ViewVC Help

View File | Revision Log | Show Annotations | View Changeset | Root Listing

root/OpenMD/trunk/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.
Revision 1782 by gezelter, Wed Aug 22 02:28:28 2012 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;
66	<	StuntDouble* integrableObject;
66	>	StuntDouble* sd;
67		Vector3d vel;
68		Vector3d pos;
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;
75	<	integrableObject = mol->nextIntegrableObject(j)) {
74	>	for (mol = info_->beginMolecule(i); mol != NULL;
75	>	mol = info_->nextMolecule(i)) {
76
77	<	vel =integrableObject->getVel();
78	<	pos = integrableObject->getPos();
79	<	frc = integrableObject->getFrc();
80	<	mass = integrableObject->getMass();
77	>	for (sd = mol->beginIntegrableObject(j); sd != NULL;
78	>	sd = mol->nextIntegrableObject(j)) {
79	>
80	>	vel = sd->getVel();
81	>	pos = sd->getPos();
82	>	frc = sd->getFrc();
83	>	mass = sd->getMass();
84
85	<	// velocity half step
86	<	vel += (dt2 /mass * OOPSEConstant::energyConvert) * frc;
85	>	// velocity half step
86	>	vel += (dt2 /mass * PhysicalConstants::energyConvert) * frc;
87
88	<	// position whole step
89	<	pos += dt * vel;
88	>	// position whole step
89	>	pos += dt * vel;
90
91	<	integrableObject->setVel(vel);
92	<	integrableObject->setPos(pos);
91	>	sd->setVel(vel);
92	>	sd->setPos(pos);
93
94	<	if (integrableObject->isDirectional()){
94	>	if (sd->isDirectional()){
95
96	<	// get and convert the torque to body frame
96	>	// get and convert the torque to body frame
97
98	<	Tb = integrableObject->lab2Body(integrableObject->getTrq());
98	>	Tb = sd->lab2Body(sd->getTrq());
99
100	<	// get the angular momentum, and propagate a half step
100	>	// get the angular momentum, and propagate a half step
101
102	<	ji = integrableObject->getJ();
102	>	ji = sd->getJ();
103
104	<	ji += (dt2  * OOPSEConstant::energyConvert) * Tb;
104	>	ji += (dt2  * PhysicalConstants::energyConvert) * Tb;
105
106	<	rotAlgo->rotate(integrableObject, ji, dt);
106	>	rotAlgo_->rotate(sd, ji, dt);
107
108	<	integrableObject->setJ(ji);
109	<	}
108	>	sd->setJ(ji);
109	>	}
110
111
112	<	}
113	<	} //end for(mol = info_->beginMolecule(i))
114	<
115	<	rattle->constraintA();
116	<
114	<	}
112	>	}
113	>	}
114	>	flucQ_->moveA();
115	>	rattle_->constraintA();
116	>	}
117
118	<	void NVE::moveB(){
118	>	void NVE::moveB(){
119		SimInfo::MoleculeIterator i;
120		Molecule::IntegrableObjectIterator  j;
121		Molecule* mol;
122	<	StuntDouble* integrableObject;
122	>	StuntDouble* sd;
123		Vector3d vel;
124		Vector3d frc;
125		Vector3d Tb;
126		Vector3d ji;
127	<	double mass;
127	>	RealType mass;
128
129	<	for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
130	<	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
129	<	integrableObject = mol->nextIntegrableObject(j)) {
129	>	for (mol = info_->beginMolecule(i); mol != NULL;
130	>	mol = info_->nextMolecule(i)) {
131
132	<	vel =integrableObject->getVel();
133	<	frc = integrableObject->getFrc();
134	<	mass = integrableObject->getMass();
132	>	for (sd = mol->beginIntegrableObject(j); sd != NULL;
133	>	sd = mol->nextIntegrableObject(j)) {
134	>
135	>	vel = sd->getVel();
136	>	frc = sd->getFrc();
137	>	mass = sd->getMass();
138
139	<	// velocity half step
140	<	vel += (dt2 /mass * OOPSEConstant::energyConvert) * frc;
139	>	// velocity half step
140	>	vel += (dt2 /mass * PhysicalConstants::energyConvert) * frc;
141
142	<	integrableObject->setVel(vel);
142	>	sd->setVel(vel);
143
144	<	if (integrableObject->isDirectional()){
144	>	if (sd->isDirectional()){
145
146	<	// get and convert the torque to body frame
146	>	// get and convert the torque to body frame
147
148	<	Tb = integrableObject->lab2Body(integrableObject->getTrq());
148	>	Tb = sd->lab2Body(sd->getTrq());
149
150	<	// get the angular momentum, and propagate a half step
150	>	// get the angular momentum, and propagate a half step
151
152	<	ji = integrableObject->getJ();
152	>	ji = sd->getJ();
153
154	<	ji += (dt2  * OOPSEConstant::energyConvert) * Tb;
154	>	ji += (dt2  * PhysicalConstants::energyConvert) * Tb;
155
156	<	integrableObject->setJ(ji);
157	<	}
156	>	sd->setJ(ji);
157	>	}
158
159
160	<	}
161	<	} //end for(mol = info_->beginMolecule(i))
160	>	}
161	>	}
162
163	+	flucQ_->moveB();
164	+	rattle_->constraintB();
165	+	}
166
160	–	rattle->constraintB();
167
168	<	}
168	>	RealType NVE::calcConservedQuantity() {
169	>	return thermo.getTotalEnergy();
170	>	}
171
172	<
165	<	double NVE::calcConservedQuantity() {
166	<	return thermo.getTotalE();
167	<	}
168	<
169	<	} //end namespace oopse
172	>	} //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.
Revision 1782 by gezelter, Wed Aug 22 02:28:28 2012 UTC

#	Line 0 | Line 1
1	+	Author Id Revision Date

Diff Legend

–	Removed lines
+	Added lines
<	Changed lines
>	Changed lines