--- trunk/OOPSE/libmdtools/SimSetup.cpp	2003/03/27 19:21:42	422
+++ trunk/OOPSE/libmdtools/SimSetup.cpp	2003/03/27 23:33:40	432
@@ -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,
@@ -241,8 +239,6 @@ void SimSetup::createSim( void ){
   
 
   globalIndex = mpiSim->divideLabor();
-
-
 
   // set up the local variables 
   
@@ -337,8 +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;
   }
@@ -356,6 +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;
 
@@ -654,15 +655,16 @@ 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 +701,21 @@ 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 +732,7 @@ 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 +742,7 @@ 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);
@@ -806,7 +815,7 @@ void SimSetup::makeMolecules( void ){
 	  
       if( currentBend->haveExtras() ){
 	    
-	extras = current_bend->getExtras();
+	extras = currentBend->getExtras();
 	current_extra = extras;
 	    
 	while( current_extra != NULL ){
@@ -923,6 +932,9 @@ void SimSetup::makeMolecules( void ){
 
     the_molecules[i].initialize( info );
     atomOffset += info.nAtoms;
+    delete[] theBonds;
+    delete[] theBends;
+    delete[] theTorsions;
   }
 
   // clean up the forcefield