OpenMD 3.0
Molecular Dynamics in the Open
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LangevinDynamics.cpp
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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 LangevinDynamics.cpp
47 * @author tlin
48 * @date 11/08/2004
49 * @version 1.0
50 */
51
52#include "integrators/LangevinDynamics.hpp"
53
55#include "utils/Constants.hpp"
56
57namespace OpenMD {
58
59 LangevinDynamics::LangevinDynamics(SimInfo* info) :
61
62 void LangevinDynamics::moveA() {
63 SimInfo::MoleculeIterator i;
64 Molecule::IntegrableObjectIterator j;
65 Molecule* mol;
66 StuntDouble* sd;
67 Vector3d vel;
68 Vector3d pos;
69 Vector3d frc;
70 Vector3d Tb;
71 Vector3d ji;
72 RealType mass;
73
74 for (mol = info_->beginMolecule(i); mol != NULL;
75 mol = info_->nextMolecule(i)) {
76 for (sd = mol->beginIntegrableObject(j); sd != NULL;
77 sd = mol->nextIntegrableObject(j)) {
78 vel = sd->getVel();
79 pos = sd->getPos();
80 frc = sd->getFrc();
81 mass = sd->getMass();
82
83 // velocity half step
84 vel += (dt2 / mass * Constants::energyConvert) * frc;
85
86 // position whole step
87 pos += dt * vel;
88
89 sd->setVel(vel);
90 sd->setPos(pos);
91
92 if (sd->isDirectional()) {
93 // get and convert the torque to body frame
94
95 Tb = sd->lab2Body(sd->getTrq());
96
97 // get the angular momentum, and propagate a half step
98
99 ji = sd->getJ();
100
101 ji += (dt2 * Constants::energyConvert) * Tb;
102
103 rotAlgo_->rotate(sd, ji, dt);
104
105 sd->setJ(ji);
106 }
107 }
108 } // end for(mol = info_->beginMolecule(i))
109
110 flucQ_->moveA();
111 rattle_->constraintA();
112 }
113
114 void LangevinDynamics::moveB() {
115 SimInfo::MoleculeIterator i;
116 Molecule::IntegrableObjectIterator j;
117 Molecule* mol;
118 StuntDouble* sd;
119 Vector3d vel;
120 Vector3d frc;
121 Vector3d Tb;
122 Vector3d ji;
123 RealType mass;
124
125 for (mol = info_->beginMolecule(i); mol != NULL;
126 mol = info_->nextMolecule(i)) {
127 for (sd = mol->beginIntegrableObject(j); sd != NULL;
128 sd = mol->nextIntegrableObject(j)) {
129 vel = sd->getVel();
130 frc = sd->getFrc();
131 mass = sd->getMass();
132
133 // velocity half step
134 vel += (dt2 / mass * Constants::energyConvert) * frc;
135
136 sd->setVel(vel);
137
138 if (sd->isDirectional()) {
139 // get and convert the torque to body frame
140
141 Tb = sd->lab2Body(sd->getTrq());
142
143 // get the angular momentum, and propagate a half step
144
145 ji = sd->getJ();
146
147 ji += (dt2 * Constants::energyConvert) * Tb;
148
149 sd->setJ(ji);
150 }
151 }
152 } // end for(mol = info_->beginMolecule(i))
153
154 flucQ_->moveB();
155 rattle_->constraintB();
156 }
157
158 RealType LangevinDynamics::calcConservedQuantity() { return 0.0; }
159} // namespace OpenMD
One of the heavy-weight classes of OpenMD, SimInfo maintains objects and variables relating to the cu...
Definition SimInfo.hpp:93
Molecule * beginMolecule(MoleculeIterator &i)
Returns the first molecule in this SimInfo and intialize the iterator.
Definition SimInfo.cpp:240
Molecule * nextMolecule(MoleculeIterator &i)
Returns the next avaliable Molecule based on the iterator.
Definition SimInfo.cpp:245
"Don't move, or you're dead! Stand up! Captain, we've got them!"
Vector3d getTrq()
Returns the current torque of this stuntDouble.
Vector3d lab2Body(const Vector3d &v)
Converts a lab fixed vector to a body fixed vector.
Vector3d getVel()
Returns the current velocity of this stuntDouble.
RealType getMass()
Returns the mass of this stuntDouble.
Vector3d getPos()
Returns the current position of this stuntDouble.
void setPos(const Vector3d &pos)
Sets the current position of this stuntDouble.
void setVel(const Vector3d &vel)
Sets the current velocity of this stuntDouble.
Vector3d getJ()
Returns the current angular momentum of this stuntDouble (body -fixed).
bool isDirectional()
Tests if this stuntDouble is a directional one.
Vector3d getFrc()
Returns the current force of this stuntDouble.
void setJ(const Vector3d &angMom)
Sets the current angular momentum of this stuntDouble (body-fixed).
This basic Periodic Table class was originally taken from the data.cpp file in OpenBabel.