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#ifndef PRIMITIVES_BOND_HPP |
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#define PRIMITIVES_BOND_HPP |
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#include "primitives/ShortRangeInteraction.hpp" |
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#include "primitives/Atom.hpp" |
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#include "types/BondType.hpp" |
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namespace OpenMD { |
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class Bond { |
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class Bond : public ShortRangeInteraction { |
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public: |
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Bond(Atom* atom1, Atom* atom2, BondType* bt) : atom1_(atom1), |
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atom2_(atom2), |
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bondType_(bt) {} |
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Bond(Atom* atom1, Atom* atom2, BondType* bt) : ShortRangeInteraction(), |
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bondType_(bt) { |
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atoms_.resize(2); |
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atoms_[0] = atom1; |
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atoms_[1] = atom2; |
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} |
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virtual ~Bond() {} |
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void calcForce(bool doParticlePot) { |
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RealType len; |
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Vector3d r12; |
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Vector3d force; |
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r12 = atom2_->getPos() - atom1_->getPos(); |
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r12 = atoms_[1]->getPos() - atoms_[0]->getPos(); |
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len = r12.length(); |
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bondType_->calcForce(len, potential_, dvdr); |
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force = r12 * (-dvdr / len); |
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atom1_->addFrc(-force); |
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atom2_->addFrc(force); |
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atoms_[0]->addFrc(-force); |
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atoms_[1]->addFrc(force); |
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if (doParticlePot) { |
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atom1_->addParticlePot(potential_); |
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atom2_->addParticlePot(potential_); |
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atoms_[0]->addParticlePot(potential_); |
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atoms_[1]->addParticlePot(potential_); |
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} |
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} |
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RealType getValue(int snap) { |
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Vector3d r12 = atoms_[1]->getPos(snap) - atoms_[0]->getPos(snap); |
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return r12.length(); |
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} |
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RealType getPotential() { |
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return potential_; |
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} |
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Atom* getAtomA() { |
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return atom1_; |
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return atoms_[0]; |
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} |
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Atom* getAtomB() { |
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return atom2_; |
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return atoms_[1]; |
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} |
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BondType* getBondType() { |
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return bondType_; |
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} |
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virtual std::string getName() { return name_;} |
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/** Sets the name of this bond for selections */ |
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virtual void setName(const std::string& name) { name_ = name; } |
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void accept(BaseVisitor* v) { |
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v->visit(this); |
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} |
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private: |
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RealType potential_; |
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Atom* atom1_; |
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Atom* atom2_; |
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BondType* bondType_; /**< bond type */ |
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std::string name_; |
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}; |
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} //end namespace OpenMD |
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#endif //PRIMITIVES_BOND_HPP |
