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Comparing:
trunk/src/selection/SelectionManager.cpp (file contents), Revision 317 by tim, Sat Feb 12 20:09:28 2005 UTC vs.
branches/development/src/selection/SelectionManager.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   #include "selection/SelectionManager.hpp"
44   #include "primitives/Molecule.hpp"
45   #include "brains/SimInfo.hpp"
46 < namespace oopse {
47 < SelectionManager::SelectionManager(SimInfo* info) : info_(info){
46 > namespace OpenMD {
47 >  SelectionManager::SelectionManager(SimInfo* info) : info_(info){
48  
49      int nStuntDoubles = info_->getNGlobalAtoms() + info_->getNGlobalRigidBodies();
50  
# Line 60 | Line 61 | SelectionManager::SelectionManager(SimInfo* info) : in
61      
62      for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
63          
64 <        for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
65 <            stuntdoubles_[atom->getGlobalIndex()] = atom;
66 <        }
64 >      for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
65 >        stuntdoubles_[atom->getGlobalIndex()] = atom;
66 >      }
67  
68 <        for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
69 <            stuntdoubles_[rb->getGlobalIndex()] = rb;
70 <        }
68 >      for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
69 >        stuntdoubles_[rb->getGlobalIndex()] = rb;
70 >      }
71          
72      }    
73      
74 < }
74 >  }
75  
76  
77 < StuntDouble* SelectionManager::beginSelected(int& i) {
77 >  StuntDouble* SelectionManager::beginSelected(int& i) {
78      i = bsSelection_.firstOnBit();
79      return i == -1 ? NULL : stuntdoubles_[i];
80 < }
81 < StuntDouble* SelectionManager::nextSelected(int& i) {
80 >  }
81 >  StuntDouble* SelectionManager::nextSelected(int& i) {
82      i = bsSelection_.nextOnBit(i);
83      return i == -1 ? NULL : stuntdoubles_[i];
84 < }
84 >  }
85  
86 < StuntDouble* SelectionManager::beginUnselected(int& i) {
86 >  StuntDouble* SelectionManager::beginUnselected(int& i){
87      i = bsSelection_.firstOffBit();
88      return i == -1 ? NULL : stuntdoubles_[i];
89 < }
90 < StuntDouble* SelectionManager::nextUnSelected(int& i) {
89 >  }
90 >  StuntDouble* SelectionManager::nextUnSelected(int& i) {
91      i = bsSelection_.nextOffBit(i);
92      return i == -1 ? NULL : stuntdoubles_[i];
93 < }
93 >  }
94  
95 +
96 +  SelectionManager operator| (const SelectionManager& sman1, const SelectionManager& sman2) {
97 +    SelectionManager result(sman1);
98 +    result |= sman2;
99 +    return result;
100 +  }
101 +  SelectionManager operator& (const SelectionManager& sman1, const SelectionManager& sman2) {
102 +    SelectionManager result(sman1);
103 +    result &= sman2;
104 +    return result;
105 +
106 +  }
107 +  SelectionManager operator^ (const SelectionManager& sman1, const SelectionManager& sman2) {
108 +    SelectionManager result(sman1);
109 +    result ^= sman2;
110 +    return result;
111 +
112 +  }
113 +  SelectionManager operator-(const SelectionManager& sman1, const SelectionManager& sman2){
114 +    SelectionManager result(sman1);
115 +    result -= sman2;
116 +    return result;
117 +
118 +  }
119 +
120   }

Comparing:
trunk/src/selection/SelectionManager.cpp (property svn:keywords), Revision 317 by tim, Sat Feb 12 20:09:28 2005 UTC vs.
branches/development/src/selection/SelectionManager.cpp (property svn:keywords), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

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1 + Author Id Revision Date

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