--- trunk/src/brains/SimInfo.cpp	2013/08/19 13:12:00	1929
+++ trunk/src/brains/SimInfo.cpp	2013/10/31 15:32:17	1938
@@ -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 {
@@ -372,10 +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;
@@ -418,6 +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)) {