Bond.hpp

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 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the following paper when you publish your work:
 *
 * [1] Drisko et al., J. Open Source Softw. 9, 7004 (2024).
 *
 * Good starting points for code and simulation methodology are:
 *
 * [2] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
 * [3] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
 * [4] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
 * [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 * [6] Kuang & Gezelter, Mol. Phys., 110, 691-701 (2012).
 * [7] Lamichhane, Gezelter & Newman, J. Chem. Phys. 141, 134109 (2014).
 * [8] Bhattarai, Newman & Gezelter, Phys. Rev. B 99, 094106 (2019).
 * [9] Drisko & Gezelter, J. Chem. Theory Comput. 20, 4986-4997 (2024).
 */
 
/**
 * @file Bond.hpp
 * @author    tlin
 * @date  11/01/2004
 * @version 1.0
 */
 
#ifndef PRIMITIVES_BOND_HPP
#define PRIMITIVES_BOND_HPP
 
#include "primitives/Atom.hpp"
#include "primitives/ShortRangeInteraction.hpp"
#include "types/BondType.hpp"
 
namespace OpenMD {
 
  class Bond : public ShortRangeInteraction {
  public:
    using ShortRangeInteraction::getPrevValue;
    using ShortRangeInteraction::getValue;
    Bond(Atom* atom1, Atom* atom2, BondType* bt) :
        ShortRangeInteraction(), bondType_(bt) {
      atoms_.resize(2);
      atoms_[0] = atom1;
      atoms_[1] = atom2;
    }
    virtual ~Bond() {}
    void calcForce(bool doParticlePot) {
      RealType len;
      RealType dvdr;
      Vector3d r12;
      Vector3d force;
 
      r12 = atoms_[1]->getPos() - atoms_[0]->getPos();
      snapshotMan_->getCurrentSnapshot()->wrapVector(r12);
      len = r12.length();
      bondType_->calcForce(len, potential_, dvdr);
 
      force = r12 * (-dvdr / len);
 
      atoms_[0]->addFrc(-force);
      atoms_[1]->addFrc(force);
      if (doParticlePot) {
        atoms_[0]->addParticlePot(potential_);
        atoms_[1]->addParticlePot(potential_);
      }
    }
 
    RealType getValue(int snap) {
      Vector3d r12 = atoms_[1]->getPos(snap) - atoms_[0]->getPos(snap);
      snapshotMan_->getSnapshot(snap)->wrapVector(r12);
      return r12.length();
    }
 
    RealType getPotential() { return potential_; }
 
    Atom* getAtomA() { return atoms_[0]; }
 
    Atom* getAtomB() { return atoms_[1]; }
 
    BondType* getBondType() { return bondType_; }
 
    virtual std::string getName() { return name_; }
    /** Sets the name of this bond for selections */
    virtual void setName(const std::string& name) { name_ = name; }
 
    void accept(BaseVisitor* v) { v->visit(this); }
 
  private:
    RealType potential_ {};
    BondType* bondType_; /**< bond type */
    std::string name_;
  };
}  // namespace OpenMD
 
#endif  // PRIMITIVES_BOND_HPP