Atoms_in_Boxes.h

#ifndef QNANO_NEW_ATOMS_IN_BOXES_DEFINED_H
#define QNANO_NEW_ATOMS_IN_BOXES_DEFINED_H

#include "structure/Atom_List.h"
#include "structure/Neighborhood_Criterion.h"
#include <vector>

class Atoms_in_Boxes{

private:
  std::vector<int> *boxes;
  double dx, dy, dz;
  Vec3d origin;
  
public: 
  int Nx, Ny, Nz;
  
  std::vector<int> & operator() (int ix, int iy, int iz);
  const std::vector<int> & operator() (int ix, int iy, int iz)const;
  void allocate();
  void deallocate();
  void resize(int Nx_, int Ny_, int Nz_);

  void calculate(const Atom_List &atlist, double boxwidth);
  void set_N_from_boxwidth(const Atom_List &atlist, double boxwidth);

  std::vector<int> find(const Atom_List &atlist, const Atom &a, const Neighborhood_Criterion & criterion) const;
  std::vector<int> find(const Atom_List &atlist, const Atom &a, double radius) const;

  Atoms_in_Boxes();
  Atoms_in_Boxes(const Atom_List &atlist, double boxwidth);
  ~Atoms_in_Boxes();
  
};

#endif