EndtoEnd.h

#ifndef END_TO_END_H
#define END_TO_END_H

/*
* Simpatico - Simulation Package for Polymeric and Molecular Liquids
*
* Copyright 2010 - 2014, 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 EndtoEnd : public SystemAnalyzer<System>
   {
   
   public:

      EndtoEnd(System &system);
   
      virtual void readParameters(std::istream& in);
   
      virtual void setup();
   
      virtual void sample(long iStep);
   
      virtual void output();

   private:

      std::ofstream outputFile_;

      Average  accumulator_;

      DArray<Vector> positions_;
   
      Species *speciesPtr_;
   
      int nSamplePerBlock_;

      int     speciesId_;
   
      int     nAtom_;
   
   };

}
#endif