--- trunk/mdtools/interface_implementation/SimSetup.cpp	2002/10/17 21:59:12	144
+++ trunk/mdtools/interface_implementation/SimSetup.cpp	2002/11/05 22:04:46	164
@@ -15,6 +15,11 @@ SimSetup::SimSetup(){
 SimSetup::SimSetup(){
   stamps = new MakeStamps();
   globals = new Globals();
+  
+#ifdef IS_MPI
+  strcpy( checkPointMsg, "SimSetup creation successful" );
+  MPIcheckPoint();
+#endif IS_MPI
 }
 
 SimSetup::~SimSetup(){
@@ -24,14 +29,23 @@ void SimSetup::parseFile( char* fileName ){
 
 void SimSetup::parseFile( char* fileName ){
 
-  inFileName = fileName;
-  set_interface_stamps( stamps, globals );
 #ifdef IS_MPI
-  mpiEventInit();
-#endif
-  yacc_BASS( fileName );
+  if( worldRank == 0 ){
+#endif // is_mpi
+    
+    inFileName = fileName;
+    set_interface_stamps( stamps, globals );
+    
+#ifdef IS_MPI
+    mpiEventInit();
+#endif
+
+    yacc_BASS( fileName );
+
 #ifdef IS_MPI
-  throwMPIEvent(NULL);
+    throwMPIEvent(NULL);
+  }
+  else recieveParse();
 #endif
 
 }
@@ -41,6 +55,7 @@ void SimSetup::receiveParse(void){
 
     set_interface_stamps( stamps, globals );
     mpiEventInit();
+    MPIcheckPoint();
     mpiEventLoop();
 
 }
@@ -156,6 +171,7 @@ void SimSetup::createSim( void ){
   // create the atom and short range interaction arrays
 
   the_atoms = new Atom*[tot_atoms];
+  Atom::createArrays(tot_atoms);
   the_molecules = new Molecule[tot_nmol];
 
 
@@ -392,7 +408,7 @@ void SimSetup::makeAtoms( void ){
 	current_atom = comp_stamps[i]->getAtom( k );
 	if( current_atom->haveOrientation() ){
 
-	  dAtom = new DirectionalAtom;
+	  dAtom = new DirectionalAtom(index);
 	  simnfo->n_oriented++;
 	  the_atoms[index] = dAtom;
 
@@ -412,7 +428,7 @@ void SimSetup::makeAtoms( void ){
 	  dAtom->setSUz( uz );
 	}
 	else{
-	  the_atoms[index] = new GeneralAtom;
+	  the_atoms[index] = new GeneralAtom(index);
 	}
 	the_atoms[index]->setType( current_atom->getType() );
 	the_atoms[index]->setIndex( index );