--- branches/development/src/brains/SimInfo.cpp	2011/01/05 14:49:05	1536
+++ branches/development/src/brains/SimInfo.cpp	2011/03/18 19:31:52	1544
@@ -132,7 +132,13 @@ namespace OpenMD {
     //equal to the total number of atoms minus number of atoms belong to 
     //cutoff group defined in meta-data file plus the number of cutoff 
     //groups defined in meta-data file
+    std::cerr << "nGA = " << nGlobalAtoms_ << "\n";
+    std::cerr << "nCA = " << nCutoffAtoms << "\n";
+    std::cerr << "nG = " << nGroups << "\n";
+
     nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
+
+    std::cerr << "nGCG = " << nGlobalCutoffGroups_ << "\n";
     
     //every free atom (atom does not belong to rigid bodies) is an 
     //integrable object therefore the total number of integrable objects 
@@ -818,16 +824,13 @@ namespace OpenMD {
       }       
     }
 
-    //fill ident array of local atoms (it is actually ident of
-    //AtomType, it is so confusing !!!)
-    vector<int> identArray;
+    // Build the identArray_
 
-    //to avoid memory reallocation, reserve enough space identArray
-    identArray.reserve(getNAtoms());
-    
+    identArray_.clear();
+    identArray_.reserve(getNAtoms());    
     for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {        
       for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
-	identArray.push_back(atom->getIdent());
+	identArray_.push_back(atom->getIdent());
       }
     }    
 
@@ -970,9 +973,11 @@ namespace OpenMD {
     Molecule* mol;
     RigidBody* rb;
     Atom* atom;
+    CutoffGroup* cg;
     SimInfo::MoleculeIterator mi;
     Molecule::RigidBodyIterator rbIter;
-    Molecule::AtomIterator atomIter;;
+    Molecule::AtomIterator atomIter;
+    Molecule::CutoffGroupIterator cgIter;
  
     for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
         
@@ -983,6 +988,10 @@ namespace OpenMD {
       for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
 	rb->setSnapshotManager(sman_);
       }
+
+      for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
+	cg->setSnapshotManager(sman_);
+      }
     }    
     
   }