MoleculeExtractor.h

// Copyright (C) 2015 Technische Universitaet Muenchen
// This file is part of the Mamico project. For conditions of distribution
// and use, please see the copyright notice in Mamico's main folder, or at
// www5.in.tum.de/mamico
#ifndef _MOLECULARDYNAMICS_COUPLING_CELLMAPPINGS_MOLECULEEXTRACTOR_H_
#define _MOLECULARDYNAMICS_COUPLING_CELLMAPPINGS_MOLECULEEXTRACTOR_H_
#include "coupling/interface/MDSolverInterface.h"
#include "coupling/interface/MoleculeIterator.h"
#include <iostream>
 
namespace coupling {
namespace cellmappings {
template <class LinkedCell, unsigned int dim> class MoleculeExtractor;
}
} // namespace coupling

template <class LinkedCell, unsigned int dim> class coupling::cellmappings::MoleculeExtractor {
public:
  MoleculeExtractor(coupling::interface::MDSolverInterface<LinkedCell, dim>* const mdSolverInterface) : _mdSolverInterface(mdSolverInterface) {
    _molecules.clear();
  }

  ~MoleculeExtractor() {}

  void beginCellIteration() { _molecules.clear(); }

  void endCellIteration() {}

  void handleCell(LinkedCell& cell) {
    coupling::interface::MoleculeIterator<LinkedCell, dim>* it = _mdSolverInterface->getMoleculeIterator(cell);
    it->begin();
    while (it->continueIteration()) {
      _molecules.push_back(it->getConst().getPosition());
      it->next();
    }
    delete it;
  }

  const std::vector<tarch::la::Vector<dim, double>>& getExtractedMolecules() const { return _molecules; }
 
private:
  coupling::interface::MDSolverInterface<LinkedCell, dim>* const _mdSolverInterface;
  std::vector<tarch::la::Vector<dim, double>> _molecules;
};
 
#endif // _MOLECULARDYNAMICS_COUPLING_CELLMAPPINGS_MOLECULEEXTRACTOR_H_