--- trunk/mdtools/interface_implementation/SimSetup.cpp	2002/11/26 21:04:43	189
+++ 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;
@@ -161,15 +161,51 @@ void SimSetup::createSim( void ){
 #endif // is_mpi
 
   // make an array of molecule stamps that match the components used.
+  // also extract the used stamps out into a separate linked list
 
+  simnfo->nComponents = n_components;
+  simnfo->componentsNmol = components_nmol;
+  simnfo->compStamps = comp_stamps;
+  simnfo->headStamp = new LinkedMolStamp();
+  
+  char* id;
+  LinkedMolStamp* headStamp = simnfo->headStamp;
+  LinkedMolStamp* currentStamp = NULL;
   for( i=0; i<n_components; i++ ){
 
-    comp_stamps[i] =
-      the_stamps->getMolecule( the_components[i]->getType() );
+    id = the_components[i]->getType();
+    comp_stamps[i] = NULL;
+    
+    // check to make sure the component isn't already in the list
+
+    comp_stamps[i] = headStamp->match( id );
+    if( comp_stamps[i] == NULL ){
+      
+      // extract the component from the list;
+      
+      currentStamp = the_stamps->extractMolStamp( id );
+      if( currentStamp == NULL ){
+	sprintf( painCave.errMsg,
+		 "SimSetup error: Component \"%s\" was not found in the "
+		 "list of declared molecules\n"
+		 id );
+	painCave.isFatal = 1;
+	simError();
+      }
+      
+      headStamp->add( currentStamp );
+      comp_stamps[i] = headStamp->match( id );
+    }
   }
 
+#ifdef IS_MPI
+  strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
+  MPIcheckPoint();
+#endif // is_mpi
+  
 
 
+
   // caclulate the number of atoms, bonds, bends and torsions
 
   tot_atoms = 0;
@@ -177,10 +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();
   }
 
@@ -191,17 +227,61 @@ void SimSetup::createSim( void ){
   simnfo->n_bends = tot_bends;
   simnfo->n_torsions = tot_torsions;
   simnfo->n_SRI = tot_SRI;
+  simnfo->n_mol = tot_nmol;
 
+  
+#ifdef IS_MPI
+
+  // divide the molecules among processors here.
+  
+  mpiSimulation* mpiSim = new mpiSimulation( simnfo );
+  
+  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
+  
+
   // create the atom and short range interaction arrays
 
-  Atom::createArrays(tot_atoms);
-  the_atoms = new Atom*[tot_atoms];
-  the_molecules = new Molecule[tot_nmol];
+  Atom::createArrays(simnfo->n_atoms);
+  the_atoms = new Atom*[simnfo->n_atoms];
+  the_molecules = new Molecule[simnfo->n_mol];
 
 
-  if( tot_SRI ){
-    the_sris = new SRI*[tot_SRI];
-    the_excludes = new ex_pair[tot_SRI];
+  if( simnfo->n_SRI ){
+    the_sris = new SRI*[simnfo->n_SRI];
+    the_excludes = new ex_pair[simnfo->n_SRI];
   }
 
   // set the arrays into the SimInfo object
@@ -230,7 +310,6 @@ void SimSetup::createSim( void ){
     makeTorsions();
   }
 
-  //  makeMolecules();
 
   // get some of the tricky things that may still be in the globals
 
@@ -314,11 +393,24 @@ void SimSetup::createSim( void ){
 //     delete fileInit;
 //   }
 //   else{
+
+#ifdef IS_MPI 
+
+  // no init from bass
+  
+  sprintf( painCave.errMsg,
+	   "Cannot intialize a parallel simulation without an initial configuration file.\n" );
+  painCave.isFatal;
+  simError();
+  
+#else
 
   initFromBass();
+
+#endif // is_mpi
  
 #ifdef IS_MPI
-  strcpy( checkPointMsg, "initFromBass successfully created the lattice" );
+  strcpy( checkPointMsg, "Successfully read in the initial configuration" );
   MPIcheckPoint();
 #endif // is_mpi
 
@@ -501,6 +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++;
 
     }