--- trunk/OOPSE/libmdtools/Molecule.cpp	2004/04/28 22:34:02	1140
+++ trunk/OOPSE/libmdtools/Molecule.cpp	2004/08/23 15:11:36	1452
@@ -12,11 +12,12 @@ Molecule::Molecule( void ){
   myBonds = NULL;
   myBends = NULL;
   myTorsions = NULL;
-  hasMassRatio = false;
 }
 
 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];
@@ -38,11 +39,24 @@ Molecule::~Molecule( void ){
     delete[] myTorsions;
   }
 
+  for(cg = beginCutoffGroup(iter);  cg != NULL; cg = nextCutoffGroup(iter))
+    delete cg;
+  myCutoffGroups.clear();
+  
 }
 
 
 void Molecule::initialize( molInit &theInit ){
 
+  CutoffGroup* curCutoffGroup;
+  vector<CutoffGroup*>::iterator iterCutoff;
+  Atom* cutoffAtom;
+  vector<Atom*>::iterator iterAtom;
+  int atomIndex;
+  GenericData* gdata;
+  ConsRbData* rbData;
+  RigidBody* oldRb;
+  
   nAtoms = theInit.nAtoms;
   nMembers = nAtoms;
   nBonds = theInit.nBonds;
@@ -59,9 +73,28 @@ 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();
+
+  myConstraintPairs = theInit.myConstraintPairs;
+  
 }
 
 void Molecule::calcForces( void ){
@@ -73,19 +106,10 @@ void Molecule::calcForces( void ){
     myRigidBodies[i]->updateAtoms();
   }
 
-  //the mass ratio will never change during the simulation. Thus, we could
-  //just calculate it at the begining of the simulation
-  if (!hasMassRatio){
-    double totMass = getTotalMass();
-    for(int i = 0; i < nAtoms; i ++)
-      myAtoms[i]->setMassRatio(myAtoms[i]->getMass()/totMass);  
-    hasMassRatio =  true;
-  }
-
   //calculate the center of mass of the molecule
-  getCOM(com);  
-  for(int i = 0; i < nAtoms; i ++)
-    myAtoms[i]->setRc(com);  
+  //getCOM(com);  
+  //for(int i = 0; i < nAtoms; i ++)
+  //  myAtoms[i]->setRc(com);  
   
 
   for(i=0; i<nBonds; i++){