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Comparing branches/development/src/selection/NameFinder.cpp (file contents):
Revision 1767 by gezelter, Fri Jul 6 22:01:58 2012 UTC vs.
Revision 1850 by gezelter, Wed Feb 20 15:39:39 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 54 | Line 54 | namespace OpenMD {
54      children.clear();
55    }
56  
57 –
57    NameFinder::NameFinder(SimInfo* info) : info_(info), root_(NULL){
58      nStuntDouble_ = info_->getNGlobalAtoms() + info_->getNGlobalRigidBodies();
59      loadNames();
60    }
61  
63 –
62    NameFinder::~NameFinder(){
63      delete root_;
64    }
# Line 79 | Line 77 | namespace OpenMD {
77      root_->bs.resize(nStuntDouble_);
78      root_->bs.setAll(); //
79      
80 <    for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
80 >    for (mol = info_->beginMolecule(mi); mol != NULL;
81 >         mol = info_->nextMolecule(mi)) {
82            
83        std::string molName = mol->getMoleculeName();
84        TreeNode* currentMolNode = createNode(root_, molName);
# Line 92 | Line 91 | namespace OpenMD {
91          currentAtomNode->bs.setBitOn(atom->getGlobalIndex());
92        }
93  
94 <      for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
94 >      for (rb = mol->beginRigidBody(rbIter); rb != NULL;
95 >           rb = mol->nextRigidBody(rbIter)) {
96          std::string rbName = rb->getType();
97          TreeNode* currentRbNode = createNode(currentMolNode, rbName);
98              
# Line 106 | Line 106 | namespace OpenMD {
106  
107            currentRbAtomNode->bs.setBitOn(atom->getGlobalIndex());
108          }
109 –
109        }
110 <        
112 <    }    
113 <
110 >    }
111    }
112  
113    TreeNode* NameFinder::createNode(TreeNode* parent, const std::string& name) {
# Line 236 | Line 233 | namespace OpenMD {
233      SimInfo::MoleculeIterator mi;
234      Molecule* mol;
235  
236 <    for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
236 >    for (mol = info_->beginMolecule(mi); mol != NULL;
237 >         mol = info_->nextMolecule(mi)) {
238            
239        if (isMatched(mol->getMoleculeName(), name) ) {
240          int natoms = mol->getNAtoms();
# Line 250 | Line 248 | namespace OpenMD {
248            bs.setBitOn(mol->getRigidBodyAt(internalIndex - natoms)->getGlobalIndex());
249          }
250        }
251 <        
254 <    }    
255 <    
251 >    }
252    }
253  
254    bool NameFinder::isInteger(const std::string str) {
# Line 261 | Line 257 | namespace OpenMD {
257          return false;
258        }
259      }
264 –
260      return true;
261    }
267 –
262   }

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