--- trunk/OOPSE/libmdtools/SimSetup.cpp	2003/03/27 23:33:40	432
+++ trunk/OOPSE/libmdtools/SimSetup.cpp	2003/04/02 22:19:03	443
@@ -314,6 +314,7 @@ void SimSetup::createSim( void ){
     
     if(mol2proc[i] == worldRank ){
       the_molecules[molIndex].setStampID( molCompType[i] );
+      the_molecules[molIndex].setMyIndex( molIndex );
       molIndex++;
     }
   }
@@ -324,6 +325,7 @@ void SimSetup::createSim( void ){
   for(i=0; i<n_components; i++){
     for(j=0; j<components_nmol[i]; j++ ){
       the_molecules[molIndex].setStampID( i );
+      the_molecules[molIndex].setMyIndex( molIndex );
       molIndex++;
     }
   }
@@ -333,14 +335,12 @@ void SimSetup::createSim( void ){
 
 
   if( simnfo->n_SRI ){
-    
-    std::cerr << "n_SRI = " << simnfo->n_SRI << "\n";
     
     Exclude::createArray(simnfo->n_SRI);
     the_excludes = new Exclude*[simnfo->n_SRI];
     for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
     simnfo->globalExcludes = new int;
-    simnfo->n_exclude = tot_SRI;
+    simnfo->n_exclude = simnfo->n_SRI;
   }
   else{
     
@@ -783,8 +783,8 @@ void SimSetup::makeMolecules( void ){
       theBonds[j].a = currentBond->getA() + atomOffset;
       theBonds[j].b = currentBond->getB() + atomOffset;
 
-      exI = theBonds[i].a;
-      exJ = theBonds[i].b;
+      exI = theBonds[j].a;
+      exJ = theBonds[j].b;
 
       // exclude_I must always be the smaller of the pair
       if( exI > exJ ){
@@ -800,6 +800,7 @@ void SimSetup::makeMolecules( void ){
       
       the_excludes[j+excludeOffset]->setPair( exI, exJ );
 #else  // isn't MPI
+
       the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
 #endif  //is_mpi
     }
@@ -837,7 +838,7 @@ void SimSetup::makeMolecules( void ){
 	      
 	    default:
 	      sprintf( painCave.errMsg,
-		       "SimSetup Error: ghostVectorSource was neiter a "
+		       "SimSetup Error: ghostVectorSource was neither a "
 		       "double nor an int.\n"
 		       "-->Bend[%d] in %s\n",
 		       j, comp_stamps[stampID]->getID() );
@@ -931,15 +932,23 @@ void SimSetup::makeMolecules( void ){
 
 
     the_molecules[i].initialize( info );
+
+
     atomOffset += info.nAtoms;
     delete[] theBonds;
     delete[] theBends;
     delete[] theTorsions;
   }
+
+#ifdef IS_MPI
+  sprintf( checkPointMsg, "all molecules initialized succesfully" );
+  MPIcheckPoint();
+#endif // is_mpi
 
   // clean up the forcefield
   the_ff->calcRcut();
   the_ff->cleanMe();
+
 }
 
 void SimSetup::initFromBass( void ){