--- trunk/src/selection/IndexFinder.cpp	2009/11/25 20:02:06	1390
+++ branches/development/src/selection/IndexFinder.cpp	2012/10/03 14:20:07	1803
@@ -36,21 +36,19 @@
  * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
  * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
  * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
- * [4]  Vardeman & Gezelter, in progress (2009).                        
+ * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
+ * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
  */
 #include "selection/IndexFinder.hpp"
 #include "primitives/Molecule.hpp"
 namespace OpenMD {
 
-
-
   IndexFinder::IndexFinder(SimInfo* info) : info_(info){
     nStuntDoubles_ = info_->getNGlobalAtoms() + info_->getNGlobalRigidBodies();
     bitSets_.resize(info_->getNGlobalMolecules());
     init();
   }
 
-
   void IndexFinder::init() {
 
     SimInfo::MoleculeIterator mi;
@@ -60,20 +58,19 @@ namespace OpenMD {
     Molecule::RigidBodyIterator rbIter;
     RigidBody* rb;
     
-    for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
+    for (mol = info_->beginMolecule(mi); mol != NULL; 
+         mol = info_->nextMolecule(mi)) {
            
       OpenMDBitSet bs(nStuntDoubles_);
       for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
 	bs.setBitOn(atom->getGlobalIndex());
       }
-
-      for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
+      for (rb = mol->beginRigidBody(rbIter); rb != NULL; 
+           rb = mol->nextRigidBody(rbIter)) {
 	bs.setBitOn(rb->getGlobalIndex());
       }
-
       bitSets_[mol->getGlobalIndex()] = bs;
-    }    
-
+    }
   }
 
   OpenMDBitSet IndexFinder::find(int molIndex){
@@ -85,11 +82,8 @@ namespace OpenMD {
         
     for (int i = begMolIndex; i < endMolIndex; ++i) {
       bs |= bitSets_[i];
-    }
-    
+    }    
     return bs;
   }
-
-
 }