--- trunk/OOPSE/libmdtools/SimSetup.cpp	2003/04/07 20:06:31	469
+++ trunk/OOPSE/libmdtools/SimSetup.cpp	2003/04/10 20:08:56	489
@@ -87,10 +87,58 @@ void SimSetup::createSim( void ){
   if( !strcasecmp( ensemble, "NPT" ) ) {
     the_extendedsystem = new ExtendedSystem( simnfo );
     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
-    the_extendedsystem->setTargetPressure(the_globals->getTargetPressure());
+    if (the_globals->haveTargetPressure())
+      the_extendedsystem->setTargetPressure(the_globals->getTargetPressure());
+    else {
+      sprintf( painCave.errMsg,
+               "SimSetup error: If you use the constant pressure\n"
+               "    ensemble, you must set targetPressure.\n"
+               "    This was found in the BASS file.\n");
+      painCave.isFatal = 1;
+      simError();
+    }
+
+    if (the_globals->haveTauThermostat()) 
+      the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
+    else if (the_globals->haveQmass())
+      the_extendedsystem->setQmass(the_globals->getQmass());
+    else {
+      sprintf( painCave.errMsg,
+               "SimSetup error: If you use one of the constant temperature\n"
+               "    ensembles, you must set either tauThermostat or qMass.\n"
+               "    Neither of these was found in the BASS file.\n");
+      painCave.isFatal = 1;
+      simError();
+    }
+
+    if (the_globals->haveTauBarostat())
+      the_extendedsystem->setTauBarostat(the_globals->getTauBarostat());
+    else {
+      sprintf( painCave.errMsg,
+               "SimSetup error: If you use the constant pressure\n"
+               "    ensemble, you must set tauBarostat.\n"
+               "    This was found in the BASS file.\n");
+      painCave.isFatal = 1;
+      simError();
+    }
+
   } else if ( !strcasecmp( ensemble, "NVT") ) {
     the_extendedsystem = new ExtendedSystem( simnfo );
     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
+
+    if (the_globals->haveTauThermostat()) 
+      the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
+    else if (the_globals->haveQmass())
+      the_extendedsystem->setQmass(the_globals->getQmass());
+    else {
+      sprintf( painCave.errMsg,
+               "SimSetup error: If you use one of the constant temperature\n"
+               "    ensembles, you must set either tauThermostat or qMass.\n"
+               "    Neither of these was found in the BASS file.\n");
+      painCave.isFatal = 1;
+      simError();
+    }
+
   } else if ( !strcasecmp( ensemble, "NVE") ) {
   } else {
     sprintf( painCave.errMsg,
@@ -280,7 +328,7 @@ void SimSetup::createSim( void ){
 
     for( j=0; j<components_nmol[i]; j++ ){
       
-      if( mol2proc[j] == worldRank ){
+      if( mol2proc[allMol] == worldRank ){
 	
 	local_atoms +=    comp_stamps[i]->getNAtoms();
 	local_bonds +=    comp_stamps[i]->getNBonds();
@@ -337,6 +385,7 @@ void SimSetup::createSim( void ){
     if(mol2proc[i] == worldRank ){
       the_molecules[molIndex].setStampID( molCompType[i] );
       the_molecules[molIndex].setMyIndex( molIndex );
+      the_molecules[molIndex].setGlobalIndex( i );
       molIndex++;
     }
   }
@@ -348,6 +397,7 @@ void SimSetup::createSim( void ){
     for(j=0; j<components_nmol[i]; j++ ){
       the_molecules[molIndex].setStampID( i );
       the_molecules[molIndex].setMyIndex( molIndex );
+      the_molecules[molIndex].setGlobalIndex( molIndex );
       molIndex++;
     }
   }
@@ -437,9 +487,13 @@ void SimSetup::createSim( void ){
 
   makeMolecules();
   simnfo->identArray = new int[simnfo->n_atoms];
+  simnfo->molMembershipArray = new int[simnfo->n_atoms];
   for(i=0; i<simnfo->n_atoms; i++){
     simnfo->identArray[i] = the_atoms[i]->getIdent();
   }
+  for(i=0; i< simnfo->n_mol; i++) {
+    the_molecules[i].atomicRollCall(simnfo->molMembershipArray);
+  }
   
   if (the_globals->getUseRF() ) {
     simnfo->useReactionField = 1;
@@ -680,13 +734,9 @@ void SimSetup::createSim( void ){
 
   if( !strcmp( force_field, "TraPPE_Ex" ) ){
     new Symplectic(simnfo, the_ff, the_extendedsystem);
-    std::cerr << "called new Symplecic\n";
-    fprintf( stderr, "called new Symplectic. stderr\n" );
   }
   else if( !strcmp( force_field, "LJ" ) ){
     new Verlet( *simnfo, the_ff, the_extendedsystem );
-    std::cerr << "called new Verlet\n";
-    fprintf( stderr, "called new Verlet. stderr\n" );
   }
   else {
     std::cerr << "I'm a bug.\n";