--- branches/development/src/parallel/ForceMatrixDecomposition.cpp	2012/06/18 18:23:20	1756
+++ trunk/src/parallel/ForceMatrixDecomposition.cpp	2012/09/10 18:38:44	1796
@@ -176,6 +176,9 @@ namespace OpenMD {
     pot_row.resize(nAtomsInRow_);
     pot_col.resize(nAtomsInCol_);
 
+    expot_row.resize(nAtomsInRow_);
+    expot_col.resize(nAtomsInCol_);
+
     AtomRowToGlobal.resize(nAtomsInRow_);
     AtomColToGlobal.resize(nAtomsInCol_);
     AtomPlanIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
@@ -307,7 +310,6 @@ namespace OpenMD {
     
     RealType tol = 1e-6;
     largestRcut_ = 0.0;
-    RealType rc;
     int atid;
     set<AtomType*> atypes = info_->getSimulatedAtomTypes();
     
@@ -392,7 +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;
@@ -417,8 +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:
@@ -474,7 +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];
     }
@@ -484,6 +486,8 @@ namespace OpenMD {
   void ForceMatrixDecomposition::zeroWorkArrays() {
     pairwisePot = 0.0;
     embeddingPot = 0.0;
+    excludedPot = 0.0;
+    excludedSelfPot = 0.0;
 
 #ifdef IS_MPI
     if (storageLayout_ & DataStorage::dslForce) {
@@ -500,6 +504,12 @@ namespace OpenMD {
          Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
 
     fill(pot_col.begin(), pot_col.end(), 
+         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));   
+
+    fill(expot_row.begin(), expot_row.end(), 
+         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
+
+    fill(expot_col.begin(), expot_col.end(), 
          Vector<RealType, N_INTERACTION_FAMILIES> (0.0));   
 
     if (storageLayout_ & DataStorage::dslParticlePot) {    
@@ -780,13 +790,19 @@ namespace OpenMD {
 
     vector<potVec> pot_temp(nLocal_, 
                             Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
+    vector<potVec> expot_temp(nLocal_, 
+                              Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
 
     // scatter/gather pot_row into the members of my column
           
     AtomPlanPotRow->scatter(pot_row, pot_temp);
+    AtomPlanPotRow->scatter(expot_row, expot_temp);
 
-    for (int ii = 0;  ii < pot_temp.size(); ii++ )
+    for (int ii = 0;  ii < pot_temp.size(); ii++ ) 
       pairwisePot += pot_temp[ii];
+
+    for (int ii = 0;  ii < expot_temp.size(); ii++ ) 
+      excludedPot += expot_temp[ii];
         
     if (storageLayout_ & DataStorage::dslParticlePot) {
       // This is the pairwise contribution to the particle pot.  The
@@ -804,12 +820,18 @@ namespace OpenMD {
 
     fill(pot_temp.begin(), pot_temp.end(), 
          Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
+    fill(expot_temp.begin(), expot_temp.end(), 
+         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
       
     AtomPlanPotColumn->scatter(pot_col, pot_temp);    
+    AtomPlanPotColumn->scatter(expot_col, expot_temp);    
     
     for (int ii = 0;  ii < pot_temp.size(); ii++ )
       pairwisePot += pot_temp[ii];    
 
+    for (int ii = 0;  ii < expot_temp.size(); ii++ )
+      excludedPot += expot_temp[ii];    
+
     if (storageLayout_ & DataStorage::dslParticlePot) {
       // This is the pairwise contribution to the particle pot.  The
       // embedding contribution is added in each of the low level
@@ -851,6 +873,13 @@ namespace OpenMD {
       pairwisePot[ii] = ploc2;
     }
 
+    for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
+      RealType ploc1 = excludedPot[ii];
+      RealType ploc2 = 0.0;
+      MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
+      excludedPot[ii] = ploc2;
+    }
+
     // Here be dragons.
     MPI::Intracomm col = colComm.getComm();
 
@@ -878,6 +907,12 @@ namespace OpenMD {
       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
     
   }
@@ -1007,19 +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;
@@ -1194,6 +1229,8 @@ namespace OpenMD {
 #ifdef IS_MPI
     pot_row[atom1] += RealType(0.5) *  *(idat.pot);
     pot_col[atom2] += RealType(0.5) *  *(idat.pot);
+    expot_row[atom1] += RealType(0.5) *  *(idat.excludedPot);
+    expot_col[atom2] += RealType(0.5) *  *(idat.excludedPot);
 
     atomRowData.force[atom1] += *(idat.f1);
     atomColData.force[atom2] -= *(idat.f1);
@@ -1210,6 +1247,7 @@ namespace OpenMD {
 
 #else
     pairwisePot += *(idat.pot);
+    excludedPot += *(idat.excludedPot);
 
     snap_->atomData.force[atom1] += *(idat.f1);
     snap_->atomData.force[atom2] -= *(idat.f1);
@@ -1257,7 +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);
@@ -1301,6 +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.
@@ -1325,6 +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.
@@ -1351,6 +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.