--- trunk/OOPSE/libmdtools/SimInfo.cpp	2004/05/11 20:33:41	1157
+++ trunk/OOPSE/libmdtools/SimInfo.cpp	2004/05/12 15:02:03	1164
@@ -453,8 +453,8 @@ 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 +579,7 @@ void getFortranGroupArray(SimInfo* info, vector<double
   Atom* cutoffAtom;
   vector<Atom*>::iterator iterAtom;
   int atomIndex;
+  double totalMass;
   
   mfact.clear();
   groupList.clear();
@@ -606,7 +607,8 @@ void getFortranGroupArray(SimInfo* info, vector<double
       if(myMols[i].belongToCutoffGroup(atomIndex))
         continue;
       else{
-        mfact.push_back(myAtoms[j]->getMass());
+        // this is a fraction of the cutoff group's mass, not the mass itself!
+        mfact.push_back(1.0);
         groupList.push_back(myAtoms[j]->getIndex() + 1);
         groupStart.push_back(curIndex++);   
       }
@@ -615,17 +617,21 @@ void getFortranGroupArray(SimInfo* info, vector<double
     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);
         groupList.push_back(cutoffAtom->getIndex() + 1);
       }  
                               
       groupStart.push_back(curIndex);
       curIndex += myCutoffGroup->getNumAtom();
-    }
-    
-  }
 
+    }//end for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff))
+
+  }//end for(int i  = 0; i < numMol; i++)
+  
   ngroup = groupStart.size();
 }