--- trunk/mdtools/interface_implementation/SimSetup.cpp	2002/10/09 22:29:40	131
+++ trunk/mdtools/interface_implementation/SimSetup.cpp	2002/11/14 22:00:44	176
@@ -6,14 +6,21 @@
 #include "parse_me.h"
 #include "LRI.hpp"
 #include "Integrator.hpp"
+#include "simError.h"
+
 #ifdef IS_MPI
-#include "mpiInterface.h"
+#include "mpiBASS.h"
 #include "bassDiag.hpp"
 #endif
 
 SimSetup::SimSetup(){
   stamps = new MakeStamps();
   globals = new Globals();
+  
+#ifdef IS_MPI
+  strcpy( checkPointMsg, "SimSetup creation successful" );
+  MPIcheckPoint();
+#endif // IS_MPI
 }
 
 SimSetup::~SimSetup(){
@@ -23,14 +30,23 @@ void SimSetup::parseFile( char* fileName ){
 
 void SimSetup::parseFile( char* fileName ){
 
-  inFileName = fileName;
-  set_interface_stamps( stamps, globals );
 #ifdef IS_MPI
-  mpiEventInit();
+  if( worldRank == 0 ){
+#endif // is_mpi
+    
+    inFileName = fileName;
+    set_interface_stamps( stamps, globals );
+    
+#ifdef IS_MPI
+    mpiEventInit();
 #endif
-  yacc_BASS( fileName );
+
+    yacc_BASS( fileName );
+
 #ifdef IS_MPI
-  throwMPIEvent(NULL);
+    throwMPIEvent(NULL);
+  }
+  else receiveParse();
 #endif
 
 }
@@ -40,6 +56,7 @@ void SimSetup::receiveParse(void){
 
     set_interface_stamps( stamps, globals );
     mpiEventInit();
+    MPIcheckPoint();
     mpiEventLoop();
 
 }
@@ -51,6 +68,7 @@ void SimSetup::createSim( void ){
   delete dumpMe;
 }
 #endif
+
 void SimSetup::createSim( void ){
 
   MakeStamps *the_stamps;
@@ -75,10 +93,17 @@ void SimSetup::createSim( void ){
   else if( !strcmp( force_field, "DipoleTest" ) ) the_ff = new DipoleTestFF();
   else if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF();
   else{
-    std::cerr<< "SimSetup Error. Unrecognized force field -> "
-	     << force_field << "\n";
-    exit(8);
+    sprintf( painCave.errMsg,
+	     "SimSetup Error. Unrecognized force field -> %s\n",
+	     force_field );
+    painCave.isFatal = 1;
+    simError();
   }
+
+#ifdef IS_MPI
+  strcpy( checkPointMsg, "ForceField creation successful" );
+  MPIcheckPoint();
+#endif // is_mpi
 
   // get the components and calculate the tot_nMol and indvidual n_mol
   the_components = the_globals->getComponents();
@@ -155,6 +180,7 @@ 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];
 
 
@@ -391,7 +417,7 @@ 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;
 
@@ -411,7 +437,7 @@ 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 );