--- trunk/src/brains/SimCreator.cpp	2008/04/25 15:14:47	1241
+++ trunk/src/brains/SimCreator.cpp	2008/09/10 18:11:32	1287
@@ -145,7 +145,6 @@ namespace oopse {
       treeParser.initializeASTFactory(factory);
       treeParser.setASTFactory(&factory);
       simParams = treeParser.walkTree(parser.getAST());
-
     }
 
       
@@ -264,7 +263,7 @@ namespace oopse {
       ++lineNo;
       std::string line = trimLeftCopy(buffer);
       i = CaseInsensitiveFind(line, "<OOPSE");
-      if (i == string::npos) {
+      if (static_cast<size_t>(i) == string::npos) {
         sprintf(painCave.errMsg, 
                 "SimCreator: File: %s is not an OOPSE file!\n", 
                 mdFileName.c_str()); 
@@ -330,9 +329,8 @@ namespace oopse {
     Globals* simParams = parseFile(rawMetaDataStream, mdFileName, metaDataBlockStart+1);
     
     //create the force field
-    ForceField * ff = ForceFieldFactory::getInstance()
-      ->createForceField(simParams->getForceField());
-    
+    ForceField * ff = ForceFieldFactory::getInstance()->createForceField(simParams->getForceField());
+
     if (ff == NULL) {
       sprintf(painCave.errMsg, 
               "ForceField Factory can not create %s force field\n",
@@ -395,16 +393,16 @@ namespace oopse {
     //responsibility to LocalIndexManager.
     setGlobalIndex(info);
     
-    //Although addExcludePairs is called inside SimInfo's addMolecule
+    //Although addInteractionPairs is called inside SimInfo's addMolecule
     //method, at that point atoms don't have the global index yet
     //(their global index are all initialized to -1).  Therefore we
-    //have to call addExcludePairs explicitly here. A way to work
+    //have to call addInteractionPairs explicitly here. A way to work
     //around is that we can determine the beginning global indices of
     //atoms before they get created.
     SimInfo::MoleculeIterator mi;
     Molecule* mol;
     for (mol= info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
-      info->addExcludePairs(mol);
+      info->addInteractionPairs(mol);
     }
     
     if (loadInitCoords)