--- trunk/src/brains/SimCreator.cpp	2008/04/25 15:14:47	1241
+++ trunk/src/brains/SimCreator.cpp	2008/10/22 20:01:49	1313
@@ -108,7 +108,7 @@ namespace oopse {
       } else {
         //get stream size
         commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);   
-                
+
         char* buf = new char[streamSize];
         assert(buf);
                 
@@ -116,7 +116,7 @@ namespace oopse {
         commStatus = MPI_Bcast(buf, streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD); 
                 
         ppStream.str(buf);
-        delete buf;
+        delete [] buf;
 
       }
 #endif            
@@ -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)
@@ -724,7 +722,7 @@ namespace oopse {
     // to get the full globalGroupMembership array (We think).
     // This would be prettier if we could use MPI_IN_PLACE like the MPI-2
     // docs said we could.
-    std::vector<int> tmpGroupMembership(nGlobalAtoms, 0);
+    std::vector<int> tmpGroupMembership(info->getNGlobalAtoms(), 0);
     MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms,
                   MPI_INT, MPI_SUM, MPI_COMM_WORLD);
     info->setGlobalGroupMembership(tmpGroupMembership);
@@ -736,14 +734,13 @@ namespace oopse {
     std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0);
     
     for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
-      
       for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
         globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
       }
     }
     
 #ifdef IS_MPI
-    std::vector<int> tmpMolMembership(nGlobalAtoms, 0);
+    std::vector<int> tmpMolMembership(info->getNGlobalAtoms(), 0);
     
     MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms,
                   MPI_INT, MPI_SUM, MPI_COMM_WORLD);
@@ -769,28 +766,28 @@ namespace oopse {
     std::vector<int> numIntegrableObjectsPerMol = nIOPerMol;
 #endif    
 
- std::vector<int> startingIOIndexForMol(info->getNGlobalMolecules());
-
-int startingIndex = 0;
- for (int i = 0; i < info->getNGlobalMolecules(); i++) {
-  startingIOIndexForMol[i] = startingIndex;
-  startingIndex += numIntegrableObjectsPerMol[i];
- }
-
- std::vector<StuntDouble*> IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL);
- for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
+    std::vector<int> startingIOIndexForMol(info->getNGlobalMolecules());
+    
+    int startingIndex = 0;
+    for (int i = 0; i < info->getNGlobalMolecules(); i++) {
+      startingIOIndexForMol[i] = startingIndex;
+      startingIndex += numIntegrableObjectsPerMol[i];
+    }
+    
+    std::vector<StuntDouble*> IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL);
+    for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
       int myGlobalIndex = mol->getGlobalIndex();
       int globalIO = startingIOIndexForMol[myGlobalIndex];
       for (StuntDouble* integrableObject = mol->beginIntegrableObject(ioi); integrableObject != NULL;
            integrableObject = mol->nextIntegrableObject(ioi)) {
-            integrableObject->setGlobalIntegrableObjectIndex(globalIO);
-            IOIndexToIntegrableObject[globalIO] = integrableObject;
-            globalIO++;
+        integrableObject->setGlobalIntegrableObjectIndex(globalIO);
+        IOIndexToIntegrableObject[globalIO] = integrableObject;
+        globalIO++;
       }
     }
-
-  info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject);
-  
+    
+    info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject);
+    
   }
   
   void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) {