--- trunk/OOPSE/libmdtools/Molecule.cpp	2004/04/15 16:18:26	1113
+++ trunk/OOPSE/libmdtools/Molecule.cpp	2004/06/04 03:15:31	1234
@@ -12,11 +12,12 @@ Molecule::Molecule( void ){
   myBonds = NULL;
   myBends = NULL;
   myTorsions = NULL;
-
 }
 
 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 +39,21 @@ 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;
+  
   nAtoms = theInit.nAtoms;
   nMembers = nAtoms;
   nBonds = theInit.nBonds;
@@ -61,17 +72,29 @@ void Molecule::initialize( molInit &theInit ){
 
   for (int i = 0; i < myRigidBodies.size(); i++) 
       myRigidBodies[i]->calcRefCoords();
-    
+
+  myCutoffGroups = theInit.myCutoffGroups;
+  nCutoffGroups = myCutoffGroups.size();
+
+  myConstraintPairs = theInit.myConstraintPairs;
+  
 }
 
 void Molecule::calcForces( void ){
   
   int i;
+  double com[3];
 
   for(i=0; i<myRigidBodies.size(); i++) {
     myRigidBodies[i]->updateAtoms();
   }
 
+  //calculate the center of mass of the molecule
+  //getCOM(com);  
+  //for(int i = 0; i < nAtoms; i ++)
+  //  myAtoms[i]->setRc(com);  
+  
+
   for(i=0; i<nBonds; i++){
     myBonds[i]->calc_forces();
   }