--- trunk/OOPSE/libmdtools/SimSetup.cpp	2003/03/27 19:21:42	422
+++ trunk/OOPSE/libmdtools/SimSetup.cpp	2003/03/31 21:50:59	438
@@ -88,9 +88,7 @@ void SimSetup::createSim( void ){
 	  
 
 
-  if( !strcmp( force_field, "TraPPE" ) ) the_ff = new TraPPEFF();
-  else if( !strcmp( force_field, "DipoleTest" ) ) the_ff = new DipoleTestFF();
-  else if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF();
+  if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF();
   else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
   else{
     sprintf( painCave.errMsg,
@@ -242,8 +240,6 @@ void SimSetup::createSim( void ){
 
   globalIndex = mpiSim->divideLabor();
 
-
-
   // set up the local variables 
   
   int localMol, allMol;
@@ -318,6 +314,7 @@ void SimSetup::createSim( void ){
     
     if(mol2proc[i] == worldRank ){
       the_molecules[molIndex].setStampID( molCompType[i] );
+      the_molecules[molIndex].setMyIndex( molIndex );
       molIndex++;
     }
   }
@@ -328,6 +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++;
     }
   }
@@ -337,10 +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{
     
@@ -356,6 +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;
 
@@ -654,15 +657,16 @@ void SimSetup::createSim( void ){
 
 //   new AllLong( simnfo );
 
-  if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff );
-  if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff );
   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") ){
@@ -699,14 +703,21 @@ void SimSetup::makeMolecules( void ){
   BondStamp* currentBond;
   BendStamp* currentBend;
   TorsionStamp* currentTorsion;
+
+  bond_pair* theBonds;
+  bend_set* theBends;
+  torsion_set* theTorsions;
+
   
   //init the forceField paramters
 
   the_ff->readParams();
 
   
-  // init the molecules
+  // init the atoms
 
+  double ux, uy, uz, u, uSqr;
+  
   atomOffset = 0;
   excludeOffset = 0;
   for(i=0; i<simnfo->n_mol; i++){
@@ -723,7 +734,7 @@ void SimSetup::makeMolecules( void ){
     info.myExcludes = &the_excludes[excludeOffset];
     info.myBonds = new Bond*[info.nBonds];
     info.myBends = new Bend*[info.nBends];
-    info.myTorsions = new Torsions*[info.nTorsions];
+    info.myTorsions = new Torsion*[info.nTorsions];
 
     theBonds = new bond_pair[info.nBonds];
     theBends = new bend_set[info.nBends];
@@ -733,7 +744,7 @@ void SimSetup::makeMolecules( void ){
     
     for(j=0; j<info.nAtoms; j++){
       
-      currentAtom = theComponents[stampID]->getAtom( j );
+      currentAtom = comp_stamps[stampID]->getAtom( j );
       if( currentAtom->haveOrientation() ){
 	
 	dAtom = new DirectionalAtom(j + atomOffset);
@@ -774,8 +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 ){
@@ -791,6 +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
     }
@@ -806,7 +818,7 @@ void SimSetup::makeMolecules( void ){
 	  
       if( currentBend->haveExtras() ){
 	    
-	extras = current_bend->getExtras();
+	extras = currentBend->getExtras();
 	current_extra = extras;
 	    
 	while( current_extra != NULL ){
@@ -828,7 +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() );
@@ -922,12 +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 ){