--- trunk/OOPSE/libmdtools/SimSetup.cpp	2003/03/27 21:52:21	429
+++ trunk/OOPSE/libmdtools/SimSetup.cpp	2003/03/28 19:30:59	434
@@ -239,8 +239,6 @@ void SimSetup::createSim( void ){
   
 
   globalIndex = mpiSim->divideLabor();
-
-
 
   // set up the local variables 
   
@@ -335,8 +333,12 @@ 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;
   }
@@ -656,10 +658,13 @@ void SimSetup::createSim( void ){
   if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff );
   if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff );
 
-
+#ifdef IS_MPI
+  mpiSim->mpiRefresh();
+#endif
 
   // initialize the Fortran
-  
+
+
   simnfo->refreshSim();
   
   if( !strcmp( simnfo->mixingRule, "standard") ){
@@ -832,7 +837,7 @@ 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() );
@@ -931,10 +936,16 @@ void SimSetup::makeMolecules( void ){
     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 ){