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root/OpenMD/trunk/src/integrators/NVE.cpp
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Comparing trunk/src/integrators/NVE.cpp (file contents):
Revision 507 by gezelter, Fri Apr 15 22:04:00 2005 UTC vs.
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 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, 24107 (2008).          
39 + * [4]  Vardeman & Gezelter, in progress (2009).                        
40   */
41  
42   /**
# Line 49 | Line 49
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){
# Line 68 | Line 68 | namespace oopse {
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;
# Line 80 | Line 80 | namespace oopse {
80          mass = integrableObject->getMass();
81                  
82          // velocity half step
83 <        vel += (dt2 /mass * OOPSEConstant::energyConvert) * frc;
83 >        vel += (dt2 /mass * PhysicalConstants::energyConvert) * frc;
84  
85          // position whole step
86          pos += dt * vel;
# Line 98 | Line 98 | namespace oopse {
98  
99            ji = integrableObject->getJ();
100  
101 <          ji += (dt2  * OOPSEConstant::energyConvert) * Tb;
101 >          ji += (dt2  * PhysicalConstants::energyConvert) * Tb;
102  
103            rotAlgo->rotate(integrableObject, ji, dt);
104  
# Line 122 | Line 122 | namespace oopse {
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;
# Line 133 | Line 133 | namespace oopse {
133          mass = integrableObject->getMass();
134                  
135          // velocity half step
136 <        vel += (dt2 /mass * OOPSEConstant::energyConvert) * frc;
136 >        vel += (dt2 /mass * PhysicalConstants::energyConvert) * frc;
137                  
138          integrableObject->setVel(vel);
139  
# Line 147 | Line 147 | namespace oopse {
147  
148            ji = integrableObject->getJ();
149  
150 <          ji += (dt2  * OOPSEConstant::energyConvert) * Tb;
150 >          ji += (dt2  * PhysicalConstants::energyConvert) * Tb;
151  
152            integrableObject->setJ(ji);
153          }
# Line 162 | Line 162 | namespace oopse {
162    }
163  
164  
165 <  double NVE::calcConservedQuantity() {
166 <    return thermo.getTotalE();
165 >  RealType NVE::calcConservedQuantity() {
166 >    return thermo.getTotalE() ;
167    }
168  
169 < } //end namespace oopse
169 > } //end namespace OpenMD

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