OpenMD 3.0
Molecular Dynamics in the Open
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Inversion.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).
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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 Inversion.hpp
47 * @author tlin
48 * @date 11/01/2004
49 * @version 1.0
50 */
51
52#ifndef PRIMITIVES_INVERSION_HPP
53#define PRIMITIVES_INVERSION_HPP
54
55#include "primitives/Atom.hpp"
56#include "primitives/ShortRangeInteraction.hpp"
58
59namespace OpenMD {
61 RealType angle;
62 RealType potential;
63 };
64
66 RealType deltaV;
67 InversionData prev;
68 InversionData curr;
69 };
70
71 /**
72 * @class Inversion Inversion.hpp "primitives/Inversion.hpp"
73 */
75 public:
78
79 Inversion(Atom* atom1, Atom* atom2, Atom* atom3, Atom* atom4,
80 InversionType* it);
81 virtual ~Inversion() {}
82 virtual void calcForce(RealType& angle, bool doParticlePot);
83
84 RealType getValue(int snapshotNo) {
85 // In OpenMD's version of an inversion, the central atom
86 // comes first. However, to get the planarity in a typical cosine
87 // version of this potential (i.e. Amber-style), the central atom
88 // is treated as atom *3* in a standard torsion form:
89
90 Vector3d pos1 = atoms_[1]->getPos(snapshotNo);
91 Vector3d pos2 = atoms_[2]->getPos(snapshotNo);
92 Vector3d pos3 = atoms_[0]->getPos(snapshotNo);
93 Vector3d pos4 = atoms_[3]->getPos(snapshotNo);
94
95 Vector3d r31 = pos1 - pos3;
96 snapshotMan_->getSnapshot(snapshotNo)->wrapVector(r31);
97 Vector3d r23 = pos3 - pos2;
98 snapshotMan_->getSnapshot(snapshotNo)->wrapVector(r23);
99 Vector3d r43 = pos3 - pos4;
100 snapshotMan_->getSnapshot(snapshotNo)->wrapVector(r43);
101
102 // Calculate the cross products and distances
103 Vector3d A = cross(r31, r43);
104 Vector3d B = cross(r43, r23);
105
106 A.normalize();
107 B.normalize();
108
109 // Calculate the sin and cos
110 RealType cos_phi = dot(A, B);
111 if (cos_phi > 1.0) cos_phi = 1.0;
112 if (cos_phi < -1.0) cos_phi = -1.0;
113 return acos(cos_phi);
114 }
115
116 RealType getPotential() { return potential_; }
117
118 Atom* getAtomA() { return atoms_[0]; }
119
120 Atom* getAtomB() { return atoms_[1]; }
121
122 Atom* getAtomC() { return atoms_[2]; }
123
124 Atom* getAtomD() { return atoms_[3]; }
125
126 InversionType* getInversionType() { return inversionType_; }
127 virtual std::string getName() { return name_; }
128 /** Sets the name of this inversion for selections */
129 virtual void setName(const std::string& name) { name_ = name; }
130
131 void accept(BaseVisitor* v) { v->visit(this); }
132
133 protected:
134 InversionType* inversionType_;
135 InversionKey inversionKey_;
136 std::string name_;
137
138 RealType potential_;
139 };
140} // namespace OpenMD
141
142#endif // PRIMITIVES_INVERSION_HPP
virtual std::string getName()
Returns the name of this ShortRangeInteraction.
RealType getValue(int snapshotNo)
Returns the value of this ShortRangeInteraction in specified snapshot.
Definition Inversion.hpp:84
virtual void setName(const std::string &name)
Sets the name of this inversion for selections.
void accept(BaseVisitor *v)
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 normalize()
Normalizes this vector in place.
Definition Vector.hpp:402
This basic Periodic Table class was originally taken from the data.cpp file in OpenBabel.
Vector3< Real > cross(const Vector3< Real > &v1, const Vector3< Real > &v2)
Returns the cross product of two Vectors.
Definition Vector3.hpp:136
Real dot(const DynamicVector< Real > &v1, const DynamicVector< Real > &v2)
Returns the dot product of two DynamicVectors.