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Comparing trunk/src/integrators/LangevinDynamics.cpp (file contents):
Revision 895 by tim, Mon Mar 13 22:42:40 2006 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
36	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	+	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43		/**
44		* @file LangevinDynamics.cpp
45		* @author tlin
46		* @date 11/08/2004
46	–	* @time 15:13am
47		* @version 1.0
48		*/
49
50		#include "integrators/LangevinDynamics.hpp"
51		#include "primitives/Molecule.hpp"
52	<	#include "utils/OOPSEConstant.hpp"
52	>	#include "utils/PhysicalConstants.hpp"
53		#include "integrators/LDForceManager.hpp"
54	<	namespace oopse {
54	>	namespace OpenMD {
55
56	<
56	>
57		LangevinDynamics::LangevinDynamics(SimInfo* info) : VelocityVerletIntegrator(info){
58		setForceManager(new LDForceManager(info));
59	–	}
59
60	+	// Langevin Dynamics Force Manager needs to know about the half-time step
61	+	// size to get convergence on the friction forces:
62	+	dynamic_cast<LDForceManager*>(forceMan_)->setDt2(dt2);
63	+	}
64	+
65		void LangevinDynamics::moveA(){
66		SimInfo::MoleculeIterator i;
67		Molecule::IntegrableObjectIterator  j;
68		Molecule* mol;
69	<	StuntDouble* integrableObject;
69	>	StuntDouble* sd;
70		Vector3d vel;
71		Vector3d pos;
72		Vector3d frc;
73		Vector3d Tb;
74		Vector3d ji;
75	<	double mass;
75	>	RealType mass;
76
77	<	for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
78	<	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
75	<	integrableObject = mol->nextIntegrableObject(j)) {
77	>	for (mol = info_->beginMolecule(i); mol != NULL;
78	>	mol = info_->nextMolecule(i)) {
79
80	<	vel =integrableObject->getVel();
81	<	pos = integrableObject->getPos();
82	<	frc = integrableObject->getFrc();
83	<	mass = integrableObject->getMass();
80	>	for (sd = mol->beginIntegrableObject(j); sd != NULL;
81	>	sd = mol->nextIntegrableObject(j)) {
82	>
83	>	vel = sd->getVel();
84	>	pos = sd->getPos();
85	>	frc = sd->getFrc();
86	>	mass = sd->getMass();
87
88		// velocity half step
89	<	vel += (dt2 /mass * OOPSEConstant::energyConvert) * frc;
89	>	vel += (dt2 /mass * PhysicalConstants::energyConvert) * frc;
90
91		// position whole step
92		pos += dt * vel;
93
94	<	integrableObject->setVel(vel);
95	<	integrableObject->setPos(pos);
94	>	sd->setVel(vel);
95	>	sd->setPos(pos);
96
97	<	if (integrableObject->isDirectional()){
97	>	if (sd->isDirectional()){
98
99		// get and convert the torque to body frame
100
101	<	Tb = integrableObject->lab2Body(integrableObject->getTrq());
101	>	Tb = sd->lab2Body(sd->getTrq());
102
103		// get the angular momentum, and propagate a half step
104
105	<	ji = integrableObject->getJ();
105	>	ji = sd->getJ();
106
107	<	ji += (dt2  * OOPSEConstant::energyConvert) * Tb;
107	>	ji += (dt2  * PhysicalConstants::energyConvert) * Tb;
108
109	<	rotAlgo->rotate(integrableObject, ji, dt);
109	>	rotAlgo_->rotate(sd, ji, dt);
110
111	<	integrableObject->setJ(ji);
111	>	sd->setJ(ji);
112		}
113
114
115		}
116		} //end for(mol = info_->beginMolecule(i))
117
118	<	rattle->constraintA();
119	<
118	>	flucQ_->moveA();
119	>	rattle_->constraintA();
120		}
121
122		void LangevinDynamics::moveB(){
123		SimInfo::MoleculeIterator i;
124		Molecule::IntegrableObjectIterator  j;
125		Molecule* mol;
126	<	StuntDouble* integrableObject;
126	>	StuntDouble* sd;
127		Vector3d vel;
128		Vector3d frc;
129		Vector3d Tb;
130		Vector3d ji;
131	<	double mass;
131	>	RealType mass;
132
133	<	for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
134	<	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
129	<	integrableObject = mol->nextIntegrableObject(j)) {
133	>	for (mol = info_->beginMolecule(i); mol != NULL;
134	>	mol = info_->nextMolecule(i)) {
135
136	<	vel =integrableObject->getVel();
137	<	frc = integrableObject->getFrc();
138	<	mass = integrableObject->getMass();
136	>	for (sd = mol->beginIntegrableObject(j); sd != NULL;
137	>	sd = mol->nextIntegrableObject(j)) {
138	>
139	>	vel = sd->getVel();
140	>	frc = sd->getFrc();
141	>	mass = sd->getMass();
142
143		// velocity half step
144	<	vel += (dt2 /mass * OOPSEConstant::energyConvert) * frc;
144	>	vel += (dt2 /mass * PhysicalConstants::energyConvert) * frc;
145
146	<	integrableObject->setVel(vel);
146	>	sd->setVel(vel);
147
148	<	if (integrableObject->isDirectional()){
148	>	if (sd->isDirectional()){
149
150		// get and convert the torque to body frame
151
152	<	Tb = integrableObject->lab2Body(integrableObject->getTrq());
152	>	Tb = sd->lab2Body(sd->getTrq());
153
154		// get the angular momentum, and propagate a half step
155
156	<	ji = integrableObject->getJ();
156	>	ji = sd->getJ();
157
158	<	ji += (dt2  * OOPSEConstant::energyConvert) * Tb;
158	>	ji += (dt2  * PhysicalConstants::energyConvert) * Tb;
159
160	<	integrableObject->setJ(ji);
160	>	sd->setJ(ji);
161		}
162
163
164		}
165		} //end for(mol = info_->beginMolecule(i))
166
167	<
168	<	rattle->constraintB();
161	<
167	>	flucQ_->moveB();
168	>	rattle_->constraintB();
169		}
170
171
172	<	double LangevinDynamics::calcConservedQuantity() {
172	>	RealType LangevinDynamics::calcConservedQuantity() {
173		return 0.0;
174		}
175
176	<	} //end namespace oopse
176	>	} //end namespace OpenMD
177

Comparing trunk/src/integrators/LangevinDynamics.cpp (property svn:keywords):
Revision 895 by tim, Mon Mar 13 22:42:40 2006 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

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