--- trunk/OOPSE/libmdtools/SimSetup.cpp	2003/03/27 20:48:37	427
+++ trunk/OOPSE/libmdtools/SimSetup.cpp	2003/03/31 21:50:59	438
@@ -239,8 +239,6 @@ void SimSetup::createSim( void ){
   
 
   globalIndex = mpiSim->divideLabor();
-
-
 
   // set up the local variables 
   
@@ -316,6 +314,7 @@ void SimSetup::createSim( void ){
     
     if(mol2proc[i] == worldRank ){
       the_molecules[molIndex].setStampID( molCompType[i] );
+      the_molecules[molIndex].setMyIndex( molIndex );
       molIndex++;
     }
   }
@@ -326,6 +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++;
     }
   }
@@ -335,10 +335,14 @@ 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{
     
@@ -354,6 +358,7 @@ 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;
 
@@ -654,11 +659,14 @@ 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") ){
@@ -777,8 +785,8 @@ 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 ){
@@ -794,6 +802,7 @@ 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
     }
@@ -831,7 +840,7 @@ 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() );
@@ -925,15 +934,23 @@ 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 ){