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root/OpenMD/trunk/src/selection/SelectionManager.cpp
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Comparing trunk/src/selection/SelectionManager.cpp (file contents):
Revision 1801 by gezelter, Mon Oct 1 18:21:15 2012 UTC vs.
Revision 1953 by gezelter, Thu Dec 5 18:19:26 2013 UTC

# Line 35 | Line 35
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).
38 > * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39   * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40   * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
# Line 45 | Line 45 | namespace OpenMD {
45   #include "brains/SimInfo.hpp"
46   namespace OpenMD {
47    SelectionManager::SelectionManager(SimInfo* info) : info_(info){
48 +    nObjects_.push_back(info_->getNGlobalAtoms()+info_->getNGlobalRigidBodies());
49 +    nObjects_.push_back(info_->getNGlobalBonds());
50 +    nObjects_.push_back(info_->getNGlobalBends());
51 +    nObjects_.push_back(info_->getNGlobalTorsions());
52 +    nObjects_.push_back(info_->getNGlobalInversions());
53  
54 <    int nStuntDoubles = info_->getNGlobalAtoms() + info_->getNGlobalRigidBodies();
55 <
56 <    bsSelection_.resize(nStuntDoubles);
57 <    stuntdoubles_.resize(nStuntDoubles, NULL);
54 >    stuntdoubles_.resize(nObjects_[STUNTDOUBLE]);
55 >    bonds_.resize(nObjects_[BOND]);
56 >    bends_.resize(nObjects_[BEND]);
57 >    torsions_.resize(nObjects_[TORSION]);
58 >    inversions_.resize(nObjects_[INVERSION]);
59      
60      SimInfo::MoleculeIterator mi;
55 –    Molecule* mol;
61      Molecule::AtomIterator ai;
57 –    Atom* atom;
62      Molecule::RigidBodyIterator rbIter;
63 +    Molecule::BondIterator bondIter;
64 +    Molecule::BendIterator bendIter;
65 +    Molecule::TorsionIterator torsionIter;
66 +    Molecule::InversionIterator inversionIter;
67 +
68 +    Molecule* mol;
69 +    Atom* atom;
70      RigidBody* rb;
71 <    
71 >    Bond* bond;
72 >    Bend* bend;
73 >    Torsion* torsion;
74 >    Inversion* inversion;    
75 >        
76      for (mol = info_->beginMolecule(mi); mol != NULL;
77           mol = info_->nextMolecule(mi)) {
78 <        
78 >      
79        for(atom = mol->beginAtom(ai); atom != NULL;
80            atom = mol->nextAtom(ai)) {
81          stuntdoubles_[atom->getGlobalIndex()] = atom;
82 <      }
68 <      
82 >      }  
83        for (rb = mol->beginRigidBody(rbIter); rb != NULL;
84             rb = mol->nextRigidBody(rbIter)) {
85          stuntdoubles_[rb->getGlobalIndex()] = rb;
86        }  
87 +      for (bond = mol->beginBond(bondIter); bond != NULL;
88 +           bond = mol->nextBond(bondIter)) {
89 +        bonds_[bond->getGlobalIndex()] = bond;
90 +      }  
91 +      for (bend = mol->beginBend(bendIter); bend != NULL;
92 +           bend = mol->nextBend(bendIter)) {
93 +        bends_[bend->getGlobalIndex()] = bend;
94 +      }  
95 +      for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
96 +           torsion = mol->nextTorsion(torsionIter)) {
97 +        torsions_[torsion->getGlobalIndex()] = torsion;
98 +      }  
99 +      for (inversion = mol->beginInversion(inversionIter); inversion != NULL;
100 +           inversion = mol->nextInversion(inversionIter)) {
101 +        inversions_[inversion->getGlobalIndex()] = inversion;
102 +      }  
103      }
104    }
105  
106    StuntDouble* SelectionManager::beginSelected(int& i) {
107 <    i = bsSelection_.firstOnBit();
107 >    i = ss_.bitsets_[STUNTDOUBLE].firstOnBit();
108      return i == -1 ? NULL : stuntdoubles_[i];
109    }
110  
111    StuntDouble* SelectionManager::nextSelected(int& i) {
112 <    i = bsSelection_.nextOnBit(i);
112 >    i = ss_.bitsets_[STUNTDOUBLE].nextOnBit(i);
113      return i == -1 ? NULL : stuntdoubles_[i];
114    }
115  
116    StuntDouble* SelectionManager::beginUnselected(int& i){
117 <    i = bsSelection_.firstOffBit();
117 >    i = ss_.bitsets_[STUNTDOUBLE].firstOffBit();
118      return i == -1 ? NULL : stuntdoubles_[i];
119    }
120  
121    StuntDouble* SelectionManager::nextUnSelected(int& i) {
122 <    i = bsSelection_.nextOffBit(i);
122 >    i = ss_.bitsets_[STUNTDOUBLE].nextOffBit(i);
123      return i == -1 ? NULL : stuntdoubles_[i];
124    }
125  
126 +  Bond* SelectionManager::beginSelectedBond(int& i) {
127 +    i = ss_.bitsets_[BOND].firstOnBit();
128 +    return i == -1 ? NULL : bonds_[i];
129 +  }
130 +
131 +  Bond* SelectionManager::nextSelectedBond(int& i) {
132 +    i = ss_.bitsets_[BOND].nextOnBit(i);
133 +    return i == -1 ? NULL : bonds_[i];
134 +  }
135 +
136 +  Bond* SelectionManager::beginUnselectedBond(int& i){
137 +    i = ss_.bitsets_[BOND].firstOffBit();
138 +    return i == -1 ? NULL : bonds_[i];
139 +  }
140 +
141 +  Bond* SelectionManager::nextUnSelectedBond(int& i) {
142 +    i = ss_.bitsets_[BOND].nextOffBit(i);
143 +    return i == -1 ? NULL : bonds_[i];
144 +  }
145 +
146 +  Bend* SelectionManager::beginSelectedBend(int& i) {
147 +    i = ss_.bitsets_[BEND].firstOnBit();
148 +    return i == -1 ? NULL : bends_[i];
149 +  }
150 +
151 +  Bend* SelectionManager::nextSelectedBend(int& i) {
152 +    i = ss_.bitsets_[BEND].nextOnBit(i);
153 +    return i == -1 ? NULL : bends_[i];
154 +  }
155 +
156 +  Bend* SelectionManager::beginUnselectedBend(int& i){
157 +    i = ss_.bitsets_[BEND].firstOffBit();
158 +    return i == -1 ? NULL : bends_[i];
159 +  }
160 +
161 +  Bend* SelectionManager::nextUnSelectedBend(int& i) {
162 +    i = ss_.bitsets_[BEND].nextOffBit(i);
163 +    return i == -1 ? NULL : bends_[i];
164 +  }
165 +
166 +  Torsion* SelectionManager::beginSelectedTorsion(int& i) {
167 +    i = ss_.bitsets_[TORSION].firstOnBit();
168 +    return i == -1 ? NULL : torsions_[i];
169 +  }
170 +
171 +  Torsion* SelectionManager::nextSelectedTorsion(int& i) {
172 +    i = ss_.bitsets_[TORSION].nextOnBit(i);
173 +    return i == -1 ? NULL : torsions_[i];
174 +  }
175 +
176 +  Torsion* SelectionManager::beginUnselectedTorsion(int& i){
177 +    i = ss_.bitsets_[TORSION].firstOffBit();
178 +    return i == -1 ? NULL : torsions_[i];
179 +  }
180 +
181 +  Torsion* SelectionManager::nextUnSelectedTorsion(int& i) {
182 +    i = ss_.bitsets_[TORSION].nextOffBit(i);
183 +    return i == -1 ? NULL : torsions_[i];
184 +  }
185 +
186 +  Inversion* SelectionManager::beginSelectedInversion(int& i) {
187 +    i = ss_.bitsets_[INVERSION].firstOnBit();
188 +    return i == -1 ? NULL : inversions_[i];
189 +  }
190 +
191 +  Inversion* SelectionManager::nextSelectedInversion(int& i) {
192 +    i = ss_.bitsets_[INVERSION].nextOnBit(i);
193 +    return i == -1 ? NULL : inversions_[i];
194 +  }
195 +
196 +  Inversion* SelectionManager::beginUnselectedInversion(int& i){
197 +    i = ss_.bitsets_[INVERSION].firstOffBit();
198 +    return i == -1 ? NULL : inversions_[i];
199 +  }
200 +
201 +  Inversion* SelectionManager::nextUnSelectedInversion(int& i) {
202 +    i = ss_.bitsets_[INVERSION].nextOffBit(i);
203 +    return i == -1 ? NULL : inversions_[i];
204 +  }
205 +
206    SelectionManager operator| (const SelectionManager& sman1,
207                                const SelectionManager& sman2) {
208      SelectionManager result(sman1);

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