tools/analyzers/AtomMSD.h

#ifndef TOOLS_ATOM_MSD_H
#define TOOLS_ATOM_MSD_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 <tools/analyzers/Analyzer.h>           // base class template
#include <util/accumulators/MeanSqDispArray.h>  // member template 
#include <util/space/Vector.h>                  // member template parameter
#include <util/containers/DArray.h>             // member template

namespace Tools
{

   using namespace Util;

   class AtomMSD : public Analyzer
   {
   
   public:
  
      AtomMSD(Processor &processor);
  
      AtomMSD(Configuration &configuration, FileMaster& fileMaster);
  
      virtual void readParameters(std::istream& in);
  
      virtual void setup();
   
      virtual void sample(long iStep);

      virtual void output();

   private:
 
      std::ofstream outputFile_;

      MeanSqDispArray<Vector> accumulator_;

      DArray<Vector> truePositions_;
   
      DArray<Vector> oldPositions_;
   
      DArray<IntVector> shifts_;
   
      int speciesId_;
   
      int atomId_;
   
      int nMolecule_;
   
      int capacity_;
   
      int isInitialized_;
   
   };

}
#endif