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root/OpenMD/trunk/src/selection/SelectionManager.cpp
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Comparing trunk/src/selection/SelectionManager.cpp (file contents):
Revision 1442 by gezelter, Mon May 10 17:28:26 2010 UTC vs.
Revision 1801 by gezelter, Mon Oct 1 18:21:15 2012 UTC

# Line 33 | Line 33
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).                        
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"
# Line 48 | Line 49 | namespace OpenMD {
49      int nStuntDoubles = info_->getNGlobalAtoms() + info_->getNGlobalRigidBodies();
50  
51      bsSelection_.resize(nStuntDoubles);
52 <    stuntdoubles_.resize(nStuntDoubles);
52 >    stuntdoubles_.resize(nStuntDoubles, NULL);
53      
54      SimInfo::MoleculeIterator mi;
55      Molecule* mol;
# Line 56 | Line 57 | namespace OpenMD {
57      Atom* atom;
58      Molecule::RigidBodyIterator rbIter;
59      RigidBody* rb;
59 –
60      
61 <    for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
61 >    for (mol = info_->beginMolecule(mi); mol != NULL;
62 >         mol = info_->nextMolecule(mi)) {
63          
64 <      for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
64 >      for(atom = mol->beginAtom(ai); atom != NULL;
65 >          atom = mol->nextAtom(ai)) {
66          stuntdoubles_[atom->getGlobalIndex()] = atom;
67        }
68 <
69 <      for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
68 >      
69 >      for (rb = mol->beginRigidBody(rbIter); rb != NULL;
70 >           rb = mol->nextRigidBody(rbIter)) {
71          stuntdoubles_[rb->getGlobalIndex()] = rb;
72 <      }
73 <        
71 <    }    
72 <    
72 >      }  
73 >    }
74    }
75  
75 –
76    StuntDouble* SelectionManager::beginSelected(int& i) {
77      i = bsSelection_.firstOnBit();
78      return i == -1 ? NULL : stuntdoubles_[i];
79    }
80 +
81    StuntDouble* SelectionManager::nextSelected(int& i) {
82      i = bsSelection_.nextOnBit(i);
83      return i == -1 ? NULL : stuntdoubles_[i];
# Line 86 | Line 87 | namespace OpenMD {
87      i = bsSelection_.firstOffBit();
88      return i == -1 ? NULL : stuntdoubles_[i];
89    }
90 +
91    StuntDouble* SelectionManager::nextUnSelected(int& i) {
92      i = bsSelection_.nextOffBit(i);
93      return i == -1 ? NULL : stuntdoubles_[i];
94    }
95  
96 <
97 <  SelectionManager operator| (const SelectionManager& sman1, const SelectionManager& sman2) {
96 >  SelectionManager operator| (const SelectionManager& sman1,
97 >                              const SelectionManager& sman2) {
98      SelectionManager result(sman1);
99      result |= sman2;
100      return result;
101    }
102 <  SelectionManager operator& (const SelectionManager& sman1, const SelectionManager& sman2) {
102 >
103 >  SelectionManager operator& (const SelectionManager& sman1,
104 >                              const SelectionManager& sman2) {
105      SelectionManager result(sman1);
106      result &= sman2;
107      return result;
104 –
108    }
109 <  SelectionManager operator^ (const SelectionManager& sman1, const SelectionManager& sman2) {
109 >
110 >  SelectionManager operator^ (const SelectionManager& sman1,
111 >                              const SelectionManager& sman2) {
112      SelectionManager result(sman1);
113      result ^= sman2;
114      return result;
110 –
115    }
116 <  SelectionManager operator-(const SelectionManager& sman1, const SelectionManager& sman2){
116 >
117 >  SelectionManager operator-(const SelectionManager& sman1,
118 >                             const SelectionManager& sman2){
119      SelectionManager result(sman1);
120      result -= sman2;
121      return result;
116 –
122    }
123  
124   }

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