--- trunk/src/brains/SimInfo.cpp	2013/07/19 21:25:45	1908
+++ trunk/src/brains/SimInfo.cpp	2013/11/01 19:31:41	1940
@@ -47,6 +47,9 @@
  * @version 1.0
  */
 
+#ifdef IS_MPI
+#include <mpi.h>
+#endif
 #include <algorithm>
 #include <set>
 #include <map>
@@ -61,9 +64,6 @@
 #include "io/ForceFieldOptions.hpp"
 #include "brains/ForceField.hpp"
 #include "nonbonded/SwitchingFunction.hpp"
-#ifdef IS_MPI
-#include <mpi.h>
-#endif
 
 using namespace std;
 namespace OpenMD {
@@ -418,6 +418,7 @@ namespace OpenMD {
         atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));        
       }
     }  
+
            
     for (bond= mol->beginBond(bondIter); bond != NULL; 
          bond = mol->nextBond(bondIter)) {
@@ -938,16 +939,21 @@ 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);
       }
     }    
-    
+       
     topologyDone_ = true;
   }