--- trunk/OOPSE/libmdtools/Molecule.cpp	2004/04/28 22:34:02	1140
+++ trunk/OOPSE/libmdtools/Molecule.cpp	2004/05/11 21:14:26	1158
@@ -12,7 +12,6 @@ Molecule::Molecule( void ){
   myBonds = NULL;
   myBends = NULL;
   myTorsions = NULL;
-  hasMassRatio = false;
 }
 
 Molecule::~Molecule( void ){
@@ -43,6 +42,12 @@ void Molecule::initialize( molInit &theInit ){
 
 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;
@@ -50,6 +55,7 @@ void Molecule::initialize( molInit &theInit ){
   nTorsions = theInit.nTorsions;
   nRigidBodies = theInit.nRigidBodies;
   nOriented = theInit.nOriented;
+  nCutoffGroups = theInit.nCutoffGroups;
 
   myAtoms = theInit.myAtoms;
   myBonds = theInit.myBonds;
@@ -62,6 +68,26 @@ void Molecule::initialize( molInit &theInit ){
   for (int i = 0; i < myRigidBodies.size(); i++) 
       myRigidBodies[i]->calcRefCoords();
 
+  myCutoffGroups = theInit.myCutoffGroups;
+
+  //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)
+  
 }
 
 void Molecule::calcForces( void ){
@@ -73,19 +99,10 @@ 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++){