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Comparing:
trunk/src/integrators/LangevinDynamics.cpp (file contents), Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
branches/development/src/integrators/LangevinDynamics.cpp (file contents), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 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]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40 + * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
42  
43   /**
# Line 49 | Line 50
50  
51   #include "integrators/LangevinDynamics.hpp"
52   #include "primitives/Molecule.hpp"
53 < #include "utils/OOPSEConstant.hpp"
53 > #include "utils/PhysicalConstants.hpp"
54   #include "integrators/LDForceManager.hpp"
55 < namespace oopse {
55 > namespace OpenMD {
56  
57    
58    LangevinDynamics::LangevinDynamics(SimInfo* info) : VelocityVerletIntegrator(info){
59      setForceManager(new LDForceManager(info));
60 +
61 +    // Langevin Dynamics Force Manager needs to know about the half-time step
62 +    // size to get convergence on the friction forces:
63 +    dynamic_cast<LDForceManager*>(forceMan_)->setDt2(dt2);
64    }
65    
66    void LangevinDynamics::moveA(){
# Line 80 | Line 85 | namespace oopse {
85          mass = integrableObject->getMass();
86                  
87          // velocity half step
88 <        vel += (dt2 /mass * OOPSEConstant::energyConvert) * frc;
88 >        vel += (dt2 /mass * PhysicalConstants::energyConvert) * frc;
89  
90          // position whole step
91          pos += dt * vel;
# Line 98 | Line 103 | namespace oopse {
103  
104            ji = integrableObject->getJ();
105  
106 <          ji += (dt2  * OOPSEConstant::energyConvert) * Tb;
106 >          ji += (dt2  * PhysicalConstants::energyConvert) * Tb;
107  
108            rotAlgo->rotate(integrableObject, ji, dt);
109  
# Line 133 | Line 138 | namespace oopse {
138          mass = integrableObject->getMass();
139                  
140          // velocity half step
141 <        vel += (dt2 /mass * OOPSEConstant::energyConvert) * frc;
141 >        vel += (dt2 /mass * PhysicalConstants::energyConvert) * frc;
142                  
143          integrableObject->setVel(vel);
144  
# Line 147 | Line 152 | namespace oopse {
152  
153            ji = integrableObject->getJ();
154  
155 <          ji += (dt2  * OOPSEConstant::energyConvert) * Tb;
155 >          ji += (dt2  * PhysicalConstants::energyConvert) * Tb;
156  
157            integrableObject->setJ(ji);
158          }
# Line 166 | Line 171 | namespace oopse {
171      return 0.0;
172    }
173  
174 < } //end namespace oopse
174 > } //end namespace OpenMD
175  

Comparing:
trunk/src/integrators/LangevinDynamics.cpp (property svn:keywords), Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
branches/development/src/integrators/LangevinDynamics.cpp (property svn:keywords), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

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