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root/OpenMD/trunk/src/integrators/LangevinDynamics.cpp
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Comparing trunk/src/integrators/LangevinDynamics.cpp (file contents):
Revision 945 by gezelter, Tue Apr 25 02:09:01 2006 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/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    
57    LangevinDynamics::LangevinDynamics(SimInfo* info) : VelocityVerletIntegrator(info){
58      setForceManager(new LDForceManager(info));
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(){
# Line 68 | Line 72 | namespace oopse {
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;
# Line 80 | Line 84 | namespace oopse {
84          mass = integrableObject->getMass();
85                  
86          // velocity half step
87 <        vel += (dt2 /mass * OOPSEConstant::energyConvert) * frc;
87 >        vel += (dt2 /mass * PhysicalConstants::energyConvert) * frc;
88  
89          // position whole step
90          pos += dt * vel;
# Line 98 | Line 102 | namespace oopse {
102  
103            ji = integrableObject->getJ();
104  
105 <          ji += (dt2  * OOPSEConstant::energyConvert) * Tb;
105 >          ji += (dt2  * PhysicalConstants::energyConvert) * Tb;
106  
107            rotAlgo->rotate(integrableObject, ji, dt);
108  
# Line 122 | Line 126 | namespace oopse {
126      Vector3d frc;
127      Vector3d Tb;
128      Vector3d ji;
129 <    double mass;
129 >    RealType mass;
130      
131      for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
132        for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
# Line 133 | Line 137 | namespace oopse {
137          mass = integrableObject->getMass();
138                  
139          // velocity half step
140 <        vel += (dt2 /mass * OOPSEConstant::energyConvert) * frc;
140 >        vel += (dt2 /mass * PhysicalConstants::energyConvert) * frc;
141                  
142          integrableObject->setVel(vel);
143  
# Line 147 | Line 151 | namespace oopse {
151  
152            ji = integrableObject->getJ();
153  
154 <          ji += (dt2  * OOPSEConstant::energyConvert) * Tb;
154 >          ji += (dt2  * PhysicalConstants::energyConvert) * Tb;
155  
156            integrableObject->setJ(ji);
157          }
# Line 162 | Line 166 | namespace oopse {
166    }
167  
168  
169 <  double LangevinDynamics::calcConservedQuantity() {
169 >  RealType LangevinDynamics::calcConservedQuantity() {
170      return 0.0;
171    }
172  
173 < } //end namespace oopse
173 > } //end namespace OpenMD
174  

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