MdSimulation.h

#ifndef MCMD_MD_SIMULATION_H
#define MCMD_MD_SIMULATION_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/simulation/Simulation.h>     // base class
#include "MdSystem.h"                       // member
#include "MdAnalyzerManager.h"              // member
#include "MdCommandManager.h"               // member

namespace McMd
{

   using namespace Util;

   class MdSimulation : public Simulation
   {

   public:

      using ParamComposite::load;

      #ifdef UTIL_MPI

      MdSimulation(MPI::Intracomm& communicator);
      #endif

      MdSimulation();

      virtual ~MdSimulation();



      void setOptions(int argc, char **argv);

      void readParam();

      void readParam(std::istream &in);
   
      virtual void readParameters(std::istream &in);



      void load(const std::string& filename);

      virtual void loadParameters(Serializable::IArchive &ar);

      void save(const std::string& filename);

      virtual void save(Serializable::OArchive &ar);



      void readCommands();

      void readCommands(std::istream& in);

      bool readCommand(std::string command, std::istream& in);



      void simulate(int endStep, bool isContinuation = false);

      void analyzeConfigs(int min, int max, std::string basename);

      void analyzeTrajectory(int min, int max, 
                             std::string classname, std::string filename);



      const MdSystem& system() const;

      MdSystem& system();

      virtual bool isValid() const;
 

   private:
      
      MdSystem system_;

      MdAnalyzerManager mdAnalyzerManager_;

      MdCommandManager mdCommandManager_;

      std::string saveFileName_;

      int saveInterval_;

      bool isInitialized_;

      bool isRestarting_;

   };

   // Inline method definitions

   // Get the System being simulated by const reference.
   inline const MdSystem& MdSimulation::system() const
   {  return system_; }

   // Get the System being simulated by reference.
   inline MdSystem& MdSimulation::system()
   {  return system_; }

}    
#endif