Sample.h

#ifndef QNANO_NEW_SAMPLE_DEFINED_H_
#define QNANO_NEW_SAMPLE_DEFINED_H_

#include "structure/Atom_List.h"
#include "structure/Neighbor_List.h"
#include "tools/Parameter_Map.h"
#include "tightbinding/TB_Parameter_List.h"

class Sample{
public:
  Atom_List atlist;
  Neighbor_List nn_list;
  Neighbor_List nn_list_unrelaxed;
  TB_Parameter_List parlist;

  inline size_t size() const{ return atlist.size(); }

  void read_atoms(const std::string &filename);
  void print_atoms(const std::string &filename, const std::vector<std::string> &materials = std::vector<std::string>()  ) const;
  void print_atoms(const std::string &filename, const std::string &material ) const{
    print_atoms(filename, std::vector<std::string>(1,material) );
  };


  void read(const std::string &filename, const std::string &neighborfile="", const std::string &resources_dir="");
  void setup(Parameter_Map &param_map);

  Sample();
  Sample(const std::string &positionfile, const std::string &neighborfile="", const std::string &resources_dir="");
  Sample(Parameter_Map &param_map);

};

#endif