OpenMD 3.0
Molecular Dynamics in the Open
Loading...
Searching...
No Matches
Bend.hpp
Go to the documentation of this file.
1/*
2 * Copyright (c) 2004-present, The University of Notre Dame. All rights
3 * reserved.
4 *
5 * Redistribution and use in source and binary forms, with or without
6 * modification, are permitted provided that the following conditions are met:
7 *
8 * 1. Redistributions of source code must retain the above copyright notice,
9 * this list of conditions and the following disclaimer.
10 *
11 * 2. Redistributions in binary form must reproduce the above copyright notice,
12 * this list of conditions and the following disclaimer in the documentation
13 * and/or other materials provided with the distribution.
14 *
15 * 3. Neither the name of the copyright holder nor the names of its
16 * contributors may be used to endorse or promote products derived from
17 * this software without specific prior written permission.
18 *
19 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
20 * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
21 * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
22 * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
23 * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
24 * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
25 * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
26 * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
27 * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
28 * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
29 * POSSIBILITY OF SUCH DAMAGE.
30 *
31 * SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
32 * research, please cite the appropriate papers when you publish your
33 * work. Good starting points are:
34 *
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 Bend.hpp
47 * @author tlin
48 * @date 11/01/2004
49 * @version 1.0
50 */
51
52#ifndef PRIMITIVES_BEND_HPP
53#define PRIMITIVES_BEND_HPP
54
55#include "primitives/Atom.hpp"
56#include "primitives/ShortRangeInteraction.hpp"
57#include "types/BendType.hpp"
58
59namespace OpenMD {
60 struct BendData {
61 RealType angle;
62 RealType potential;
63 };
64
65 struct BendDataSet {
66 RealType deltaV;
67 BendData prev;
68 BendData curr;
69 };
70
71 class Bend : public ShortRangeInteraction {
72 public:
75 Bend(Atom* atom1, Atom* atom2, Atom* atom3, BendType* bt) :
77 atoms_.resize(3);
78 atoms_[0] = atom1;
79 atoms_[1] = atom2;
80 atoms_[2] = atom3;
81 }
82
83 virtual ~Bend() {}
84 virtual void calcForce(RealType& angle, bool doParticlePot);
85
86 RealType getValue(int snapshotNo) {
87 Vector3d pos1 = atoms_[0]->getPos(snapshotNo);
88 Vector3d pos2 = atoms_[1]->getPos(snapshotNo);
89 Vector3d pos3 = atoms_[2]->getPos(snapshotNo);
90
91 Vector3d r21 = pos1 - pos2;
92 snapshotMan_->getSnapshot(snapshotNo)->wrapVector(r21);
93 RealType d21 = r21.length();
94
95 Vector3d r23 = pos3 - pos2;
96 snapshotMan_->getSnapshot(snapshotNo)->wrapVector(r23);
97 RealType d23 = r23.length();
98
99 RealType cosTheta = dot(r21, r23) / (d21 * d23);
100
101 // check roundoff
102 if (cosTheta > 1.0) {
103 cosTheta = 1.0;
104 } else if (cosTheta < -1.0) {
105 cosTheta = -1.0;
106 }
107
108 return acos(cosTheta);
109 }
110
111 RealType getPotential() { return potential_; }
112
113 Atom* getAtomA() { return atoms_[0]; }
114
115 Atom* getAtomB() { return atoms_[1]; }
116
117 Atom* getAtomC() { return atoms_[2]; }
118
119 BendType* getBendType() { return bendType_; }
120
121 virtual std::string getName() { return name_; }
122 /** Sets the name of this bend for selections */
123 virtual void setName(const std::string& name) { name_ = name; }
124
125 void accept(BaseVisitor* v) { v->visit(this); }
126
127 protected:
128 RealType potential_ {};
129 BendType* bendType_; /**< bend type */
130 std::string name_;
131 };
132} // namespace OpenMD
133
134#endif // PRIMITIVES_BEND_HPP
virtual std::string getName()
Returns the name of this ShortRangeInteraction.
Definition Bend.hpp:121
BendType * bendType_
bend type
Definition Bend.hpp:129
virtual void calcForce(RealType &angle, bool doParticlePot)
Definition Bend.cpp:56
RealType getValue(int snapshotNo)
Returns the value of this ShortRangeInteraction in specified snapshot.
Definition Bend.hpp:86
void accept(BaseVisitor *v)
Definition Bend.hpp:125
virtual void setName(const std::string &name)
Sets the name of this bend for selections.
Definition Bend.hpp:123
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.
This basic Periodic Table class was originally taken from the data.cpp file in OpenBabel.
Real dot(const DynamicVector< Real > &v1, const DynamicVector< Real > &v2)
Returns the dot product of two DynamicVectors.