--- trunk/OOPSE/libmdtools/SimSetup.cpp	2003/03/24 21:55:34	394
+++ trunk/OOPSE/libmdtools/SimSetup.cpp	2003/03/26 20:22:02	407
@@ -670,7 +670,129 @@ void SimSetup::createSim( void ){
   MPIcheckPoint();
 #endif // is_mpi
 }
+
+
+void SimSetup::makeMolecules( void ){
+
+  int i, j, exI, exJ, tempEx, stampID, atomOffset;
+  molInit info;
+  DirectionalAtom* dAtom;
+  AtomStamp* currentAtom;
+  BondStamp* currentBond;
+  BendStamp* currentBend;
+  TorsionStamp* currentTorsion;
+  
+  //init the forceField paramters
+
+  the_ff->readParams();
+
+  
+  // init the molecules
+
+  atomOffset = 0;
+  for(i=0; i<simnfo->n_mol; i++){
+    
+    stampID = the_molecules[i].getStampID();
+
+    info.nAtoms    = comp_stamps[stampID]->getNAtoms();
+    info.nBonds    = comp_stamps[stampID]->getNBonds();
+    info.nBends    = comp_stamps[stampID]->getNBends();
+    info.nTorsions = comp_stamps[stampID]->getNTorsions();
+    
+    info.myAtoms = &the_atoms[atomOffset];
+    info.myBonds = new Bond*[info.nBonds];
+    info.myBends = new Bend*[info.nBends];
+    info.myTorsions = new Torsions*[info.nTorsions];
+
+    theBonds = new bond_pair[info.nBonds];
+    theBends = new bend_set[info.nBends];
+    theTorsions = new torsion_set[info.nTorsions];
+    
+    // make the Atoms
+    
+    for(j=0; j<info.nAtoms; j++){
+      
+      currentAtom = theComponents[stampID]->getAtom( j );
+      if( currentAtom->haveOrientation() ){
+	
+	dAtom = new DirectionalAtom(j + atomOffset);
+	simnfo->n_oriented++;
+	info.myAtoms[j] = dAtom;
+	
+	ux = currentAtom->getOrntX();
+	uy = currentAtom->getOrntY();
+	uz = currentAtom->getOrntZ();
+	
+	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
+	
+	u = sqrt( uSqr );
+	ux = ux / u;
+	uy = uy / u;
+	uz = uz / u;
+	
+	dAtom->setSUx( ux );
+	dAtom->setSUy( uy );
+	dAtom->setSUz( uz );
+      }
+      else{
+	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
+      }
+      info.myAtoms[j]->setType( currentAtom->getType() );
+    
+#ifdef IS_MPI
+      
+      info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
+      
+#endif // is_mpi
+    } 
+    
+    // make the bonds
+    for(j=0; j<nBonds; j++){
+      
+      currentBond = comp_stamps[stampID]->getBond( j );
+      theBonds[j].a = currentBond->getA() + atomOffset;
+      theBonds[j].b = currentBond->getB() + atomOffset;
+
+      exI = theBonds[i].a;
+      exJ = theBonds[i].b;
+
+      // exclude_I must always be the smaller of the pair
+      if( exI > exJ ){
+	tempEx = exI;
+	exI = exJ;
+	exJ = tempEx;
+      }
+#ifdef IS_MPI
+      
+      the_excludes[index*2] =     
+	the_atoms[exI]->getGlobalIndex() + 1;
+      the_excludes[index*2 + 1] = 
+	the_atoms[exJ]->getGlobalIndex() + 1;
+      
+#else  // isn't MPI
+      
+      the_excludes[index*2] =     exI + 1; 
+      the_excludes[index*2 + 1] = exJ + 1;
+      // fortran index from 1 (hence the +1 in the indexing)
 
+#endif  //is_mpi
+    
+  }
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
 void SimSetup::makeAtoms( void ){
 
   int i, j, k, index;