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Comparing trunk/src/selection/SelectionManager.hpp (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  
42   #ifndef SELECTION_SELECTIONMANAGER_HPP
43   #define SELECTION_SELECTIONMANAGER_HPP
44  
45 < #include "utils/OOPSEBitSet.hpp"
45 > #include "utils/OpenMDBitSet.hpp"
46   #include "primitives/StuntDouble.hpp"
47 < namespace oopse {
47 > namespace OpenMD {
48  
49    class SimInfo;
50    /**
# Line 59 | Line 59 | namespace oopse {
59        bsSelection_.setBitOn(sd->getGlobalIndex());
60      }
61          
62 <    void addSelectionSet(const OOPSEBitSet& bs) {
62 >    void addSelectionSet(const OpenMDBitSet& bs) {
63        bsSelection_ |= bs;
64      }
65  
# Line 68 | Line 68 | namespace oopse {
68        bsSelection_.setBitOn(sd->getGlobalIndex());
69      }
70          
71 <    void setSelectionSet(const OOPSEBitSet& bs) {
71 >    void setSelectionSet(const OpenMDBitSet& bs) {
72        bsSelection_ = bs;          
73      }
74  
# Line 104 | Line 104 | namespace oopse {
104        return bsSelection_.countBits();
105      }
106  
107 <    OOPSEBitSet getSelectionSet() {
107 >    OpenMDBitSet getSelectionSet() {
108        return bsSelection_;
109      }
110  
# Line 142 | Line 142 | namespace oopse {
142          
143    private:
144      SimInfo* info_;
145 <    OOPSEBitSet bsSelection_;
145 >    OpenMDBitSet bsSelection_;
146      std::vector<StuntDouble*> stuntdoubles_;
147    };
148  

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