--- trunk/OOPSE/libmdtools/SimSetup.cpp	2003/03/27 20:48:37	427
+++ trunk/OOPSE/libmdtools/SimSetup.cpp	2003/03/27 23:33:40	432
@@ -240,8 +240,6 @@ void SimSetup::createSim( void ){
 
   globalIndex = mpiSim->divideLabor();
 
-
-
   // set up the local variables 
   
   int localMol, allMol;
@@ -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;
   }
@@ -354,6 +356,7 @@ void SimSetup::createSim( void ){
   // set the arrays into the SimInfo object
 
   simnfo->atoms = the_atoms;
+  simnfo->molecules = the_molecules;
   simnfo->nGlobalExcludes = 0;
   simnfo->excludes = the_excludes;
 
@@ -655,10 +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") ){