--- trunk/OOPSE/libmdtools/SimSetup.cpp	2003/04/10 20:08:56	489
+++ trunk/OOPSE/libmdtools/SimSetup.cpp	2003/06/17 21:56:15	555
@@ -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;
@@ -298,16 +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 
@@ -324,6 +323,9 @@ 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++ ){
@@ -336,12 +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 ){
@@ -393,11 +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++;
     }
   }
@@ -487,13 +498,9 @@ 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;
@@ -727,21 +734,16 @@ void SimSetup::createSim( void ){
   if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
 
 
-//   // make the longe range forces and the integrator
-
-//   new AllLong( simnfo );
+  // make the integrator
 
 
-  if( !strcmp( force_field, "TraPPE_Ex" ) ){
+  if( !strcmp( ensemble, "TraPPE_Ex" ) ){
     new Symplectic(simnfo, the_ff, the_extendedsystem);
   }
   else if( !strcmp( force_field, "LJ" ) ){
     new Verlet( *simnfo, the_ff, the_extendedsystem );
   }
-  else {
-    std::cerr << "I'm a bug.\n";
-    fprintf( stderr, "Ima bug. stderr %s\n", force_field);
-  }
+
 #ifdef IS_MPI
   mpiSim->mpiRefresh();
 #endif