--- trunk/mdtools/interface_implementation/SimSetup.cpp	2002/12/19 21:59:51	215
+++ trunk/mdtools/interface_implementation/SimSetup.cpp	2003/02/03 21:15:59	261
@@ -189,7 +189,7 @@ void SimSetup::createSim( void ){
       if( currentStamp == NULL ){
 	sprintf( painCave.errMsg,
 		 "SimSetup error: Component \"%s\" was not found in the "
-		 "list of declared molecules\n"
+		 "list of declared molecules\n",
 		 id );
 	painCave.isFatal = 1;
 	simError();
@@ -238,8 +238,12 @@ void SimSetup::createSim( void ){
   
   mpiSim = new mpiSimulation( simnfo );
   
-  mpiSim->divideLabor();
+  
 
+  globalIndex = mpiSim->divideLabor();
+
+
+
   // set up the local variables 
   
   int localMol, allMol;
@@ -313,27 +317,8 @@ void SimSetup::createSim( void ){
   simnfo->sr_interactions = the_sris;
   simnfo->n_exclude = tot_SRI;
   simnfo->excludes = the_excludes;
-
-
-  // initialize the arrays
 
-  the_ff->setSimInfo( simnfo );
 
-  makeAtoms();
-
-  if( tot_bonds ){
-    makeBonds();
-  }
-
-  if( tot_bends ){
-    makeBends();
-  }
-
-  if( tot_torsions ){
-    makeTorsions();
-  }
-
-
   // get some of the tricky things that may still be in the globals
 
   if( simnfo->n_dipoles ){
@@ -406,7 +391,29 @@ void SimSetup::createSim( void ){
 #endif // is_mpi
 
 
+  // initialize the arrays
 
+  the_ff->setSimInfo( simnfo );
+
+  makeAtoms();
+  //
+  if( tot_bonds ){
+    makeBonds();
+  }
+
+  if( tot_bends ){
+    makeBends();
+  }
+
+  if( tot_torsions ){
+    makeTorsions();
+  }
+
+
+
+
+
+
  if( the_globals->haveInitialConfig() ){
  
      InitializeFromFile* fileInit;
@@ -560,13 +567,15 @@ void SimSetup::createSim( void ){
   if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
 
 
-  // make the longe range forces and the integrator
+//   // make the longe range forces and the integrator
 
-  new AllLong( simnfo );
+//   new AllLong( simnfo );
 
-  if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo );
+  if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff );
   if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo );
   if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo );
+  if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff );
+
 }
 
 void SimSetup::makeAtoms( void ){
@@ -640,6 +649,14 @@ void SimSetup::makeAtoms( void ){
     }
   }
 
+#ifdef IS_MPI
+    for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] );
+    
+    delete[] globalIndex;
+
+    mpiSim->mpiRefresh();
+#endif //IS_MPI
+	  
   the_ff->initializeAtoms();
 }
 
@@ -652,7 +669,7 @@ void SimSetup::makeBonds( void ){
   the_bonds = new bond_pair[tot_bonds];
   index = 0;
   offset = 0;
-  molIndex = 0;g1
+  molIndex = 0;
 
   for( i=0; i<n_components; i++ ){
 
@@ -679,7 +696,7 @@ void SimSetup::makeBonds( void ){
 	
 #ifdef IS_MPI
       }
-#endif is_mpi
+#endif //is_mpi
       
       molIndex++;
     }