--- trunk/OOPSE/libmdtools/SimSetup.cpp	2003/03/27 17:32:03	420
+++ trunk/OOPSE/libmdtools/SimSetup.cpp	2003/03/27 19:21:42	422
@@ -248,6 +248,9 @@ void SimSetup::createSim( void ){
   
   int localMol, allMol;
   int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
+
+  int* mol2proc = mpiSim->getMolToProcMap();
+  int* molCompType = mpiSim->getMolComponentType();
   
   allMol = 0;
   localMol = 0;
@@ -259,8 +262,7 @@ void SimSetup::createSim( void ){
 
     for( j=0; j<components_nmol[i]; j++ ){
       
-      if( mpiSim->getMyMolStart() <= allMol &&
-	  allMol <= mpiSim->getMyMolEnd() ){
+      if( mol2proc[j] == worldRank ){
 	
 	local_atoms +=    comp_stamps[i]->getNAtoms();
 	local_bonds +=    comp_stamps[i]->getNBonds();
@@ -279,7 +281,7 @@ void SimSetup::createSim( void ){
   if( local_atoms != simnfo->n_atoms ){
     sprintf( painCave.errMsg,
 	     "SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
-	     " localAtom (%d) are note equal.\n",
+	     " localAtom (%d) are not equal.\n",
 	     simnfo->n_atoms,
 	     local_atoms );
     painCave.isFatal = 1;
@@ -304,8 +306,36 @@ void SimSetup::createSim( void ){
   Atom::createArrays(simnfo->n_atoms);
   the_atoms = new Atom*[simnfo->n_atoms];
   the_molecules = new Molecule[simnfo->n_mol];
+  int molIndex;
+
+  // initialize the molecule's stampID's
+
+#ifdef IS_MPI
+  
+
+  molIndex = 0;
+  for(i=0; i<mpiSim->getTotNmol(); i++){
+    
+    if(mol2proc[i] == worldRank ){
+      the_molecules[molIndex].setStampID( molCompType[i] );
+      molIndex++;
+    }
+  }
+
+#else // is_mpi
+  
+  molIndex = 0;
+  for(i=0; i<n_components; i++){
+    for(j=0; j<components_nmol[i]; j++ ){
+      the_molecules[molIndex].setStampID( i );
+      molIndex++;
+    }
+  }
+    
 
+#endif // is_mpi
 
+
   if( simnfo->n_SRI ){
     Exclude::createArray(simnfo->n_SRI);
     the_excludes = new Exclude*[simnfo->n_SRI];
@@ -326,7 +356,6 @@ void SimSetup::createSim( void ){
   // set the arrays into the SimInfo object
 
   simnfo->atoms = the_atoms;
-  simnfo->sr_interactions = the_sris;
   simnfo->nGlobalExcludes = 0;
   simnfo->excludes = the_excludes;
 
@@ -383,25 +412,12 @@ void SimSetup::createSim( void ){
 
   the_ff->setSimInfo( simnfo );
 
-  makeAtoms();
+  makeMolecules();
   simnfo->identArray = new int[simnfo->n_atoms];
   for(i=0; i<simnfo->n_atoms; i++){
     simnfo->identArray[i] = the_atoms[i]->getIdent();
   }
   
-  if( tot_bonds ){
-    makeBonds();
-  }
-
-  if( tot_bends ){
-    makeBends();
-  }
-
-  if( tot_torsions ){
-    makeTorsions();
-  }
-
-
   if (the_globals->getUseRF() ) {
     simnfo->useReactionField = 1;