ClusterIdentifier.h

#ifndef MCMD_CLUSTER_IDENTIFIER_H
#define MCMD_CLUSTER_IDENTIFIER_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/system/Cluster.h>       // member template argument
#include <mcMd/analyzers/system/ClusterLink.h>   // member template argument
#include <mcMd/neighbor/CellList.h>              // member
#include <simp/boundary/Boundary.h>              // argument (typedef)
#include <util/containers/DArray.h>              // member template
#include <util/containers/GArray.h>              // member template
#include <util/containers/GStack.h>              // member template

namespace Simp {
   class Species;
}

namespace McMd
{

   class System;

   using namespace Util;
   using namespace Simp;

   class ClusterIdentifier 
   {
   
   public:

      ClusterIdentifier(System &system);
   
      ~ClusterIdentifier();
   
      virtual 
      void initialize(int speciesId, int atomTypeId, double cutoff);
   
      void identifyClusters();

      int nCluster() const
      {  return clusters_.size(); }

      ClusterLink& link(int moleculeId)
      {  return links_[moleculeId]; }

      Cluster& cluster(int id)
      {  return clusters_[id]; }

      bool isValid() const;

   private:

      DArray<ClusterLink> links_;

      GArray<Cluster> clusters_;

      GStack<ClusterLink>  workStack_;

      CellList cellList_;

      System* systemPtr_;

      int speciesId_;

      int atomTypeId_;

      double cutoff_;

      // Private functions

      System& system()
      {  return *systemPtr_; }

      void processNextMolecule(Cluster& cluster);

   };

}
#endif