ConnectivityGenerator.h

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#ifndef MMPARAMETRIZATION_CONNECTIVITYGENERATOR_H
#define MMPARAMETRIZATION_CONNECTIVITYGENERATOR_H

#include <list>
#include <memory>
#include <vector>

namespace Scine {

namespace Core {
struct Log;
} // namespace Core

namespace Utils {
class Settings;
class BondOrderCollection;
} // namespace Utils

namespace MMParametrization {
struct ParametrizationData;

class ConnectivityGenerator {
 public:
  ConnectivityGenerator(ParametrizationData& data, std::shared_ptr<Utils::Settings> settings, Core::Log& log);
  void generateInitialListsOfNeighbors();
  void refineListsOfNeighbors();

 private:
  // Helper function to convert a lists of neighbors vector to a bond order matrix
  Utils::BondOrderCollection generateBondOrderMatrixFromListsOfNeighbors(const std::vector<std::list<int>>& listsOfNeighbors) const;
  // The data used within all MM parametrization classes
  ParametrizationData& data_;
  // The settings
  std::shared_ptr<Utils::Settings> settings_;
  // Logger
  Core::Log& log_;
  // The threshold for a bond's bond order to be considered a bond
  double bondOrderThreshold_ = 0.4;
};

} // namespace MMParametrization
} // namespace Scine

#endif // MMPARAMETRIZATION_CONNECTIVITYGENERATOR_H