--- trunk/OOPSE/libmdtools/Molecule.cpp	2004/05/11 21:14:26	1158
+++ trunk/OOPSE/libmdtools/Molecule.cpp	2004/08/23 15:11:36	1452
@@ -16,6 +16,8 @@ Molecule::~Molecule( void ){
 
 Molecule::~Molecule( void ){
   int i;
+  CutoffGroup* cg;
+  vector<CutoffGroup*>::iterator iter;
   
   if( myAtoms != NULL ){
     for(i=0; i<nAtoms; i++) if(myAtoms[i] != NULL ) delete myAtoms[i];
@@ -37,6 +39,10 @@ Molecule::~Molecule( void ){
     delete[] myTorsions;
   }
 
+  for(cg = beginCutoffGroup(iter);  cg != NULL; cg = nextCutoffGroup(iter))
+    delete cg;
+  myCutoffGroups.clear();
+  
 }
 
 
@@ -47,6 +53,9 @@ void Molecule::initialize( molInit &theInit ){
   Atom* cutoffAtom;
   vector<Atom*>::iterator iterAtom;
   int atomIndex;
+  GenericData* gdata;
+  ConsRbData* rbData;
+  RigidBody* oldRb;
   
   nAtoms = theInit.nAtoms;
   nMembers = nAtoms;
@@ -55,7 +64,6 @@ void Molecule::initialize( molInit &theInit ){
   nTorsions = theInit.nTorsions;
   nRigidBodies = theInit.nRigidBodies;
   nOriented = theInit.nOriented;
-  nCutoffGroups = theInit.nCutoffGroups;
 
   myAtoms = theInit.myAtoms;
   myBonds = theInit.myBonds;
@@ -65,28 +73,27 @@ void Molecule::initialize( molInit &theInit ){
 
   myIntegrableObjects = theInit.myIntegrableObjects;
 
-  for (int i = 0; i < myRigidBodies.size(); i++) 
+  for (int i = 0; i < myRigidBodies.size(); i++){
       myRigidBodies[i]->calcRefCoords();
+    //just a quick hack
+    
+    gdata = myRigidBodies[i]->getProperty("OldState");
+    if(gdata != NULL){
+      rbData = dynamic_cast<ConsRbData*>(gdata);
+      if(rbData ==NULL)
+        cerr << "dynamic_cast to ConsRbData Error in Molecule::initialize()" << endl;
+      else{
+        oldRb = rbData->getData();
+        oldRb->calcRefCoords();
+      }
+    }//end if(gata != NULL)
+    
+  }//end for(int i = 0; i < myRigidBodies.size(); i++)
 
   myCutoffGroups = theInit.myCutoffGroups;
+  nCutoffGroups = myCutoffGroups.size();
 
-  //creat a global index set of atoms which belong to cutoff group. 
-  //it will be use to speed up the query whether an atom belongs to cutoff group or not
-  cutoffAtomSet.clear();
-
-  for(curCutoffGroup = beginCutoffGroup(iterCutoff); curCutoffGroup != NULL;
-                                                  curCutoffGroup = nextCutoffGroup(iterCutoff)){
-
-      for(cutoffAtom = curCutoffGroup->beginAtom(iterAtom); cutoffAtom != NULL; 
-                                           cutoffAtom = curCutoffGroup->nextAtom(iterAtom)){
-#ifdef IS_MPI
-        atomIndex = cutoffAtom->getGlobalIndex();
-#else
-        atomIndex = cutoffAtom->getIndex();
-#endif
-        cutoffAtomSet.insert(atomIndex);
-     }// end for(cutoffAtom)    
-  }//end for(curCutoffGroup)
+  myConstraintPairs = theInit.myConstraintPairs;
   
 }