--- trunk/OOPSE/libmdtools/SimInfo.cpp	2004/05/01 18:52:38	1144
+++ trunk/OOPSE/libmdtools/SimInfo.cpp	2004/05/07 21:35:05	1150
@@ -448,41 +448,41 @@ void SimInfo::refreshSim(){
 #else
   n_global = n_atoms;
 #endif
-
+  
   isError = 0;
-
- getFortranGroupArray(this, mfact, ngroup, groupList, groupStart);
-
+  
+  getFortranGroupArray(this, mfact, ngroup, groupList, groupStart);
+  
   setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl, 
-		                    &nGlobalExcludes, globalExcludes, molMembershipArray, 
-		                    &mfact[0], &ngroup, &groupList[0], &groupStart[0], &isError );
-
-  if( isError ){
-
+                  &nGlobalExcludes, globalExcludes, molMembershipArray, 
+                  &mfact[0], &ngroup, &groupList[0], &groupStart[0], &isError);
+  
+  if( isError ){
+    
     sprintf( painCave.errMsg,
-	     "There was an error setting the simulation information in fortran.\n" );
+             "There was an error setting the simulation information in fortran.\n" );
     painCave.isFatal = 1;
     simError();
   }
-
+  
 #ifdef IS_MPI
   sprintf( checkPointMsg,
 	   "succesfully sent the simulation information to fortran.\n");
   MPIcheckPoint();
 #endif // is_mpi
-
+  
   this->ndf = this->getNDF();
   this->ndfRaw = this->getNDFraw();
   this->ndfTrans = this->getNDFtranslational();
 }
 
 void SimInfo::setDefaultRcut( double theRcut ){
-
+  
   haveRcut = 1;
   rCut = theRcut;
-
+  
   ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
-
+  
   notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
 }
 
@@ -596,53 +596,66 @@ void getFortranGroupArray(SimInfo* info, vector<double
 
 
 void getFortranGroupArray(SimInfo* info, vector<double>& mfact, int& ngroup, 
-                                                          vector<int>& groupList, vector<int>& groupStart){
+                          vector<int>& groupList, vector<int>& groupStart){
   Molecule* mol;
+  Atom** myAtoms;
   int numAtom;
   int curIndex;
+  double mtot;
 
   mfact.clear();
   groupList.clear();
   groupStart.clear();
-
+  
   //Be careful, fortran array begin at 1
   curIndex = 1;
-    
+  
   if(info->useMolecularCutoffs){
-    //if using molecular cutoff
+    
+#ifdef IS_MPI
+    ngroup = mpiSim->getMyNMol();
+#else
     ngroup = info->n_mol;
-
+#endif
+    
     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++)
+        mtot += myAtoms[j]->getMass();                
       
-      for(int j=0; j < numAtom; j++){
-#ifdef IS_MPI
-        groupList.push_back((info->atoms[i])->getGlobalIndex() + 1);
-#else
-        groupList.push_back((info->atoms[i])->getIndex() + 1);
-#endif
-      }//for(int j=0; j < numAtom; j++)
-            
+      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);
+
+      }
+      
       groupStart.push_back(curIndex);
       curIndex += numAtom;
       
-    }//end for(int i =0 ; i < ngroup; i++)    
+    } //end for(int i =0 ; i < ngroup; i++)    
   }
   else{
     //using atomic cutoff, every single atom is just a group
-    ngroup = info->n_atoms;
-    for(int i =0 ; i < ngroup; i++){
-      groupStart.push_back(curIndex++); 
-
+    
 #ifdef IS_MPI
-      groupList.push_back((info->atoms[i])->getGlobalIndex() + 1);
+    ngroup = mpiSim->getMyNlocal();
 #else
-      groupList.push_back((info->atoms[i])->getIndex() + 1);
+    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)
-
+  
 }