--- trunk/OOPSE/libmdtools/SimInfo.cpp	2004/05/11 20:33:41	1157
+++ trunk/OOPSE/libmdtools/SimInfo.cpp	2004/06/01 17:15:43	1212
@@ -62,7 +62,9 @@ SimInfo::SimInfo(){
   useReactionField = 0;
   useGB = 0;
   useEAM = 0;
-  
+  useSolidThermInt = 0;
+  useLiquidThermInt = 0;
+
   haveCutoffGroups = false;
 
   excludes = Exclude::Instance();
@@ -444,7 +446,7 @@ void SimInfo::refreshSim(){
   excl = excludes->getFortranArray();
   
 #ifdef IS_MPI
-  n_global = mpiSim->getTotAtoms();
+  n_global = mpiSim->getNAtomsGlobal();
 #else
   n_global = n_atoms;
 #endif
@@ -453,8 +455,8 @@ void SimInfo::refreshSim(){
   
   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
+  //since c++ standard does not require vector to be stored continuously in meomory
+  //Most of the compilers will organize the memory of vector continuously
   setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl, 
                   &nGlobalExcludes, globalExcludes, molMembershipArray, 
                   &mfact[0], &ngroup, &groupList[0], &groupStart[0], &isError);
@@ -579,6 +581,7 @@ void getFortranGroupArray(SimInfo* info, vector<double
   Atom* cutoffAtom;
   vector<Atom*>::iterator iterAtom;
   int atomIndex;
+  double totalMass;
   
   mfact.clear();
   groupList.clear();
@@ -590,42 +593,30 @@ void getFortranGroupArray(SimInfo* info, vector<double
   myMols = info->molecules;
   numMol = info->n_mol;
   for(int i  = 0; i < numMol; i++){
-    numAtom = myMols[i].getNAtoms();
-    myAtoms = myMols[i].getMyAtoms();
-
-    
-    for(int j = 0; j < numAtom; j++){
-
-    
-#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++);   
-      }
-    }
-      
     numCutoffGroups = myMols[i].getNCutoffGroups();
     for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff); myCutoffGroup != NULL; 
                                                   myCutoffGroup =myMols[i].nextCutoffGroup(iterCutoff)){
+
+      totalMass = myCutoffGroup->getMass();
       
       for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom); cutoffAtom != NULL; 
-                                           cutoffAtom = myCutoffGroup->beginAtom(iterAtom)){
+                                           cutoffAtom = myCutoffGroup->nextAtom(iterAtom)){
+        mfact.push_back(cutoffAtom->getMass()/totalMass);
+#ifdef IS_MPI        
+        groupList.push_back(cutoffAtom->getGlobalIndex() + 1);
+#else
         groupList.push_back(cutoffAtom->getIndex() + 1);
+#endif
       }  
                               
       groupStart.push_back(curIndex);
       curIndex += myCutoffGroup->getNumAtom();
-    }
-    
-  }
 
+    }//end for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff))
+
+  }//end for(int i  = 0; i < numMol; i++)
+
+
+  //The last cutoff group need more element to indicate the end of the cutoff 
   ngroup = groupStart.size();
 }