--- branches/development/src/parallel/ForceMatrixDecomposition.cpp	2012/06/22 20:01:37	1761
+++ trunk/src/parallel/ForceMatrixDecomposition.cpp	2012/09/10 18:38:44	1796
@@ -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];
     }
@@ -1043,19 +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;
@@ -1296,7 +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);
@@ -1340,6 +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.
@@ -1364,6 +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.
@@ -1390,6 +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.