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root/OpenMD/trunk/src/selection/SelectionManager.cpp
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Comparing trunk/src/selection/SelectionManager.cpp (file contents):
Revision 353 by tim, Wed Feb 16 19:36:30 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   #include "selection/SelectionManager.hpp"
43   #include "primitives/Molecule.hpp"
44   #include "brains/SimInfo.hpp"
45 < namespace oopse {
46 < SelectionManager::SelectionManager(SimInfo* info) : info_(info){
45 > namespace OpenMD {
46 >  SelectionManager::SelectionManager(SimInfo* info) : info_(info){
47  
48      int nStuntDoubles = info_->getNGlobalAtoms() + info_->getNGlobalRigidBodies();
49  
# Line 60 | Line 60 | SelectionManager::SelectionManager(SimInfo* info) : in
60      
61      for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
62          
63 <        for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
64 <            stuntdoubles_[atom->getGlobalIndex()] = atom;
65 <        }
63 >      for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
64 >        stuntdoubles_[atom->getGlobalIndex()] = atom;
65 >      }
66  
67 <        for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
68 <            stuntdoubles_[rb->getGlobalIndex()] = rb;
69 <        }
67 >      for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
68 >        stuntdoubles_[rb->getGlobalIndex()] = rb;
69 >      }
70          
71      }    
72      
73 < }
73 >  }
74  
75  
76 < StuntDouble* SelectionManager::beginSelected(int& i) {
76 >  StuntDouble* SelectionManager::beginSelected(int& i) {
77      i = bsSelection_.firstOnBit();
78      return i == -1 ? NULL : stuntdoubles_[i];
79 < }
80 < StuntDouble* SelectionManager::nextSelected(int& i) {
79 >  }
80 >  StuntDouble* SelectionManager::nextSelected(int& i) {
81      i = bsSelection_.nextOnBit(i);
82      return i == -1 ? NULL : stuntdoubles_[i];
83 < }
83 >  }
84  
85 < StuntDouble* SelectionManager::beginUnselected(int& i){
85 >  StuntDouble* SelectionManager::beginUnselected(int& i){
86      i = bsSelection_.firstOffBit();
87      return i == -1 ? NULL : stuntdoubles_[i];
88 < }
89 < StuntDouble* SelectionManager::nextUnSelected(int& i) {
88 >  }
89 >  StuntDouble* SelectionManager::nextUnSelected(int& i) {
90      i = bsSelection_.nextOffBit(i);
91      return i == -1 ? NULL : stuntdoubles_[i];
92 < }
92 >  }
93  
94  
95 < SelectionManager operator| (const SelectionManager& sman1, const SelectionManager& sman2) {
95 >  SelectionManager operator| (const SelectionManager& sman1, const SelectionManager& sman2) {
96      SelectionManager result(sman1);
97      result |= sman2;
98      return result;
99 < }
100 < SelectionManager operator& (const SelectionManager& sman1, const SelectionManager& sman2) {
99 >  }
100 >  SelectionManager operator& (const SelectionManager& sman1, const SelectionManager& sman2) {
101      SelectionManager result(sman1);
102      result &= sman2;
103      return result;
104  
105 < }
106 < SelectionManager operator^ (const SelectionManager& sman1, const SelectionManager& sman2) {
105 >  }
106 >  SelectionManager operator^ (const SelectionManager& sman1, const SelectionManager& sman2) {
107      SelectionManager result(sman1);
108      result ^= sman2;
109      return result;
110  
111 < }
112 < SelectionManager operator-(const SelectionManager& sman1, const SelectionManager& sman2){
111 >  }
112 >  SelectionManager operator-(const SelectionManager& sman1, const SelectionManager& sman2){
113      SelectionManager result(sman1);
114      result -= sman2;
115      return result;
116  
117 < }
117 >  }
118  
119   }

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