Neighbor_List.h

#ifndef QNANO_NEW_NEIGHBOR_LIST_DEFINED_H
#define QNANO_NEW_NEIGHBOR_LIST_DEFINED_H

#include "structure/Neighbor.h"
#include "tightbinding/TB_Parameter_List.h"
#include "structure/Atoms_in_Boxes.h"
#include "structure/Atom_List.h"
#include "structure/Neighborhood_Criterion_Lattice.h"
#include "structure/Periodic_Vecs.h"


class Neighbor_List: public List_Class<std::vector<Neighbor> > {
public:
  void setup(Parameter_Map &param_map, const Atom_List &atlist);
  void setup(Parameter_Map &param_map);


  void add(const Atom_List &atlist, const Neighborhood_Criterion &criterion,  double boxwidth=-1.);

  void add_shifted(const Atom_List &atlist, const Neighborhood_Criterion &criterion, const Vec3d &shift, double boxwidth=-1.);

  void calculate(const Atom_List &atlist, const Neighborhood_Criterion &criterion, const std::vector<Vec3d> & periodic_vec=std::vector<Vec3d>(), double boxwidth=-1.);
  void calculate(const Atom_List &atlist, const Lattice &lat, const std::vector<Vec3d> & periodic_vec=std::vector<Vec3d>(), double tolerance=0.20){
    Neighborhood_Criterion_Lattice criterion(lat, tolerance);
    calculate(atlist, criterion, periodic_vec, criterion.upper_bound_radius());
  }
  

  void calculate_unrelaxed(const Atom_List &atlist, const Lattice &lat, double tolerance=0.2);
  void setup_unrelaxed_from_relaxed(const Atom_List & atlist, const Neighbor_List & neilist_relaxed, const TB_Parameter_List &parlist);

  
//  bool calcualte_unrelaxed_single(const Atom_List &atlist, size_t index1, size_t index2, size_t nindex, const Lattice &lat, double tolerance=0.2, const Vec3d &shift=Vec3d());
  bool calcualte_unrelaxed_single(const Neighbor_List &other, size_t index, size_t n, const Lattice &lat, double tolerance=0.2, const Vec3d &shift=Vec3d());

  

  size_t get_max_neighbors_per_atom()const;
  //read from file
  void read(const std::string &filename, const Atom_List &atlist);
  //print neighbors file
  void print(const std::string &filename)const;
  //print neighbors file with bond vectors 'D'
  void print_withD(const std::string &filename)const;
  

  //Basic consistency check: if A is a neighbor of B, B has to be a neighbor of A
  void check_consistency()const;

  //Constructors:
  Neighbor_List(){}
  Neighbor_List(const Atom_List &atlist, const Neighborhood_Criterion &criterion, const std::vector<Vec3d> &periodic_vec=std::vector<Vec3d>(), double boxwidth=-1.){
    calculate(atlist, criterion, periodic_vec, boxwidth);
  }
  Neighbor_List(const Atom_List &atlist, const Lattice &lat, const std::vector<Vec3d> &periodic_vec=std::vector<Vec3d>(), double tolerance=0.2){
    calculate(atlist, lat, periodic_vec, tolerance);
  }
};

#endif