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root/OpenMD/branches/development/src/integrators/NVE.cpp

Comparing:
trunk/src/integrators/NVE.cpp (file contents), Revision 246 by gezelter, Wed Jan 12 22:41:40 2005 UTC vs.
branches/development/src/integrators/NVE.cpp (file contents), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

#	Line 1 | Line 1
1	<	/*
1	>	/*
2		* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3		*
4		* The University of Notre Dame grants you ("Licensee") a
#	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, 24107 (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 NVE.cpp
45	<	* @author tlin
46	<	* @date 11/08/2004
47	<	* @time 15:13am
48	<	* @version 1.0
49	<	*/
43	>	/**
44	>	* @file NVE.cpp
45	>	* @author tlin
46	>	* @date 11/08/2004
47	>	* @time 15:13am
48	>	* @version 1.0
49	>	*/
50
51		#include "integrators/NVE.hpp"
52		#include "primitives/Molecule.hpp"
53	<	#include "utils/OOPSEConstant.hpp"
53	>	#include "utils/PhysicalConstants.hpp"
54
55	<	namespace oopse {
55	>	namespace OpenMD {
56
57
58	<	NVE::NVE(SimInfo* info) : VelocityVerletIntegrator(info){
58	>	NVE::NVE(SimInfo* info) : VelocityVerletIntegrator(info){
59
60	<	}
60	>	}
61
62	<	void NVE::moveA(){
62	>	void NVE::moveA(){
63		SimInfo::MoleculeIterator i;
64		Molecule::IntegrableObjectIterator  j;
65		Molecule* mol;
#	Line 68 | Line 69 | void NVE::moveA(){
69		Vector3d frc;
70		Vector3d Tb;
71		Vector3d ji;
72	<	double mass;
72	>	RealType mass;
73
74		for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
75	<	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
76	<	integrableObject = mol->nextIntegrableObject(j)) {
75	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
76	>	integrableObject = mol->nextIntegrableObject(j)) {
77
78	<	vel =integrableObject->getVel();
79	<	pos = integrableObject->getPos();
80	<	frc = integrableObject->getFrc();
81	<	mass = integrableObject->getMass();
78	>	vel =integrableObject->getVel();
79	>	pos = integrableObject->getPos();
80	>	frc = integrableObject->getFrc();
81	>	mass = integrableObject->getMass();
82
83	<	// velocity half step
84	<	vel += (dt2 /mass * OOPSEConstant::energyConvert) * frc;
83	>	// velocity half step
84	>	vel += (dt2 /mass * PhysicalConstants::energyConvert) * frc;
85
86	<	// position whole step
87	<	pos += dt * vel;
86	>	// position whole step
87	>	pos += dt * vel;
88
89	<	integrableObject->setVel(vel);
90	<	integrableObject->setPos(pos);
89	>	integrableObject->setVel(vel);
90	>	integrableObject->setPos(pos);
91
92	<	if (integrableObject->isDirectional()){
92	>	if (integrableObject->isDirectional()){
93
94	<	// get and convert the torque to body frame
94	>	// get and convert the torque to body frame
95
96	<	Tb = integrableObject->lab2Body(integrableObject->getTrq());
96	>	Tb = integrableObject->lab2Body(integrableObject->getTrq());
97
98	<	// get the angular momentum, and propagate a half step
98	>	// get the angular momentum, and propagate a half step
99
100	<	ji = integrableObject->getJ();
100	>	ji = integrableObject->getJ();
101
102	<	ji += (dt2  * OOPSEConstant::energyConvert) * Tb;
102	>	ji += (dt2  * PhysicalConstants::energyConvert) * Tb;
103
104	<	rotAlgo->rotate(integrableObject, ji, dt);
104	>	rotAlgo->rotate(integrableObject, ji, dt);
105
106	<	integrableObject->setJ(ji);
107	<	}
106	>	integrableObject->setJ(ji);
107	>	}
108
109
110	<	}
110	>	}
111		} //end for(mol = info_->beginMolecule(i))
112
113		rattle->constraintA();
114
115	<	}
115	>	}
116
117	<	void NVE::moveB(){
117	>	void NVE::moveB(){
118		SimInfo::MoleculeIterator i;
119		Molecule::IntegrableObjectIterator  j;
120		Molecule* mol;
#	Line 122 | Line 123 | void NVE::moveB(){
123		Vector3d frc;
124		Vector3d Tb;
125		Vector3d ji;
126	<	double mass;
126	>	RealType mass;
127
128		for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
129	<	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
130	<	integrableObject = mol->nextIntegrableObject(j)) {
129	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
130	>	integrableObject = mol->nextIntegrableObject(j)) {
131
132	<	vel =integrableObject->getVel();
133	<	frc = integrableObject->getFrc();
134	<	mass = integrableObject->getMass();
132	>	vel =integrableObject->getVel();
133	>	frc = integrableObject->getFrc();
134	>	mass = integrableObject->getMass();
135
136	<	// velocity half step
137	<	vel += (dt2 /mass * OOPSEConstant::energyConvert) * frc;
136	>	// velocity half step
137	>	vel += (dt2 /mass * PhysicalConstants::energyConvert) * frc;
138
139	<	integrableObject->setVel(vel);
139	>	integrableObject->setVel(vel);
140
141	<	if (integrableObject->isDirectional()){
141	>	if (integrableObject->isDirectional()){
142
143	<	// get and convert the torque to body frame
143	>	// get and convert the torque to body frame
144
145	<	Tb = integrableObject->lab2Body(integrableObject->getTrq());
145	>	Tb = integrableObject->lab2Body(integrableObject->getTrq());
146
147	<	// get the angular momentum, and propagate a half step
147	>	// get the angular momentum, and propagate a half step
148
149	<	ji = integrableObject->getJ();
149	>	ji = integrableObject->getJ();
150
151	<	ji += (dt2  * OOPSEConstant::energyConvert) * Tb;
151	>	ji += (dt2  * PhysicalConstants::energyConvert) * Tb;
152
153	<	integrableObject->setJ(ji);
154	<	}
153	>	integrableObject->setJ(ji);
154	>	}
155
156
157	<	}
157	>	}
158		} //end for(mol = info_->beginMolecule(i))
159
160
161		rattle->constraintB();
162
163	<	}
163	>	}
164
165
166	<	double NVE::calcConservedQuantity() {
167	<	return thermo.getTotalE();
168	<	}
166	>	RealType NVE::calcConservedQuantity() {
167	>	return thermo.getTotalE() ;
168	>	}
169
170	<	} //end namespace oopse
170	>	} //end namespace OpenMD

Comparing:
trunk/src/integrators/NVE.cpp (property svn:keywords), Revision 246 by gezelter, Wed Jan 12 22:41:40 2005 UTC vs.
branches/development/src/integrators/NVE.cpp (property svn:keywords), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

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