--- branches/development/src/parallel/ForceMatrixDecomposition.cpp	2012/07/06 22:01:58	1767
+++ trunk/src/parallel/ForceMatrixDecomposition.cpp	2012/09/10 18:38:44	1796
@@ -1042,19 +1042,19 @@ namespace OpenMD {
    * the parallel decomposition.
    */
   bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2, int cg1, int cg2) {
-    int unique_id_1, unique_id_2, group1, group2;
+    int unique_id_1, unique_id_2;
         
 #ifdef IS_MPI
     // in MPI, we have to look up the unique IDs for each atom
     unique_id_1 = AtomRowToGlobal[atom1];
     unique_id_2 = AtomColToGlobal[atom2];
-    group1 = cgRowToGlobal[cg1];
-    group2 = cgColToGlobal[cg2];
+    // group1 = cgRowToGlobal[cg1];
+    // group2 = cgColToGlobal[cg2];
 #else
     unique_id_1 = AtomLocalToGlobal[atom1];
     unique_id_2 = AtomLocalToGlobal[atom2];
-    group1 = cgLocalToGlobal[cg1];
-    group2 = cgLocalToGlobal[cg2];
+    int group1 = cgLocalToGlobal[cg1];
+    int group2 = cgLocalToGlobal[cg2];
 #endif   
 
     if (unique_id_1 == unique_id_2) return true;
@@ -1295,7 +1295,6 @@ namespace OpenMD {
 #endif
 
     RealType rList_ = (largestRcut_ + skinThickness_);
-    RealType rl2 = rList_ * rList_;
     Snapshot* snap_ = sman_->getCurrentSnapshot();
     Mat3x3d Hmat = snap_->getHmat();
     Vector3d Hx = Hmat.getColumn(0);
@@ -1339,6 +1338,10 @@ 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.
@@ -1363,6 +1366,10 @@ 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.
@@ -1389,6 +1396,10 @@ 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.