--- trunk/OOPSE/libmdtools/SimSetup.cpp	2003/03/27 20:48:37	427
+++ trunk/OOPSE/libmdtools/SimSetup.cpp	2003/04/07 14:30:36	466
@@ -66,6 +66,7 @@ void SimSetup::createSim( void ){
 
   MakeStamps *the_stamps;
   Globals* the_globals;
+  ExtendedSystem* the_extendedsystem;
   int i, j;
 
   // get the stamps and globals;
@@ -80,16 +81,33 @@ void SimSetup::createSim( void ){
   // get the ones we know are there, yet still may need some work.
   n_components = the_globals->getNComponents();
   strcpy( force_field, the_globals->getForceField() );
+
+  // get the ensemble and set up an extended system if we need it:
   strcpy( ensemble, the_globals->getEnsemble() );
+  if( !strcasecmp( ensemble, "NPT" ) ) {
+    the_extendedsystem = new ExtendedSystem( simnfo );
+    the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
+    the_extendedsystem->setTargetPressure(the_globals->getTargetPressure());
+  } else if ( !strcasecmp( ensemble, "NVT") ) {
+    the_extendedsystem = new ExtendedSystem( simnfo );
+    the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
+  } else if ( !strcasecmp( ensemble, "NVE") ) {
+  } else {
+    sprintf( painCave.errMsg,
+	     "SimSetup Warning. Unrecognized Ensemble -> %s, "
+             "reverting to NVE for this simulation.\n",
+	     ensemble );
+    painCave.isFatal = 0;
+    simError();
+    strcpy( ensemble, "NVE" );
+  }  
   strcpy( simnfo->ensemble, ensemble );
 
   strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
   simnfo->usePBC = the_globals->getPBC();
 	  
-
-
   if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF();
-  else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
+  else if( !strcasecmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
   else{
     sprintf( painCave.errMsg,
 	     "SimSetup Error. Unrecognized force field -> %s\n",
@@ -240,8 +258,6 @@ void SimSetup::createSim( void ){
 
   globalIndex = mpiSim->divideLabor();
 
-
-
   // set up the local variables 
   
   int localMol, allMol;
@@ -316,6 +332,7 @@ void SimSetup::createSim( void ){
     
     if(mol2proc[i] == worldRank ){
       the_molecules[molIndex].setStampID( molCompType[i] );
+      the_molecules[molIndex].setMyIndex( molIndex );
       molIndex++;
     }
   }
@@ -326,6 +343,7 @@ 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++;
     }
   }
@@ -335,10 +353,12 @@ void SimSetup::createSim( void ){
 
 
   if( simnfo->n_SRI ){
+    
     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{
     
@@ -354,6 +374,7 @@ 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;
 
@@ -652,13 +673,20 @@ void SimSetup::createSim( void ){
 
 //   new AllLong( simnfo );
 
-  if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff );
-  if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff );
+  if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic(simnfo, 
+                                                           the_ff, 
+                                                           the_extendedsystem);
+  if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, 
+                                                 the_ff, 
+                                                 the_extendedsystem );
 
+#ifdef IS_MPI
+  mpiSim->mpiRefresh();
+#endif
 
-
   // initialize the Fortran
-  
+
+
   simnfo->refreshSim();
   
   if( !strcmp( simnfo->mixingRule, "standard") ){
@@ -777,8 +805,8 @@ 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 ){
@@ -794,6 +822,7 @@ 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
     }
@@ -831,7 +860,7 @@ 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() );
@@ -925,15 +954,23 @@ 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 ){