IntraStructureFactor.h

#ifndef MCMD_INTRA_STRUCTURE_FACTOR_H
#define MCMD_INTRA_STRUCTURE_FACTOR_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 IntraStructureFactor 
    : public SystemAnalyzer<System>
   {

   public:

      IntraStructureFactor(System &system);

      ~IntraStructureFactor();

      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_;

      DMatrix<double>          structureFactorDelta_;

      DMatrix< std::complex<double> >  fourierModes_;

      // Array of miller index vectors for wavevectors
      DArray<IntVector>  waveIntVectors_;

      // Array of wave vectors
      DArray<Vector>  waveVectors_;

      // Array of atom type indices (-1 indicates a sum of all types)
      DArray< Pair<int> >  atomTypeIdPairs_;

      int  speciesId_;

      int  nWave_;

      int  nAtomTypeIdPair_;

      int  nSample_;

      int  nAtomType_;


   private:
      bool isInitialized_;

      void makeWaveVectors();

   };

   /*
   * Serialize to/from an archive. 
   */
   template <class Archive>
   void IntraStructureFactor::serialize(Archive& ar, 
                                        const unsigned int version)
   {
      Analyzer::serialize(ar, version);
      ar & speciesId_;
      ar & nAtomTypeIdPair_;
      ar & atomTypeIdPairs_;
      ar & nWave_;
      ar & waveIntVectors_;
      ar & nAtomType_;
      ar & structureFactors_;
      ar & fourierModes_;
      ar & nSample_;
   }

}
#endif