--- trunk/OOPSE/libmdtools/SimSetup.cpp	2003/04/07 20:06:31	469
+++ trunk/OOPSE/libmdtools/SimSetup.cpp	2003/04/17 21:54:18	504
@@ -67,7 +67,7 @@ void SimSetup::createSim( void ){
   MakeStamps *the_stamps;
   Globals* the_globals;
   ExtendedSystem* the_extendedsystem;
-  int i, j;
+  int i, j, k, globalAtomIndex;
 
   // get the stamps and globals;
   the_stamps = stamps;
@@ -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,
@@ -250,16 +298,15 @@ void SimSetup::createSim( void ){
   simnfo->n_torsions = tot_torsions;
   simnfo->n_SRI = tot_SRI;
   simnfo->n_mol = tot_nmol;
-
   
+  simnfo->molMembershipArray = new int[tot_atoms];
+
 #ifdef IS_MPI
 
   // divide the molecules among processors here.
   
   mpiSim = new mpiSimulation( simnfo );
   
-  
-
   globalIndex = mpiSim->divideLabor();
 
   // set up the local variables 
@@ -276,11 +323,14 @@ void SimSetup::createSim( void ){
   local_bonds = 0;
   local_bends = 0;
   local_torsions = 0;
+  globalAtomIndex = 0;
+
+
   for( i=0; i<n_components; i++ ){
 
     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();
@@ -288,12 +338,16 @@ void SimSetup::createSim( void ){
 	local_torsions += comp_stamps[i]->getNTorsions();
 	localMol++;
       }      
-      allMol++;
+      for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
+        simnfo->molMembershipArray[globalAtomIndex] = allMol;
+        globalAtomIndex++;
+      }
+
+      allMol++;      
     }
   }
   local_SRI = local_bonds + local_bends + local_torsions;
   
-
   simnfo->n_atoms = mpiSim->getMyNlocal();  
   
   if( local_atoms != simnfo->n_atoms ){
@@ -337,6 +391,7 @@ 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++;
     }
   }
@@ -344,10 +399,16 @@ void SimSetup::createSim( void ){
 #else // is_mpi
   
   molIndex = 0;
+  globalAtomIndex = 0;
   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 );
+      the_molecules[molIndex].setGlobalIndex( molIndex );
+      for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
+        simnfo->molMembershipArray[globalAtomIndex] = molIndex;
+        globalAtomIndex++;
+      }
       molIndex++;
     }
   }
@@ -680,18 +741,11 @@ 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";
-    fprintf( stderr, "Ima bug. stderr %s\n", force_field);
-  }
+
 #ifdef IS_MPI
   mpiSim->mpiRefresh();
 #endif