LinkMSD.h

#ifndef LINK_MSD_H
#define LINK_MSD_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 <mcMd/links/LinkMaster.h>
#include <mcMd/links/LinkEvents.h>
#include <util/misc/Observer.h>
#include <util/global.h>

#include <cstdio> 
#include <cstring> 

namespace McMd {
   class Species;
}

namespace McMd
{

   using namespace Util;
   using namespace Simp;

   class LinkMSD : public SystemAnalyzer<System>,
                   public Observer<LinkAddEvent>, 
                   public Observer<LinkRemoveEvent>  
   {
   
   public:

      LinkMSD(System &system);
   
      virtual void readParameters(std::istream& in);
   
      virtual void setup();
   
      virtual void sample(long iStep);
      
      virtual void update(const LinkAddEvent& event);
      
      virtual void update(const LinkRemoveEvent& event);      
   
      virtual void output();

   private:

      std::ofstream outputFile_;

      int capacity_;
      
      int linkCapacity_;
      
      int nSamplePerBlock_;
      
      DArray<Average>  accumulator_;
            
      DArray<int> i0_;
      
      DArray<int> t0_;    
         
   };

}
#endif