int     atom2Id_;
   
      int     capacity_;
   
      bool    isInitialized_;

   };

   /*
   * Serialize to/from an archive. 
   */
   template <class Archive>
   void IntraPairAutoCorr::serialize(Archive& ar, const unsigned int version)
   {
      Analyzer::serialize(ar, version);
      ar & speciesId_;
      ar & atom1Id_;
      ar & atom2Id_;
      ar & capacity_;

      ar & nMolecule_;
      ar & accumulator_;
   }

}
#endif