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root/OpenMD/branches/development/src/selection/IndexFinder.cpp
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Comparing trunk/src/selection/IndexFinder.cpp (file contents):
Revision 770 by tim, Fri Dec 2 15:38:03 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   #include "selection/IndexFinder.hpp"
42   #include "primitives/Molecule.hpp"
43 < namespace oopse {
43 > namespace OpenMD {
44  
45  
46  
# Line 62 | Line 62 | namespace oopse {
62      
63      for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
64            
65 <      OOPSEBitSet bs(nStuntDoubles_);
65 >      OpenMDBitSet bs(nStuntDoubles_);
66        for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
67          bs.setBitOn(atom->getGlobalIndex());
68        }
# Line 76 | Line 76 | namespace oopse {
76  
77    }
78  
79 <  OOPSEBitSet IndexFinder::find(int molIndex){
79 >  OpenMDBitSet IndexFinder::find(int molIndex){
80      return bitSets_[molIndex];
81    }
82  
83 <  OOPSEBitSet IndexFinder::find(int begMolIndex, int endMolIndex){
84 <    OOPSEBitSet bs(nStuntDoubles_);
83 >  OpenMDBitSet IndexFinder::find(int begMolIndex, int endMolIndex){
84 >    OpenMDBitSet bs(nStuntDoubles_);
85          
86      for (int i = begMolIndex; i < endMolIndex; ++i) {
87        bs |= bitSets_[i];

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