--- branches/development/src/parallel/ForceMatrixDecomposition.cpp	2012/06/21 19:26:46	1760
+++ trunk/src/parallel/ForceMatrixDecomposition.cpp	2012/08/22 02:28:28	1782
@@ -310,7 +310,6 @@ namespace OpenMD {
     
     RealType tol = 1e-6;
     largestRcut_ = 0.0;
-    RealType rc;
     int atid;
     set<AtomType*> atypes = info_->getSimulatedAtomTypes();
     
@@ -395,7 +394,7 @@ namespace OpenMD {
       }
       
       bool gTypeFound = false;
-      for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
+      for (unsigned int gt = 0; gt < gTypeCutoffs.size(); gt++) {
         if (abs(groupCutoff[cg1] - gTypeCutoffs[gt]) < tol) {
           groupToGtype[cg1] = gt;
           gTypeFound = true;
@@ -420,8 +419,8 @@ namespace OpenMD {
     
     RealType tradRcut = groupMax;
 
-    for (int i = 0; i < gTypeCutoffs.size();  i++) {
-      for (int j = 0; j < gTypeCutoffs.size();  j++) {       
+    for (unsigned int i = 0; i < gTypeCutoffs.size();  i++) {
+      for (unsigned int j = 0; j < gTypeCutoffs.size();  j++) {       
         RealType thisRcut;
         switch(cutoffPolicy_) {
         case TRADITIONAL:
@@ -477,7 +476,7 @@ namespace OpenMD {
   }
 
   int ForceMatrixDecomposition::getTopologicalDistance(int atom1, int atom2) {
-    for (int j = 0; j < toposForAtom[atom1].size(); j++) {
+    for (unsigned int j = 0; j < toposForAtom[atom1].size(); j++) {
       if (toposForAtom[atom1][j] == atom2) 
         return topoDist[atom1][j];
     }
@@ -488,6 +487,7 @@ namespace OpenMD {
     pairwisePot = 0.0;
     embeddingPot = 0.0;
     excludedPot = 0.0;
+    excludedSelfPot = 0.0;
 
 #ifdef IS_MPI
     if (storageLayout_ & DataStorage::dslForce) {
@@ -906,6 +906,12 @@ namespace OpenMD {
       RealType ploc2 = 0.0;
       MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
       embeddingPot[ii] = ploc2;
+    }    
+    for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
+      RealType ploc1 = excludedSelfPot[ii];
+      RealType ploc2 = 0.0;
+      MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
+      excludedSelfPot[ii] = ploc2;
     }    
 #endif
     
@@ -1333,6 +1339,10 @@ namespace OpenMD {
         for (int j = 0; j < 3; j++) {
           scaled[j] -= roundMe(scaled[j]);
           scaled[j] += 0.5;
+          // Handle the special case when an object is exactly on the
+          // boundary (a scaled coordinate of 1.0 is the same as
+          // scaled coordinate of 0.0)
+          if (scaled[j] >= 1.0) scaled[j] -= 1.0;
         }
         
         // find xyz-indices of cell that cutoffGroup is in.
@@ -1357,6 +1367,10 @@ namespace OpenMD {
         for (int j = 0; j < 3; j++) {
           scaled[j] -= roundMe(scaled[j]);
           scaled[j] += 0.5;
+          // Handle the special case when an object is exactly on the
+          // boundary (a scaled coordinate of 1.0 is the same as
+          // scaled coordinate of 0.0)
+          if (scaled[j] >= 1.0) scaled[j] -= 1.0;
         }
         
         // find xyz-indices of cell that cutoffGroup is in.
@@ -1383,6 +1397,10 @@ namespace OpenMD {
         for (int j = 0; j < 3; j++) {
           scaled[j] -= roundMe(scaled[j]);
           scaled[j] += 0.5;
+          // Handle the special case when an object is exactly on the
+          // boundary (a scaled coordinate of 1.0 is the same as
+          // scaled coordinate of 0.0)
+          if (scaled[j] >= 1.0) scaled[j] -= 1.0;
         }
         
         // find xyz-indices of cell that cutoffGroup is in.