OpenMD 3.0
Molecular Dynamics in the Open
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Bond.hpp
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35 * [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
36 * [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
37 * [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
38 * [4] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
39 * [5] Kuang & Gezelter, Mol. Phys., 110, 691-701 (2012).
40 * [6] Lamichhane, Gezelter & Newman, J. Chem. Phys. 141, 134109 (2014).
41 * [7] Lamichhane, Newman & Gezelter, J. Chem. Phys. 141, 134110 (2014).
42 * [8] Bhattarai, Newman & Gezelter, Phys. Rev. B 99, 094106 (2019).
43 */
44
45/**
46 * @file Bond.hpp
47 * @author tlin
48 * @date 11/01/2004
49 * @version 1.0
50 */
51
52#ifndef PRIMITIVES_BOND_HPP
53#define PRIMITIVES_BOND_HPP
54
55#include "primitives/Atom.hpp"
56#include "primitives/ShortRangeInteraction.hpp"
57#include "types/BondType.hpp"
58
59namespace OpenMD {
60
61 class Bond : public ShortRangeInteraction {
62 public:
65 Bond(Atom* atom1, Atom* atom2, BondType* bt) :
66 ShortRangeInteraction(), bondType_(bt) {
67 atoms_.resize(2);
68 atoms_[0] = atom1;
69 atoms_[1] = atom2;
70 }
71 virtual ~Bond() {}
72 void calcForce(bool doParticlePot) {
73 RealType len;
74 RealType dvdr;
75 Vector3d r12;
76 Vector3d force;
77
78 r12 = atoms_[1]->getPos() - atoms_[0]->getPos();
79 snapshotMan_->getCurrentSnapshot()->wrapVector(r12);
80 len = r12.length();
81 bondType_->calcForce(len, potential_, dvdr);
82
83 force = r12 * (-dvdr / len);
84
85 atoms_[0]->addFrc(-force);
86 atoms_[1]->addFrc(force);
87 if (doParticlePot) {
88 atoms_[0]->addParticlePot(potential_);
89 atoms_[1]->addParticlePot(potential_);
90 }
91 }
92
93 RealType getValue(int snap) {
94 Vector3d r12 = atoms_[1]->getPos(snap) - atoms_[0]->getPos(snap);
95 snapshotMan_->getSnapshot(snap)->wrapVector(r12);
96 return r12.length();
97 }
98
99 RealType getPotential() { return potential_; }
100
101 Atom* getAtomA() { return atoms_[0]; }
102
103 Atom* getAtomB() { return atoms_[1]; }
104
105 BondType* getBondType() { return bondType_; }
106
107 virtual std::string getName() { return name_; }
108 /** Sets the name of this bond for selections */
109 virtual void setName(const std::string& name) { name_ = name; }
110
111 void accept(BaseVisitor* v) { v->visit(this); }
112
113 private:
114 RealType potential_ {};
115 BondType* bondType_; /**< bond type */
116 std::string name_;
117 };
118} // namespace OpenMD
119
120#endif // PRIMITIVES_BOND_HPP
virtual std::string getName()
Returns the name of this ShortRangeInteraction.
Definition Bond.hpp:107
void accept(BaseVisitor *v)
Definition Bond.hpp:111
virtual void setName(const std::string &name)
Sets the name of this bond for selections.
Definition Bond.hpp:109
RealType getValue(int snap)
Returns the value of this ShortRangeInteraction in specified snapshot.
Definition Bond.hpp:93
BondType class is responsible for calculating the force and energy of the bond.
Definition BondType.hpp:64
A ShortRangeInteraction holds some bookeeping data for bonded interactions (e.g.
virtual RealType getValue()
Returns the current value of this ShortRangeInteraction.
virtual RealType getPrevValue()
Returns the previous value of this ShortRangeInteraction.
void wrapVector(Vector3d &v)
Wrapping the vector according to periodic boundary condition.
Definition Snapshot.cpp:337
Snapshot * getCurrentSnapshot()
Returns the pointer of current snapshot.
This basic Periodic Table class was originally taken from the data.cpp file in OpenBabel.