AtomStamp.hpp

/*
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 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *
 * [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
 * [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
 * [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
 * [4] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 * [5] Kuang & Gezelter, Mol. Phys., 110, 691-701 (2012).
 * [6] Lamichhane, Gezelter & Newman, J. Chem. Phys. 141, 134109 (2014).
 * [7] Lamichhane, Newman & Gezelter, J. Chem. Phys. 141, 134110 (2014).
 * [8] Bhattarai, Newman & Gezelter, Phys. Rev. B 99, 094106 (2019).
 */
 
#ifndef TYPES_ATOMSTAMP_HPP
#define TYPES_ATOMSTAMP_HPP
 
#include <set>
#include <vector>
 
#include "types/DataHolder.hpp"
 
namespace OpenMD {
 
  class AtomStamp : public DataHolder {
    DeclareParameter(Type, std::string);
 
  public:
    AtomStamp(int index);
 
  public:
    bool setPosition(const std::vector<RealType>& pos);
    bool setOrientation(const std::vector<RealType>& ort);
    bool havePosition() { return havePos_; }
    bool haveOrientation() { return haveOrt_; }
    RealType getPosX() { return position_[0]; }
    RealType getPosY() { return position_[1]; }
    RealType getPosZ() { return position_[2]; }
    RealType getEulerPhi() { return orientation_[0]; }
    RealType getEulerTheta() { return orientation_[1]; }
    RealType getEulerPsi() { return orientation_[2]; }
    int getIndex() { return index_; }
    virtual void validate();
    using AtomIter = std::set<int>::iterator;
    using BondIter = std::vector<int>::iterator;
    int getFirstBondedAtom(AtomIter& ai) {
      ai = bondedAtoms_.begin();
      return ai != bondedAtoms_.end() ? *ai : -1;
    }
    int getNextBondedAtom(AtomIter& ai) {
      ++ai;
      return ai != bondedAtoms_.end() ? *ai : -1;
    }
    int getFirstBond(BondIter& bi) {
      bi = bonds_.begin();
      return bi != bonds_.end() ? *bi : -1;
    }
    int getNextBond(BondIter& bi) {
      ++bi;
      return bi != bonds_.end() ? *bi : -1;
    }
    void addBond(int bondIndex) { bonds_.push_back(bondIndex); }
    void addBondedAtom(int atomIndex) { bondedAtoms_.insert(atomIndex); }
    size_t getCoordination() { return bonds_.size(); }
    void overrideCharge(RealType c) {
      orCharge_    = c;
      hasOverride_ = true;
    }
 
    bool hasOverride() { return hasOverride_; }
    RealType getOverrideCharge() { return orCharge_; }
 
  private:
    Vector3d position_;
    Vector3d orientation_;
    RealType orCharge_;
    bool havePos_;
    bool haveOrt_;
    bool hasOverride_;
    int index_;
    std::vector<int> bonds_;
    std::set<int> bondedAtoms_;
  };
}  // namespace OpenMD
 
#endif