--- trunk/mdtools/interface_implementation/SimSetup.cpp	2002/12/06 21:20:42	198
+++ trunk/mdtools/interface_implementation/SimSetup.cpp	2002/12/10 21:41:26	202
@@ -73,7 +73,7 @@ void SimSetup::createSim( void ){
 
   MakeStamps *the_stamps;
   Globals* the_globals;
-  int i;
+  int i, j;
 
   // get the stamps and globals;
   the_stamps = stamps;
@@ -213,10 +213,10 @@ void SimSetup::createSim( void ){
   tot_bends = 0;
   tot_torsions = 0;
   for( i=0; i<n_components; i++ ){
-
-    tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
-    tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
-    tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
+    
+    tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
+    tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
+    tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
     tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
   }
 
@@ -234,9 +234,40 @@ void SimSetup::createSim( void ){
 
   // divide the molecules among processors here.
   
-  new mpiSimulation( simnfo );
+  mpiSimulation* mpiSim = new mpiSimulation( simnfo );
   
-  simnfo->mpiSim->divideLabor( n_components, comp_stamps, components_nmol );
+  mpiSim->divideLabor();
+
+  // set up the local variables 
+  
+  int localMol;
+  int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
+  
+  localMol = 0;
+  local_atoms = 0;
+  local_bonds = 0;
+  local_bends = 0;
+  local_torsions = 0;
+  for( i=0; i<n_components; i++ ){
+
+    for( j=0; j<components_nmol[i]; j++ ){
+      
+      if( mpiSim->getMyMolStart() <= j &&
+	  j <= mpiSim->getMyMolEnd() ){
+	
+	local_atoms +=    comp_stamps[i]->getNAtoms();
+	local_bonds +=    comp_stamps[i]->getNBonds();
+	local_bends +=    comp_stamps[i]->getNBends();
+	local_torsions += comp_stamps[i]->getNTorsions();
+	localMol++;
+      }      
+    }
+  }
+
+  
+
+  simnfo->n_atoms = mpiSim->getMyNlocal();  
+  
 
 #endif // is_mpi
   
@@ -562,6 +593,7 @@ void SimSetup::makeAtoms( void ){
       the_molecules[molIndex].setNMembers( nMemb );
       the_molecules[molIndex].setStartAtom( molStart );
       the_molecules[molIndex].setEndAtom( molEnd );
+      the_molecules[molIndex].setStampID( i );
       molIndex++;
 
     }