--- branches/development/src/nonbonded/InteractionManager.cpp	2011/10/11 19:46:51	1656
+++ branches/development/src/nonbonded/InteractionManager.cpp	2013/01/09 19:27:52	1825
@@ -36,7 +36,8 @@
  * [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).          
- * [4]  Vardeman & Gezelter, in progress (2009).                        
+ * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
+ * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
  */
  
 #include "nonbonded/InteractionManager.hpp"
@@ -59,7 +60,9 @@ namespace OpenMD {
   }
 
   void InteractionManager::initialize() {
-    
+
+    if (initialized_) return; 
+
     ForceField* forceField_ = info_->getForceField();
     
     lj_->setForceField(forceField_);
@@ -84,14 +87,13 @@ namespace OpenMD {
          atype1 = atomTypes->nextType(i1)) {
       
       // add it to the map:
-      AtomTypeProperties atp = atype1->getATP();    
       
       pair<map<int,AtomType*>::iterator,bool> ret;    
-      ret = typeMap_.insert( pair<int, AtomType*>(atp.ident, atype1) );
+      ret = typeMap_.insert( pair<int, AtomType*>(atype1->getIdent(), atype1) );
       if (ret.second == false) {
         sprintf( painCave.errMsg,
                  "InteractionManager already had a previous entry with ident %d\n",
-                 atp.ident);
+                 atype1->getIdent());
         painCave.severity = OPENMD_INFO;
         painCave.isFatal = 0;
         simError();                 
@@ -109,7 +111,7 @@ namespace OpenMD {
         
         bool vdwExplicit = false;
         bool metExplicit = false;
-        bool hbExplicit = false;
+        // bool hbExplicit = false;
                        
         key = make_pair(atype1, atype2);
         
@@ -302,10 +304,6 @@ namespace OpenMD {
     eam_->setCutoffRadius(rcut);
   }
 
-  void InteractionManager::setSwitchingRadius(RealType rswitch) {
-    electrostatic_->setSwitchingRadius(rswitch);
-  }
-  
   void InteractionManager::doPrePair(InteractionData idat){
     
     if (!initialized_) initialize();
@@ -379,7 +377,7 @@ namespace OpenMD {
 
   RealType InteractionManager::getSuggestedCutoffRadius(int *atid) {
     if (!initialized_) initialize();
-    
+
     AtomType* atype = typeMap_[*atid];
 
     pair<AtomType*, AtomType*> key = make_pair(atype, atype);