StructureFactorP.h

#ifndef MCMD_STRUCTURE_FACTOR_P_H
#define MCMD_STRUCTURE_FACTOR_P_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/SystemAnalyzer.h>   // base class template
#include <mcMd/simulation/System.h>              // base class template parameter
#include <util/containers/DMatrix.h>             // member template
#include <util/containers/DArray.h>              // member template
#include <util/containers/Pair.h>                // member template parameter

#include <util/global.h>

#include <iostream>
#include <complex>

namespace McMd
{

   using namespace Util;

   class StructureFactorP 
    : public SystemAnalyzer<System>
   {

   public:

      StructureFactorP(System &system);

      ~StructureFactorP();

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

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

      virtual void save(Serializable::OArchive& ar);
  
      template <class Archive>
      void serialize(Archive& ar, const unsigned int version);

      virtual void setup();
   
      void sample(long iStep);

      virtual void output();

   protected:

      std::ofstream outputFile_;

      DMatrix<double>  structureFactors_;

      /*
      * Fourier modes (temporary).
      *
      * First index is wavevector, second is atom type.
      */
      DMatrix< std::complex<double> > fourierModes_;

      DArray<IntVector>  waveIntVectors_;

      DArray<Vector> waveVectors_;

      DArray< Pair<int> >  atomTypeIdPairs_;

      int  nWave_;

      int  nAtomTypeIdPair_;

      int  nSample_;

      int  nAtomType_;

      bool  isInitialized_;

      void makeWaveVectors();

   };

   template <class Archive>
   void StructureFactorP::serialize(Archive& ar, const unsigned int version)
   {
      Analyzer::serialize(ar, version);
      ar & nAtomType_;
      ar & nAtomTypeIdPair_;
      ar & atomTypeIdPairs_;
      ar & nWave_;
      ar & waveIntVectors_;

      ar & structureFactors_;
      ar & nSample_;
   }

}
#endif