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root/OpenMD/trunk/src/integrators/NVE.cpp
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Comparing trunk/src/integrators/NVE.cpp (file contents):
Revision 246 by gezelter, Wed Jan 12 22:41:40 2005 UTC vs.
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 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]  Vardeman & Gezelter, in progress (2009).                        
40   */
41  
42 < /**
43 <  * @file NVE.cpp
44 <  * @author tlin
45 <  * @date 11/08/2004
46 <  * @time 15:13am
47 <  * @version 1.0
48 <  */
42 > /**
43 > * @file NVE.cpp
44 > * @author tlin
45 > * @date 11/08/2004
46 > * @time 15:13am
47 > * @version 1.0
48 > */
49  
50   #include "integrators/NVE.hpp"
51   #include "primitives/Molecule.hpp"
52 < #include "utils/OOPSEConstant.hpp"
52 > #include "utils/PhysicalConstants.hpp"
53  
54 < namespace oopse {
54 > namespace OpenMD {
55  
56  
57 < NVE::NVE(SimInfo* info) : VelocityVerletIntegrator(info){
57 >  NVE::NVE(SimInfo* info) : VelocityVerletIntegrator(info){
58  
59 < }
59 >  }
60  
61 < void NVE::moveA(){
61 >  void NVE::moveA(){
62      SimInfo::MoleculeIterator i;
63      Molecule::IntegrableObjectIterator  j;
64      Molecule* mol;
# Line 68 | Line 68 | void NVE::moveA(){
68      Vector3d frc;
69      Vector3d Tb;
70      Vector3d ji;
71 <    double mass;
71 >    RealType mass;
72      
73      for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
74 <        for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
75 <               integrableObject = mol->nextIntegrableObject(j)) {
74 >      for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
75 >           integrableObject = mol->nextIntegrableObject(j)) {
76  
77 <                vel =integrableObject->getVel();
78 <                pos = integrableObject->getPos();
79 <                frc = integrableObject->getFrc();
80 <                mass = integrableObject->getMass();
77 >        vel =integrableObject->getVel();
78 >        pos = integrableObject->getPos();
79 >        frc = integrableObject->getFrc();
80 >        mass = integrableObject->getMass();
81                  
82 <                // velocity half step
83 <                vel += (dt2 /mass * OOPSEConstant::energyConvert) * frc;
82 >        // velocity half step
83 >        vel += (dt2 /mass * PhysicalConstants::energyConvert) * frc;
84  
85 <                // position whole step
86 <                pos += dt * vel;
85 >        // position whole step
86 >        pos += dt * vel;
87  
88 <                integrableObject->setVel(vel);
89 <                integrableObject->setPos(pos);
88 >        integrableObject->setVel(vel);
89 >        integrableObject->setPos(pos);
90  
91 <                if (integrableObject->isDirectional()){
91 >        if (integrableObject->isDirectional()){
92  
93 <                    // get and convert the torque to body frame
93 >          // get and convert the torque to body frame
94  
95 <                    Tb = integrableObject->lab2Body(integrableObject->getTrq());
95 >          Tb = integrableObject->lab2Body(integrableObject->getTrq());
96  
97 <                    // get the angular momentum, and propagate a half step
97 >          // get the angular momentum, and propagate a half step
98  
99 <                    ji = integrableObject->getJ();
99 >          ji = integrableObject->getJ();
100  
101 <                    ji += (dt2  * OOPSEConstant::energyConvert) * Tb;
101 >          ji += (dt2  * PhysicalConstants::energyConvert) * Tb;
102  
103 <                    rotAlgo->rotate(integrableObject, ji, dt);
103 >          rotAlgo->rotate(integrableObject, ji, dt);
104  
105 <                    integrableObject->setJ(ji);
106 <                }
105 >          integrableObject->setJ(ji);
106 >        }
107  
108              
109 <        }
109 >      }
110      } //end for(mol = info_->beginMolecule(i))
111      
112      rattle->constraintA();
113      
114 < }    
114 >  }    
115  
116 < void NVE::moveB(){
116 >  void NVE::moveB(){
117      SimInfo::MoleculeIterator i;
118      Molecule::IntegrableObjectIterator  j;
119      Molecule* mol;
# Line 122 | Line 122 | void NVE::moveB(){
122      Vector3d frc;
123      Vector3d Tb;
124      Vector3d ji;
125 <    double mass;
125 >    RealType mass;
126      
127      for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
128 <        for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
129 <               integrableObject = mol->nextIntegrableObject(j)) {
128 >      for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
129 >           integrableObject = mol->nextIntegrableObject(j)) {
130  
131 <                vel =integrableObject->getVel();
132 <                frc = integrableObject->getFrc();
133 <                mass = integrableObject->getMass();
131 >        vel =integrableObject->getVel();
132 >        frc = integrableObject->getFrc();
133 >        mass = integrableObject->getMass();
134                  
135 <                // velocity half step
136 <                vel += (dt2 /mass * OOPSEConstant::energyConvert) * frc;
135 >        // velocity half step
136 >        vel += (dt2 /mass * PhysicalConstants::energyConvert) * frc;
137                  
138 <                integrableObject->setVel(vel);
138 >        integrableObject->setVel(vel);
139  
140 <                if (integrableObject->isDirectional()){
140 >        if (integrableObject->isDirectional()){
141  
142 <                    // get and convert the torque to body frame
142 >          // get and convert the torque to body frame
143  
144 <                    Tb = integrableObject->lab2Body(integrableObject->getTrq());
144 >          Tb = integrableObject->lab2Body(integrableObject->getTrq());
145  
146 <                    // get the angular momentum, and propagate a half step
146 >          // get the angular momentum, and propagate a half step
147  
148 <                    ji = integrableObject->getJ();
148 >          ji = integrableObject->getJ();
149  
150 <                    ji += (dt2  * OOPSEConstant::energyConvert) * Tb;
150 >          ji += (dt2  * PhysicalConstants::energyConvert) * Tb;
151  
152 <                    integrableObject->setJ(ji);
153 <                }
152 >          integrableObject->setJ(ji);
153 >        }
154  
155              
156 <        }
156 >      }
157      } //end for(mol = info_->beginMolecule(i))
158    
159  
160      rattle->constraintB();
161  
162 < }
162 >  }
163  
164  
165 < double NVE::calcConservedQuantity() {
166 <    return thermo.getTotalE();
167 < }
165 >  RealType NVE::calcConservedQuantity() {
166 >    return thermo.getTotalE() ;
167 >  }
168  
169 < } //end namespace oopse
169 > } //end namespace OpenMD

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