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root/OpenMD/trunk/src/selection/NameFinder.cpp
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Comparing trunk/src/selection/NameFinder.cpp (file contents):
Revision 1782 by gezelter, Wed Aug 22 02:28:28 2012 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 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    }
65  
66    void NameFinder::loadNames() {
67  
70 –    std::map<std::string, TreeNode*>::iterator foundIter;
68      SimInfo::MoleculeIterator mi;
69      Molecule* mol;
70      Molecule::AtomIterator ai;
# Line 79 | Line 76 | namespace OpenMD {
76      root_->bs.resize(nStuntDouble_);
77      root_->bs.setAll(); //
78      
79 <    for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
79 >    for (mol = info_->beginMolecule(mi); mol != NULL;
80 >         mol = info_->nextMolecule(mi)) {
81            
82        std::string molName = mol->getMoleculeName();
83        TreeNode* currentMolNode = createNode(root_, molName);
# Line 92 | Line 90 | namespace OpenMD {
90          currentAtomNode->bs.setBitOn(atom->getGlobalIndex());
91        }
92  
93 <      for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
93 >      for (rb = mol->beginRigidBody(rbIter); rb != NULL;
94 >           rb = mol->nextRigidBody(rbIter)) {
95          std::string rbName = rb->getType();
96          TreeNode* currentRbNode = createNode(currentMolNode, rbName);
97              
# Line 106 | Line 105 | namespace OpenMD {
105  
106            currentRbAtomNode->bs.setBitOn(atom->getGlobalIndex());
107          }
109 –
108        }
109 <        
112 <    }    
113 <
109 >    }
110    }
111  
112    TreeNode* NameFinder::createNode(TreeNode* parent, const std::string& name) {
# Line 232 | Line 228 | namespace OpenMD {
228  
229    void NameFinder::matchInternalIndex(const std::string& name, int internalIndex, OpenMDBitSet& bs){
230  
235 –    std::map<std::string, TreeNode*>::iterator foundIter;
231      SimInfo::MoleculeIterator mi;
232      Molecule* mol;
233  
234 <    for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
234 >    for (mol = info_->beginMolecule(mi); mol != NULL;
235 >         mol = info_->nextMolecule(mi)) {
236            
237        if (isMatched(mol->getMoleculeName(), name) ) {
238          int natoms = mol->getNAtoms();
# Line 250 | Line 246 | namespace OpenMD {
246            bs.setBitOn(mol->getRigidBodyAt(internalIndex - natoms)->getGlobalIndex());
247          }
248        }
249 <        
254 <    }    
255 <    
249 >    }
250    }
251  
252 <  bool NameFinder::isInteger(const std::string str) {
252 >  bool NameFinder::isInteger(const std::string &str) {
253      for(unsigned int i = 0; i < str.size(); ++i){
254        if (!std::isdigit(str[i])) {
255          return false;
256        }
257      }
264 –
258      return true;
259    }
267 –
260   }

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