--- branches/development/src/brains/SimInfo.cpp	2012/07/09 14:15:52	1769
+++ branches/development/src/brains/SimInfo.cpp	2013/01/09 19:27:52	1825
@@ -88,7 +88,8 @@ namespace OpenMD {
     
     vector<Component*> components = simParams->getComponents();
     
-    for (vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
+    for (vector<Component*>::iterator i = components.begin(); 
+         i !=components.end(); ++i) {
       molStamp = (*i)->getMoleculeStamp();
       nMolWithSameStamp = (*i)->getNMol();
       
@@ -267,8 +268,9 @@ namespace OpenMD {
     ndf_local -= nConstraints_;
 
 #ifdef IS_MPI
-    MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
-    MPI_Allreduce(&nfq_local,&nGlobalFluctuatingCharges_,1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
+    MPI::COMM_WORLD.Allreduce(&ndf_local, &ndf_, 1, MPI::INT,MPI::SUM);
+    MPI::COMM_WORLD.Allreduce(&nfq_local, &nGlobalFluctuatingCharges_, 1,
+                              MPI::INT, MPI::SUM);
 #else
     ndf_ = ndf_local;
     nGlobalFluctuatingCharges_ = nfq_local;
@@ -282,7 +284,7 @@ namespace OpenMD {
 
   int SimInfo::getFdf() {
 #ifdef IS_MPI
-    MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
+    MPI::COMM_WORLD.Allreduce(&fdf_local, &fdf_, 1, MPI::INT, MPI::SUM);
 #else
     fdf_ = fdf_local;
 #endif
@@ -338,7 +340,7 @@ namespace OpenMD {
     }
     
 #ifdef IS_MPI
-    MPI_Allreduce(&ndfRaw_local,&ndfRaw_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
+    MPI::COMM_WORLD.Allreduce(&ndfRaw_local, &ndfRaw_, 1, MPI::INT, MPI::SUM);
 #else
     ndfRaw_ = ndfRaw_local;
 #endif
@@ -351,7 +353,8 @@ namespace OpenMD {
 
 
 #ifdef IS_MPI
-    MPI_Allreduce(&ndfTrans_local,&ndfTrans_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
+    MPI::COMM_WORLD.Allreduce(&ndfTrans_local, &ndfTrans_, 1, 
+                              MPI::INT, MPI::SUM);
 #else
     ndfTrans_ = ndfTrans_local;
 #endif
@@ -781,7 +784,8 @@ namespace OpenMD {
 
   void SimInfo::setupSimVariables() {
     useAtomicVirial_ = simParams_->getUseAtomicVirial();
-    // we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
+    // we only call setAccumulateBoxDipole if the accumulateBoxDipole
+    // parameter is true
     calcBoxDipole_ = false;
     if ( simParams_->haveAccumulateBoxDipole() ) 
       if ( simParams_->getAccumulateBoxDipole() ) {
@@ -875,7 +879,6 @@ namespace OpenMD {
 
 
   void SimInfo::prepareTopology() {
-    int nExclude, nOneTwo, nOneThree, nOneFour;
 
     //calculate mass ratio of cutoff group
     SimInfo::MoleculeIterator mi;
@@ -924,11 +927,6 @@ namespace OpenMD {
     
     //scan topology 
 
-    nExclude = excludedInteractions_.getSize();
-    nOneTwo = oneTwoInteractions_.getSize();
-    nOneThree = oneThreeInteractions_.getSize();
-    nOneFour = oneFourInteractions_.getSize();
-
     int* excludeList = excludedInteractions_.getPairList();
     int* oneTwoList = oneTwoInteractions_.getPairList();
     int* oneThreeList = oneThreeInteractions_.getPairList();
@@ -979,15 +977,18 @@ namespace OpenMD {
  
     for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
         
-      for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
+      for (atom = mol->beginAtom(atomIter); atom != NULL; 
+           atom = mol->nextAtom(atomIter)) {
 	atom->setSnapshotManager(sman_);
       }
         
-      for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
+      for (rb = mol->beginRigidBody(rbIter); rb != NULL; 
+           rb = mol->nextRigidBody(rbIter)) {
 	rb->setSnapshotManager(sman_);
       }
 
-      for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
+      for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; 
+           cg = mol->nextCutoffGroup(cgIter)) {
 	cg->setSnapshotManager(sman_);
       }
     }    
@@ -1002,28 +1003,26 @@ namespace OpenMD {
    
   
   StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
-    return IOIndexToIntegrableObject.at(index);
+    if (index >= IOIndexToIntegrableObject.size()) {
+      sprintf(painCave.errMsg,
+              "SimInfo::getIOIndexToIntegrableObject Error: Integrable Object\n"
+              "\tindex exceeds number of known objects!\n");
+      painCave.isFatal = 1;
+      simError();
+      return NULL;
+    } else
+      return IOIndexToIntegrableObject.at(index);
   }
   
   void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
     IOIndexToIntegrableObject= v;
   }
-/*
-   void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
-      assert( v.size() == nAtoms_ + nRigidBodies_);
-      sdByGlobalIndex_ = v;
-    }
 
-    StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
-      //assert(index < nAtoms_ + nRigidBodies_);
-      return sdByGlobalIndex_.at(index);
-    }   
-*/   
   int SimInfo::getNGlobalConstraints() {
     int nGlobalConstraints;
 #ifdef IS_MPI
-    MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
-                  MPI_COMM_WORLD);    
+    MPI::COMM_WORLD.Allreduce(&nConstraints_, &nGlobalConstraints, 1, 
+                              MPI::INT, MPI::SUM);
 #else
     nGlobalConstraints =  nConstraints_;
 #endif