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Comparing trunk/src/integrators/Velocitizer.cpp (file contents):
Revision 1079 by gezelter, Thu Oct 19 15:57:07 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   #include "integrators/Velocitizer.hpp"
# Line 51 | Line 51
51   #endif
52  
53   /* Remove me after testing*/
54 + /*
55   #include <cstdio>
56   #include <iostream>
57 + */
58   /*End remove me*/
59  
60 < namespace oopse {
60 > namespace OpenMD {
61    
62    Velocitizer::Velocitizer(SimInfo* info) : info_(info) {
63      
# Line 103 | Line 105 | namespace oopse {
105      Molecule::IntegrableObjectIterator j;
106      Molecule * mol;
107      StuntDouble * integrableObject;
108 <        
108 >
109      kebar = kb * temperature * info_->getNdfRaw() / (2.0 * info_->getNdf());
110      for( mol = info_->beginMolecule(i); mol != NULL;
111           mol = info_->nextMolecule(i) ) {
# Line 203 | Line 205 | namespace oopse {
205                << angularMomentum <<  std::endl;
206      std::cerr << "Inertia Tensor before is "
207                << inertiaTensor <<  std::endl;
208 <    */  
208 >    */
209      inertiaTensor =inertiaTensor.inverse();
210      /*
211      std::cerr << "Inertia Tensor after inverse is "
# Line 233 | Line 235 | namespace oopse {
235      /*
236      std::cerr << "Angular Momentum after is "
237                << angularMomentum <<  std::endl;
238 <    */
237 <      
238 >    */
239    }
240    
241    

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