--- trunk/src/selection/DistanceFinder.cpp	2010/04/14 14:41:33	1434
+++ trunk/src/selection/DistanceFinder.cpp	2012/10/01 18:21:15	1801
@@ -36,7 +36,8 @@
  * [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/DistanceFinder.hpp"
@@ -56,18 +57,19 @@ namespace OpenMD {
     RigidBody* rb;
 
     
-    for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
+    for (mol = info_->beginMolecule(mi); mol != NULL; 
+         mol = info_->nextMolecule(mi)) {
         
-      for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
+      for(atom = mol->beginAtom(ai); atom != NULL; 
+          atom = mol->nextAtom(ai)) {
 	stuntdoubles_[atom->getGlobalIndex()] = atom;
       }
 
-      for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
+      for (rb = mol->beginRigidBody(rbIter); rb != NULL; 
+           rb = mol->nextRigidBody(rbIter)) {
 	stuntdoubles_[rb->getGlobalIndex()] = rb;
       }
-        
-    }    
-
+    }
   }
 
   OpenMDBitSet DistanceFinder::find(const OpenMDBitSet& bs, RealType distance) {
@@ -77,17 +79,19 @@ namespace OpenMD {
     OpenMDBitSet bsResult(nStuntDoubles_);
     assert(bsResult.size() == bs.size());
    
-    for (int j = 0; j < stuntdoubles_.size(); ++j) {
+    for (unsigned int j = 0; j < stuntdoubles_.size(); ++j) {
       if (stuntdoubles_[j]->isRigidBody()) {
         RigidBody* rb = static_cast<RigidBody*>(stuntdoubles_[j]);
         rb->updateAtoms();
       }
     }
    
+    // This will fail in parallel because i might not be on this processor.
+
     for (int i = bs.firstOnBit(); i != -1; i = bs.nextOnBit(i)) {
       center = stuntdoubles_[i];
       centerPos = center->getPos();
-      for (int j = 0; j < stuntdoubles_.size(); ++j) {
+      for (unsigned int j = 0; j < stuntdoubles_.size(); ++j) {
 	Vector3d r =centerPos - stuntdoubles_[j]->getPos();
 	currSnapshot->wrapVector(r);
 	if (r.length() <= distance) {