Atom_List.h

#ifndef QNANO_NEW_ATOM_LIST_DEFINED_H
#define QNANO_NEW_ATOM_LIST_DEFINED_H

#include "structure/Atom.h"
#include "tools/List_Class.h"
#include "tools/Parameter_Map.h"
#include "structure/Lattice.h"

class Atom_List: public List_Class<Atom> {
public:

  Vec3d bbox_min() const;
  Vec3d bbox_max() const;
  Vec3d bbox_center() const;
  Vec3d bbox_width() const;
  std::pair<Vec3d,Vec3d> bbox() const;

  void read(const std::string &filename);
  void setup(Parameter_Map &param_map, bool *successful=NULL);
  void print(const std::string &filename, const std::vector<std::string> &materials = std::vector<std::string>() ) const;
  static std::vector<std::string> get_material_names_from_file(const std::string &filename);
  
  void generate_from_lattice(const Lattice &lat, int Nx, int Ny, int Nz);
  void generate_from_material_file(const std::string &res_dir, const std::string &material, int Nx, int Ny, int Nz);
  void replace_elements(int from, int to);
  
  //cutting and shaping
  void cut_radius(double radius, const Vec3d &center);
  void cut_plane(double a, double b, double c, double d, const Vec3d &center);
  void cut_plane(const std::vector<double> &v, const Vec3d &center);
  void cut_plane(const Vec3d &v, const Vec3d &center);
  

  //constructors
  Atom_List(){}
  Atom_List(const std::string &filename){ read(filename);}
  Atom_List(Parameter_Map &param_map, bool *successful=NULL){setup(param_map, successful);}

};

#endif