BlockRadiusGyration.h

#ifndef MCMD_BLOCK_RADIUS_GYRATION_H
#define MCMD_BLOCK_RADIUS_GYRATION_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>        // class template parameter
#include <util/accumulators/Average.h>     // member
#include <util/containers/DArray.h>        // member template
#include <util/space/Vector.h>             // member template parameter

#include <cstdio> 
#include <cstring> 

namespace Simp {
   class Species;
}

namespace McMd
{

   using namespace Util;
   using namespace Simp;

   class BlockRadiusGyration : public SystemAnalyzer<System>
   {
   
   public:

      BlockRadiusGyration(System &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:

      std::ofstream outputFile_;

      DArray<Average>  accumulators_;

      DArray<Vector> positions_;
      
      DArray<Vector> rCom_;
      
      DArray<int>  iTypeNAtom_;
      
      DArray<double> dRSq_; 

      DArray<double> dRSqPair_;  

      Species*  speciesPtr_;

      int  nAtomType_;
      
      int  nAtomTypePairs_;
      
      int  nSamplePerBlock_;

      int  speciesId_;
   
      int  nAtom_;
   
      bool  isInitialized_;

   };

   template <class Archive>
   void BlockRadiusGyration::serialize(Archive& ar, const unsigned int version)
   {  
      Analyzer::serialize(ar, version);
      ar & nSamplePerBlock_;
      ar & speciesId_;
      ar & nAtom_;
      ar & nAtomType_;
      ar & nAtomTypePairs_;
      ar & accumulators_;
   }

}
#endif