--- trunk/OOPSE/libmdtools/SimInfo.cpp	2004/05/11 20:07:56	1156
+++ trunk/OOPSE/libmdtools/SimInfo.cpp	2004/05/11 20:33:41	1157
@@ -62,6 +62,8 @@ SimInfo::SimInfo(){
   useReactionField = 0;
   useGB = 0;
   useEAM = 0;
+  
+  haveCutoffGroups = false;
 
   excludes = Exclude::Instance();
 
@@ -450,7 +452,9 @@ void SimInfo::refreshSim(){
   isError = 0;
   
   getFortranGroupArray(this, mfact, ngroup, groupList, groupStart);
-  
+  //it may not be a good idea to pass the address of first element in vector
+  //since c++ standard does not require vector to be stored continously in meomory
+  //Most of the compilers will organize the memory of vector continously
   setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl, 
                   &nGlobalExcludes, globalExcludes, molMembershipArray, 
                   &mfact[0], &ngroup, &groupList[0], &groupStart[0], &isError);
@@ -563,65 +567,65 @@ void getFortranGroupArray(SimInfo* info, vector<double
 
 void getFortranGroupArray(SimInfo* info, vector<double>& mfact, int& ngroup, 
                           vector<int>& groupList, vector<int>& groupStart){
-  Molecule* mol;
+  Molecule* myMols;
   Atom** myAtoms;
   int numAtom;
   int curIndex;
   double mtot;
-
+  int numMol;
+  int numCutoffGroups;
+  CutoffGroup* myCutoffGroup;
+  vector<CutoffGroup*>::iterator iterCutoff;
+  Atom* cutoffAtom;
+  vector<Atom*>::iterator iterAtom;
+  int atomIndex;
+  
   mfact.clear();
   groupList.clear();
   groupStart.clear();
   
   //Be careful, fortran array begin at 1
   curIndex = 1;
-  
-  if(info->useMolecularCutoffs){
-    
-#ifdef IS_MPI
-    ngroup = mpiSim->getMyNMol();
-#else
-    ngroup = info->n_mol;
-#endif
+
+  myMols = info->molecules;
+  numMol = info->n_mol;
+  for(int i  = 0; i < numMol; i++){
+    numAtom = myMols[i].getNAtoms();
+    myAtoms = myMols[i].getMyAtoms();
+
     
-    for(int i = 0; i < ngroup; i ++){
-      mol = &(info->molecules[i]);
-      numAtom = mol->getNAtoms();
-      myAtoms = mol->getMyAtoms();
-      mtot = 0.0;
+    for(int j = 0; j < numAtom; j++){
 
-      for(int j=0; j < numAtom; j++)
-        mtot += myAtoms[j]->getMass();                
-      
-      for(int j=0; j < numAtom; j++){ 
-               
-        // We want the local Index:
-        groupList.push_back(myAtoms[j]->getIndex() + 1);
-        mfact.push_back(myAtoms[j]->getMass() / mtot);
+    
+#ifdef IS_MPI      
+      atomIndex = myAtoms[j]->getGlobalIndex();
+#else
+      atomIndex = myAtoms[j]->getIndex();
+#endif
 
+      if(myMols[i].belongToCutoffGroup(atomIndex))
+        continue;
+      else{
+        mfact.push_back(myAtoms[j]->getMass());
+        groupList.push_back(myAtoms[j]->getIndex() + 1);
+        groupStart.push_back(curIndex++);   
       }
+    }
       
-      groupStart.push_back(curIndex);
-      curIndex += numAtom;
+    numCutoffGroups = myMols[i].getNCutoffGroups();
+    for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff); myCutoffGroup != NULL; 
+                                                  myCutoffGroup =myMols[i].nextCutoffGroup(iterCutoff)){
       
-    } //end for(int i =0 ; i < ngroup; i++)    
-  }
-  else{
-    //using atomic cutoff, every single atom is just a group
+      for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom); cutoffAtom != NULL; 
+                                           cutoffAtom = myCutoffGroup->beginAtom(iterAtom)){
+        groupList.push_back(cutoffAtom->getIndex() + 1);
+      }  
+                              
+      groupStart.push_back(curIndex);
+      curIndex += myCutoffGroup->getNumAtom();
+    }
     
-#ifdef IS_MPI
-    ngroup = mpiSim->getMyNlocal();
-#else
-    ngroup = info->n_atoms;
-#endif
-    
-    for(int i =0 ; i < ngroup; i++){
-      groupStart.push_back(curIndex++);       
-      groupList.push_back((info->atoms[i])->getIndex() + 1);
-      mfact.push_back(1.0);
-      
-    }//end for(int i =0 ; i < ngroup; i++)
-    
-  }//end if (info->useMolecularCutoffs)
-  
+  }
+
+  ngroup = groupStart.size();
 }