--- trunk/src/brains/SimInfo.cpp	2012/09/10 18:38:44	1796
+++ trunk/src/brains/SimInfo.cpp	2013/08/19 13:51:04	1930
@@ -35,7 +35,7 @@
  *                                                                      
  * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
  * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
- * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
+ * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
  * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
  * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
  */
@@ -91,6 +91,13 @@ namespace OpenMD {
     for (vector<Component*>::iterator i = components.begin(); 
          i !=components.end(); ++i) {
       molStamp = (*i)->getMoleculeStamp();
+      if ( (*i)->haveRegion() ) {        
+        molStamp->setRegion( (*i)->getRegion() );
+      } else {
+        // set the region to a disallowed value:
+        molStamp->setRegion( -1 );
+      }
+
       nMolWithSameStamp = (*i)->getNMol();
       
       addMoleculeStamp(molStamp, nMolWithSameStamp);
@@ -365,10 +372,12 @@ namespace OpenMD {
 
   void SimInfo::addInteractionPairs(Molecule* mol) {
     ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
+    vector<Atom*>::iterator atomIter;
     vector<Bond*>::iterator bondIter;
     vector<Bend*>::iterator bendIter;
     vector<Torsion*>::iterator torsionIter;
     vector<Inversion*>::iterator inversionIter;
+    Atom* atom;
     Bond* bond;
     Bend* bend;
     Torsion* torsion;
@@ -411,6 +420,7 @@ namespace OpenMD {
         atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));        
       }
     }  
+
            
     for (bond= mol->beginBond(bondIter); bond != NULL; 
          bond = mol->nextBond(bondIter)) {
@@ -780,6 +790,22 @@ namespace OpenMD {
 #endif
 
     return atomTypes;        
+  }
+
+
+  int getGlobalCountOfType(AtomType* atype) {
+    /*
+    set<AtomType*> atypes = getSimulatedAtomTypes();
+    map<AtomType*, int> counts_;
+
+    for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
+      for(atom = mol->beginAtom(ai); atom != NULL;
+          atom = mol->nextAtom(ai)) {
+	atom->getAtomType();
+      }      
+    }    
+    */
+    return 0;
   }
 
   void SimInfo::setupSimVariables() {
@@ -915,23 +941,21 @@ namespace OpenMD {
       }       
     }
 
-    // Build the identArray_
+    // Build the identArray_ and regions_
 
     identArray_.clear();
-    identArray_.reserve(getNAtoms());    
-    for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {        
+    identArray_.reserve(getNAtoms());   
+    regions_.clear();
+    regions_.reserve(getNAtoms());
+ 
+    for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {      
+      int reg = mol->getRegion();      
       for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
 	identArray_.push_back(atom->getIdent());
+        regions_.push_back(reg);
       }
     }    
-    
-    //scan topology 
-
-    int* excludeList = excludedInteractions_.getPairList();
-    int* oneTwoList = oneTwoInteractions_.getPairList();
-    int* oneThreeList = oneThreeInteractions_.getPairList();
-    int* oneFourList = oneFourInteractions_.getPairList();
-
+       
     topologyDone_ = true;
   }
 
@@ -1003,7 +1027,7 @@ namespace OpenMD {
    
   
   StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
-    if (index >= IOIndexToIntegrableObject.size()) {
+    if (index >= int(IOIndexToIntegrableObject.size())) {
       sprintf(painCave.errMsg,
               "SimInfo::getIOIndexToIntegrableObject Error: Integrable Object\n"
               "\tindex exceeds number of known objects!\n");