--- branches/development/src/parallel/ForceMatrixDecomposition.cpp	2011/06/13 22:13:12	1581
+++ trunk/src/parallel/ForceMatrixDecomposition.cpp	2013/10/31 18:18:57	1939
@@ -35,8 +35,9 @@
  *                                                                      
  * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
  * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
- * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
- * [4]  Vardeman & Gezelter, in progress (2009).                        
+ * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
+ * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
+ * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
  */
 #include "parallel/ForceMatrixDecomposition.hpp"
 #include "math/SquareMatrix3.hpp"
@@ -47,54 +48,102 @@ namespace OpenMD {
 using namespace std;
 namespace OpenMD {
 
+  ForceMatrixDecomposition::ForceMatrixDecomposition(SimInfo* info, InteractionManager* iMan) : ForceDecomposition(info, iMan) {
+
+    // In a parallel computation, row and colum scans must visit all
+    // surrounding cells (not just the 14 upper triangular blocks that
+    // are used when the processor can see all pairs)
+#ifdef IS_MPI
+    cellOffsets_.clear();
+    cellOffsets_.push_back( Vector3i(-1,-1,-1) );
+    cellOffsets_.push_back( Vector3i( 0,-1,-1) );
+    cellOffsets_.push_back( Vector3i( 1,-1,-1) );                          
+    cellOffsets_.push_back( Vector3i(-1, 0,-1) );
+    cellOffsets_.push_back( Vector3i( 0, 0,-1) );
+    cellOffsets_.push_back( Vector3i( 1, 0,-1) );
+    cellOffsets_.push_back( Vector3i(-1, 1,-1) );
+    cellOffsets_.push_back( Vector3i( 0, 1,-1) );      
+    cellOffsets_.push_back( Vector3i( 1, 1,-1) );
+    cellOffsets_.push_back( Vector3i(-1,-1, 0) );
+    cellOffsets_.push_back( Vector3i( 0,-1, 0) );
+    cellOffsets_.push_back( Vector3i( 1,-1, 0) );
+    cellOffsets_.push_back( Vector3i(-1, 0, 0) );       
+    cellOffsets_.push_back( Vector3i( 0, 0, 0) );
+    cellOffsets_.push_back( Vector3i( 1, 0, 0) );
+    cellOffsets_.push_back( Vector3i(-1, 1, 0) );
+    cellOffsets_.push_back( Vector3i( 0, 1, 0) );
+    cellOffsets_.push_back( Vector3i( 1, 1, 0) );
+    cellOffsets_.push_back( Vector3i(-1,-1, 1) );
+    cellOffsets_.push_back( Vector3i( 0,-1, 1) );
+    cellOffsets_.push_back( Vector3i( 1,-1, 1) );
+    cellOffsets_.push_back( Vector3i(-1, 0, 1) );
+    cellOffsets_.push_back( Vector3i( 0, 0, 1) );
+    cellOffsets_.push_back( Vector3i( 1, 0, 1) );
+    cellOffsets_.push_back( Vector3i(-1, 1, 1) );
+    cellOffsets_.push_back( Vector3i( 0, 1, 1) );
+    cellOffsets_.push_back( Vector3i( 1, 1, 1) );
+#endif    
+  }
+
+
   /**
    * distributeInitialData is essentially a copy of the older fortran 
    * SimulationSetup
    */
-  
   void ForceMatrixDecomposition::distributeInitialData() {
     snap_ = sman_->getCurrentSnapshot();
     storageLayout_ = sman_->getStorageLayout();
     ff_ = info_->getForceField();
     nLocal_ = snap_->getNumberOfAtoms();
-
+   
     nGroups_ = info_->getNLocalCutoffGroups();
-    cerr << "in dId, nGroups = " << nGroups_ << "\n";
     // gather the information for atomtype IDs (atids):
-    identsLocal = info_->getIdentArray();
+    idents = info_->getIdentArray();
+    regions = info_->getRegions();
     AtomLocalToGlobal = info_->getGlobalAtomIndices();
     cgLocalToGlobal = info_->getGlobalGroupIndices();
     vector<int> globalGroupMembership = info_->getGlobalGroupMembership();
+
     massFactors = info_->getMassFactors();
-    PairList excludes = info_->getExcludedInteractions();
-    PairList oneTwo = info_->getOneTwoInteractions();
-    PairList oneThree = info_->getOneThreeInteractions();
-    PairList oneFour = info_->getOneFourInteractions();
 
+    PairList* excludes = info_->getExcludedInteractions();
+    PairList* oneTwo = info_->getOneTwoInteractions();
+    PairList* oneThree = info_->getOneThreeInteractions();
+    PairList* oneFour = info_->getOneFourInteractions();
+    
+    if (needVelocities_) 
+      snap_->cgData.setStorageLayout(DataStorage::dslPosition | 
+                                     DataStorage::dslVelocity);
+    else 
+      snap_->cgData.setStorageLayout(DataStorage::dslPosition);
+    
 #ifdef IS_MPI
  
-    AtomCommIntRow = new Communicator<Row,int>(nLocal_);
-    AtomCommRealRow = new Communicator<Row,RealType>(nLocal_);
-    AtomCommVectorRow = new Communicator<Row,Vector3d>(nLocal_);
-    AtomCommMatrixRow = new Communicator<Row,Mat3x3d>(nLocal_);
-    AtomCommPotRow = new Communicator<Row,potVec>(nLocal_);
+    MPI::Intracomm row = rowComm.getComm();
+    MPI::Intracomm col = colComm.getComm();
 
-    AtomCommIntColumn = new Communicator<Column,int>(nLocal_);
-    AtomCommRealColumn = new Communicator<Column,RealType>(nLocal_);
-    AtomCommVectorColumn = new Communicator<Column,Vector3d>(nLocal_);
-    AtomCommMatrixColumn = new Communicator<Column,Mat3x3d>(nLocal_);
-    AtomCommPotColumn = new Communicator<Column,potVec>(nLocal_);
+    AtomPlanIntRow = new Plan<int>(row, nLocal_);
+    AtomPlanRealRow = new Plan<RealType>(row, nLocal_);
+    AtomPlanVectorRow = new Plan<Vector3d>(row, nLocal_);
+    AtomPlanMatrixRow = new Plan<Mat3x3d>(row, nLocal_);
+    AtomPlanPotRow = new Plan<potVec>(row, nLocal_);
 
-    cgCommIntRow = new Communicator<Row,int>(nGroups_);
-    cgCommVectorRow = new Communicator<Row,Vector3d>(nGroups_);
-    cgCommIntColumn = new Communicator<Column,int>(nGroups_);
-    cgCommVectorColumn = new Communicator<Column,Vector3d>(nGroups_);
+    AtomPlanIntColumn = new Plan<int>(col, nLocal_);
+    AtomPlanRealColumn = new Plan<RealType>(col, nLocal_);
+    AtomPlanVectorColumn = new Plan<Vector3d>(col, nLocal_);
+    AtomPlanMatrixColumn = new Plan<Mat3x3d>(col, nLocal_);
+    AtomPlanPotColumn = new Plan<potVec>(col, nLocal_);
 
-    nAtomsInRow_ = AtomCommIntRow->getSize();
-    nAtomsInCol_ = AtomCommIntColumn->getSize();
-    nGroupsInRow_ = cgCommIntRow->getSize();
-    nGroupsInCol_ = cgCommIntColumn->getSize();
+    cgPlanIntRow = new Plan<int>(row, nGroups_);
+    cgPlanVectorRow = new Plan<Vector3d>(row, nGroups_);
+    cgPlanIntColumn = new Plan<int>(col, nGroups_);
+    cgPlanVectorColumn = new Plan<Vector3d>(col, nGroups_);
 
+    nAtomsInRow_ = AtomPlanIntRow->getSize();
+    nAtomsInCol_ = AtomPlanIntColumn->getSize();
+    nGroupsInRow_ = cgPlanIntRow->getSize();
+    nGroupsInCol_ = cgPlanIntColumn->getSize();
+
     // Modify the data storage objects with the correct layouts and sizes:
     atomRowData.resize(nAtomsInRow_);
     atomRowData.setStorageLayout(storageLayout_);
@@ -103,23 +152,55 @@ namespace OpenMD {
     cgRowData.resize(nGroupsInRow_);
     cgRowData.setStorageLayout(DataStorage::dslPosition);
     cgColData.resize(nGroupsInCol_);
-    cgColData.setStorageLayout(DataStorage::dslPosition);
-        
+    if (needVelocities_)
+      // we only need column velocities if we need them.
+      cgColData.setStorageLayout(DataStorage::dslPosition |
+                                 DataStorage::dslVelocity);
+    else     
+      cgColData.setStorageLayout(DataStorage::dslPosition);
+      
     identsRow.resize(nAtomsInRow_);
     identsCol.resize(nAtomsInCol_);
     
-    AtomCommIntRow->gather(identsLocal, identsRow);
-    AtomCommIntColumn->gather(identsLocal, identsCol);
+    AtomPlanIntRow->gather(idents, identsRow);
+    AtomPlanIntColumn->gather(idents, identsCol);
+
+    regionsRow.resize(nAtomsInRow_);
+    regionsCol.resize(nAtomsInCol_);
     
-    AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
-    AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
+    AtomPlanIntRow->gather(regions, regionsRow);
+    AtomPlanIntColumn->gather(regions, regionsCol);
     
-    cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
-    cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
+    // allocate memory for the parallel objects
+    atypesRow.resize(nAtomsInRow_);
+    atypesCol.resize(nAtomsInCol_);
 
-    AtomCommRealRow->gather(massFactors, massFactorsRow);
-    AtomCommRealColumn->gather(massFactors, massFactorsCol);
+    for (int i = 0; i < nAtomsInRow_; i++) 
+      atypesRow[i] = ff_->getAtomType(identsRow[i]);
+    for (int i = 0; i < nAtomsInCol_; i++) 
+      atypesCol[i] = ff_->getAtomType(identsCol[i]);         
 
+    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);
+    AtomPlanIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
+
+    cgRowToGlobal.resize(nGroupsInRow_);
+    cgColToGlobal.resize(nGroupsInCol_);
+    cgPlanIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
+    cgPlanIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
+
+    massFactorsRow.resize(nAtomsInRow_);
+    massFactorsCol.resize(nAtomsInCol_);
+    AtomPlanRealRow->gather(massFactors, massFactorsRow);
+    AtomPlanRealColumn->gather(massFactors, massFactorsCol);
+
     groupListRow_.clear();
     groupListRow_.resize(nGroupsInRow_);
     for (int i = 0; i < nGroupsInRow_; i++) {
@@ -142,8 +223,8 @@ namespace OpenMD {
       }      
     }
 
-    skipsForAtom.clear();
-    skipsForAtom.resize(nAtomsInRow_);
+    excludesForAtom.clear();
+    excludesForAtom.resize(nAtomsInRow_);
     toposForAtom.clear();
     toposForAtom.resize(nAtomsInRow_);
     topoDist.clear();
@@ -154,42 +235,29 @@ namespace OpenMD {
       for (int j = 0; j < nAtomsInCol_; j++) {
         int jglob = AtomColToGlobal[j];
 
-        if (excludes.hasPair(iglob, jglob)) 
-          skipsForAtom[i].push_back(j);       
+        if (excludes->hasPair(iglob, jglob)) 
+          excludesForAtom[i].push_back(j);       
         
-        if (oneTwo.hasPair(iglob, jglob)) {
+        if (oneTwo->hasPair(iglob, jglob)) {
           toposForAtom[i].push_back(j);
           topoDist[i].push_back(1);
         } else {
-          if (oneThree.hasPair(iglob, jglob)) {
+          if (oneThree->hasPair(iglob, jglob)) {
             toposForAtom[i].push_back(j);
             topoDist[i].push_back(2);
           } else {
-            if (oneFour.hasPair(iglob, jglob)) {
+            if (oneFour->hasPair(iglob, jglob)) {
               toposForAtom[i].push_back(j);
               topoDist[i].push_back(3);
             }
           }
-        }
-      }      
-    }
-
-#endif
-
-    groupList_.clear();
-    groupList_.resize(nGroups_);
-    for (int i = 0; i < nGroups_; i++) {
-      int gid = cgLocalToGlobal[i];
-      for (int j = 0; j < nLocal_; j++) {
-        int aid = AtomLocalToGlobal[j];
-        if (globalGroupMembership[aid] == gid) {
-          groupList_[i].push_back(j);
         }
       }      
     }
 
-    skipsForAtom.clear();
-    skipsForAtom.resize(nLocal_);
+#else
+    excludesForAtom.clear();
+    excludesForAtom.resize(nLocal_);
     toposForAtom.clear();
     toposForAtom.resize(nLocal_);
     topoDist.clear();
@@ -201,18 +269,18 @@ namespace OpenMD {
       for (int j = 0; j < nLocal_; j++) {
         int jglob = AtomLocalToGlobal[j];
 
-        if (excludes.hasPair(iglob, jglob)) 
-          skipsForAtom[i].push_back(j);              
+        if (excludes->hasPair(iglob, jglob)) 
+          excludesForAtom[i].push_back(j);              
         
-        if (oneTwo.hasPair(iglob, jglob)) {
+        if (oneTwo->hasPair(iglob, jglob)) {
           toposForAtom[i].push_back(j);
           topoDist[i].push_back(1);
         } else {
-          if (oneThree.hasPair(iglob, jglob)) {
+          if (oneThree->hasPair(iglob, jglob)) {
             toposForAtom[i].push_back(j);
             topoDist[i].push_back(2);
           } else {
-            if (oneFour.hasPair(iglob, jglob)) {
+            if (oneFour->hasPair(iglob, jglob)) {
               toposForAtom[i].push_back(j);
               topoDist[i].push_back(3);
             }
@@ -220,28 +288,54 @@ namespace OpenMD {
         }
       }      
     }
-    
+#endif
+
+    // allocate memory for the parallel objects
+    atypesLocal.resize(nLocal_);
+
+    for (int i = 0; i < nLocal_; i++) 
+      atypesLocal[i] = ff_->getAtomType(idents[i]);
+
+    groupList_.clear();
+    groupList_.resize(nGroups_);
+    for (int i = 0; i < nGroups_; i++) {
+      int gid = cgLocalToGlobal[i];
+      for (int j = 0; j < nLocal_; j++) {
+        int aid = AtomLocalToGlobal[j];
+        if (globalGroupMembership[aid] == gid) {
+          groupList_[i].push_back(j);
+        }
+      }      
+    }
+
+
     createGtypeCutoffMap();
+
   }
    
   void ForceMatrixDecomposition::createGtypeCutoffMap() {
+    
+    GrCut.clear();
+    GrCutSq.clear();
+    GrlistSq.clear();
 
     RealType tol = 1e-6;
-    RealType rc;
+    largestRcut_ = 0.0;
     int atid;
     set<AtomType*> atypes = info_->getSimulatedAtomTypes();
-    vector<RealType> atypeCutoff;
-    atypeCutoff.resize( atypes.size() );
-
+    
+    map<int, RealType> atypeCutoff;
+      
     for (set<AtomType*>::iterator at = atypes.begin(); 
          at != atypes.end(); ++at){
-      rc = interactionMan_->getSuggestedCutoffRadius(*at);
       atid = (*at)->getIdent();
-      atypeCutoff[atid] = rc;
+      if (userChoseCutoff_) 
+        atypeCutoff[atid] = userCutoff_;
+      else
+        atypeCutoff[atid] = interactionMan_->getSuggestedCutoffRadius(*at);
     }
-
+    
     vector<RealType> gTypeCutoffs;
-
     // first we do a single loop over the cutoff groups to find the
     // largest cutoff for any atypes present in this group.
 #ifdef IS_MPI
@@ -299,49 +393,54 @@ namespace OpenMD {
 
     vector<RealType> groupCutoff(nGroups_, 0.0);
     groupToGtype.resize(nGroups_);
-
-    cerr << "nGroups = " << nGroups_ << "\n";
     for (int cg1 = 0; cg1 < nGroups_; cg1++) {
-
       groupCutoff[cg1] = 0.0;
       vector<int> atomList = getAtomsInGroupRow(cg1);
-
       for (vector<int>::iterator ia = atomList.begin(); 
            ia != atomList.end(); ++ia) {            
         int atom1 = (*ia);
-        atid = identsLocal[atom1];
-        if (atypeCutoff[atid] > groupCutoff[cg1]) {
+        atid = idents[atom1];
+        if (atypeCutoff[atid] > groupCutoff[cg1]) 
           groupCutoff[cg1] = atypeCutoff[atid];
-        }
       }
-
+      
       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;
         } 
       }
-      if (!gTypeFound) {
+      if (!gTypeFound) {      
         gTypeCutoffs.push_back( groupCutoff[cg1] );
         groupToGtype[cg1] = gTypeCutoffs.size() - 1;
       }      
     }
 #endif
 
-    cerr << "gTypeCutoffs.size() = " << gTypeCutoffs.size() << "\n";
     // Now we find the maximum group cutoff value present in the simulation
 
-    RealType groupMax = *max_element(gTypeCutoffs.begin(), gTypeCutoffs.end());
+    RealType groupMax = *max_element(gTypeCutoffs.begin(), 
+                                     gTypeCutoffs.end());
 
 #ifdef IS_MPI
-    MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE, MPI::MAX);
+    MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE, 
+                              MPI::MAX);
 #endif
     
     RealType tradRcut = groupMax;
 
-    for (int i = 0; i < gTypeCutoffs.size();  i++) {
-      for (int j = 0; j < gTypeCutoffs.size();  j++) {       
+    GrCut.resize( gTypeCutoffs.size() );
+    GrCutSq.resize( gTypeCutoffs.size() );
+    GrlistSq.resize( gTypeCutoffs.size() );
+
+
+    for (unsigned int i = 0; i < gTypeCutoffs.size();  i++) {
+      GrCut[i].resize( gTypeCutoffs.size() , 0.0);
+      GrCutSq[i].resize( gTypeCutoffs.size(), 0.0 );
+      GrlistSq[i].resize( gTypeCutoffs.size(), 0.0 );
+
+      for (unsigned int j = 0; j < gTypeCutoffs.size();  j++) {       
         RealType thisRcut;
         switch(cutoffPolicy_) {
         case TRADITIONAL:
@@ -363,22 +462,21 @@ namespace OpenMD {
           break;
         }
 
-        pair<int,int> key = make_pair(i,j);
-        gTypeCutoffMap[key].first = thisRcut;
-
+        GrCut[i][j] = thisRcut;
         if (thisRcut > largestRcut_) largestRcut_ = thisRcut;
+        GrCutSq[i][j] = thisRcut * thisRcut;
+        GrlistSq[i][j] = pow(thisRcut + skinThickness_, 2);
 
-        gTypeCutoffMap[key].second = thisRcut*thisRcut;
-        
-        gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2);
-
+        // pair<int,int> key = make_pair(i,j);
+        // gTypeCutoffMap[key].first = thisRcut;
+        // gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2);
         // sanity check
         
         if (userChoseCutoff_) {
-          if (abs(gTypeCutoffMap[key].first - userCutoff_) > 0.0001) {
+          if (abs(GrCut[i][j] - userCutoff_) > 0.0001) {
             sprintf(painCave.errMsg,
                     "ForceMatrixDecomposition::createGtypeCutoffMap " 
-                    "user-specified rCut does not match computed group Cutoff\n");
+                    "user-specified rCut (%lf) does not match computed group Cutoff\n", userCutoff_);
             painCave.severity = OPENMD_ERROR;
             painCave.isFatal = 1;
             simError();            
@@ -388,8 +486,7 @@ namespace OpenMD {
     }
   }
 
-
-  groupCutoffs ForceMatrixDecomposition::getGroupCutoffs(int cg1, int cg2) {
+  void ForceMatrixDecomposition::getGroupCutoffs(int &cg1, int &cg2, RealType &rcut, RealType &rcutsq, RealType &rlistsq) {
     int i, j;   
 #ifdef IS_MPI
     i = groupRowToGtype[cg1];
@@ -398,23 +495,27 @@ namespace OpenMD {
     i = groupToGtype[cg1];
     j = groupToGtype[cg2];
 #endif    
-    return gTypeCutoffMap[make_pair(i,j)];
+    rcut = GrCut[i][j];
+    rcutsq = GrCutSq[i][j];
+    rlistsq = GrlistSq[i][j];
+    return;
+    //return gTypeCutoffMap[make_pair(i,j)];
   }
 
   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];
-    }
+    }                                           
     return 0;
   }
 
   void ForceMatrixDecomposition::zeroWorkArrays() {
+    pairwisePot = 0.0;
+    embeddingPot = 0.0;
+    excludedPot = 0.0;
+    excludedSelfPot = 0.0;
 
-    for (int j = 0; j < N_INTERACTION_FAMILIES; j++) {
-      longRangePot_[j] = 0.0;
-    }
-
 #ifdef IS_MPI
     if (storageLayout_ & DataStorage::dslForce) {
       fill(atomRowData.force.begin(), atomRowData.force.end(), V3Zero);
@@ -430,13 +531,19 @@ 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));
-    
-    pot_local = 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) {    
-      fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(), 0.0);
-      fill(atomColData.particlePot.begin(), atomColData.particlePot.end(), 0.0);
+      fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(),
+           0.0);
+      fill(atomColData.particlePot.begin(), atomColData.particlePot.end(),
+           0.0);
     }
 
     if (storageLayout_ & DataStorage::dslDensity) {      
@@ -445,8 +552,10 @@ namespace OpenMD {
     }
 
     if (storageLayout_ & DataStorage::dslFunctional) {   
-      fill(atomRowData.functional.begin(), atomRowData.functional.end(), 0.0);
-      fill(atomColData.functional.begin(), atomColData.functional.end(), 0.0);
+      fill(atomRowData.functional.begin(), atomRowData.functional.end(),
+           0.0);
+      fill(atomColData.functional.begin(), atomColData.functional.end(),
+           0.0);
     }
 
     if (storageLayout_ & DataStorage::dslFunctionalDerivative) {      
@@ -456,8 +565,30 @@ namespace OpenMD {
            atomColData.functionalDerivative.end(), 0.0);
     }
 
-#else
-    
+    if (storageLayout_ & DataStorage::dslSkippedCharge) {      
+      fill(atomRowData.skippedCharge.begin(), 
+           atomRowData.skippedCharge.end(), 0.0);
+      fill(atomColData.skippedCharge.begin(), 
+           atomColData.skippedCharge.end(), 0.0);
+    }
+
+    if (storageLayout_ & DataStorage::dslFlucQForce) {      
+      fill(atomRowData.flucQFrc.begin(), 
+           atomRowData.flucQFrc.end(), 0.0);
+      fill(atomColData.flucQFrc.begin(), 
+           atomColData.flucQFrc.end(), 0.0);
+    }
+
+    if (storageLayout_ & DataStorage::dslElectricField) {    
+      fill(atomRowData.electricField.begin(), 
+           atomRowData.electricField.end(), V3Zero);
+      fill(atomColData.electricField.begin(), 
+           atomColData.electricField.end(), V3Zero);
+    }
+
+#endif
+    // even in parallel, we need to zero out the local arrays:
+
     if (storageLayout_ & DataStorage::dslParticlePot) {      
       fill(snap_->atomData.particlePot.begin(), 
            snap_->atomData.particlePot.end(), 0.0);
@@ -467,16 +598,26 @@ namespace OpenMD {
       fill(snap_->atomData.density.begin(), 
            snap_->atomData.density.end(), 0.0);
     }
+
     if (storageLayout_ & DataStorage::dslFunctional) {
       fill(snap_->atomData.functional.begin(), 
            snap_->atomData.functional.end(), 0.0);
     }
+
     if (storageLayout_ & DataStorage::dslFunctionalDerivative) {      
       fill(snap_->atomData.functionalDerivative.begin(), 
            snap_->atomData.functionalDerivative.end(), 0.0);
     }
-#endif
-    
+
+    if (storageLayout_ & DataStorage::dslSkippedCharge) {      
+      fill(snap_->atomData.skippedCharge.begin(), 
+           snap_->atomData.skippedCharge.end(), 0.0);
+    }
+
+    if (storageLayout_ & DataStorage::dslElectricField) {      
+      fill(snap_->atomData.electricField.begin(), 
+           snap_->atomData.electricField.end(), V3Zero);
+    }
   }
 
 
@@ -486,32 +627,62 @@ namespace OpenMD {
 #ifdef IS_MPI
     
     // gather up the atomic positions
-    AtomCommVectorRow->gather(snap_->atomData.position, 
+    AtomPlanVectorRow->gather(snap_->atomData.position, 
                               atomRowData.position);
-    AtomCommVectorColumn->gather(snap_->atomData.position, 
+    AtomPlanVectorColumn->gather(snap_->atomData.position, 
                                  atomColData.position);
     
     // gather up the cutoff group positions
-    cgCommVectorRow->gather(snap_->cgData.position, 
+
+    cgPlanVectorRow->gather(snap_->cgData.position, 
                             cgRowData.position);
-    cgCommVectorColumn->gather(snap_->cgData.position, 
+
+    cgPlanVectorColumn->gather(snap_->cgData.position, 
                                cgColData.position);
+
+
+
+    if (needVelocities_) {
+      // gather up the atomic velocities
+      AtomPlanVectorColumn->gather(snap_->atomData.velocity, 
+                                   atomColData.velocity);
+      
+      cgPlanVectorColumn->gather(snap_->cgData.velocity, 
+                                 cgColData.velocity);
+    }
+
     
     // if needed, gather the atomic rotation matrices
     if (storageLayout_ & DataStorage::dslAmat) {
-      AtomCommMatrixRow->gather(snap_->atomData.aMat, 
+      AtomPlanMatrixRow->gather(snap_->atomData.aMat, 
                                 atomRowData.aMat);
-      AtomCommMatrixColumn->gather(snap_->atomData.aMat, 
+      AtomPlanMatrixColumn->gather(snap_->atomData.aMat, 
                                    atomColData.aMat);
     }
-    
-    // if needed, gather the atomic eletrostatic frames
-    if (storageLayout_ & DataStorage::dslElectroFrame) {
-      AtomCommMatrixRow->gather(snap_->atomData.electroFrame, 
-                                atomRowData.electroFrame);
-      AtomCommMatrixColumn->gather(snap_->atomData.electroFrame, 
-                                   atomColData.electroFrame);
+
+    // if needed, gather the atomic eletrostatic information
+    if (storageLayout_ & DataStorage::dslDipole) {
+      AtomPlanVectorRow->gather(snap_->atomData.dipole, 
+                                atomRowData.dipole);
+      AtomPlanVectorColumn->gather(snap_->atomData.dipole, 
+                                   atomColData.dipole);
     }
+
+    if (storageLayout_ & DataStorage::dslQuadrupole) {
+      AtomPlanMatrixRow->gather(snap_->atomData.quadrupole, 
+                                atomRowData.quadrupole);
+      AtomPlanMatrixColumn->gather(snap_->atomData.quadrupole, 
+                                   atomColData.quadrupole);
+    }
+        
+    // if needed, gather the atomic fluctuating charge values
+    if (storageLayout_ & DataStorage::dslFlucQPosition) {
+      AtomPlanRealRow->gather(snap_->atomData.flucQPos, 
+                              atomRowData.flucQPos);
+      AtomPlanRealColumn->gather(snap_->atomData.flucQPos, 
+                                 atomColData.flucQPos);
+    }
+
 #endif      
   }
   
@@ -525,15 +696,30 @@ namespace OpenMD {
     
     if (storageLayout_ & DataStorage::dslDensity) {
       
-      AtomCommRealRow->scatter(atomRowData.density, 
+      AtomPlanRealRow->scatter(atomRowData.density, 
                                snap_->atomData.density);
       
       int n = snap_->atomData.density.size();
       vector<RealType> rho_tmp(n, 0.0);
-      AtomCommRealColumn->scatter(atomColData.density, rho_tmp);
+      AtomPlanRealColumn->scatter(atomColData.density, rho_tmp);
       for (int i = 0; i < n; i++)
         snap_->atomData.density[i] += rho_tmp[i];
     }
+
+    // this isn't necessary if we don't have polarizable atoms, but
+    // we'll leave it here for now.
+    if (storageLayout_ & DataStorage::dslElectricField) {
+      
+      AtomPlanVectorRow->scatter(atomRowData.electricField, 
+                                 snap_->atomData.electricField);
+      
+      int n = snap_->atomData.electricField.size();
+      vector<Vector3d> field_tmp(n, V3Zero);
+      AtomPlanVectorColumn->scatter(atomColData.electricField, 
+                                    field_tmp);
+      for (int i = 0; i < n; i++)
+        snap_->atomData.electricField[i] += field_tmp[i];
+    }
 #endif
   }
 
@@ -546,16 +732,16 @@ namespace OpenMD {
     storageLayout_ = sman_->getStorageLayout();
 #ifdef IS_MPI
     if (storageLayout_ & DataStorage::dslFunctional) {
-      AtomCommRealRow->gather(snap_->atomData.functional, 
+      AtomPlanRealRow->gather(snap_->atomData.functional, 
                               atomRowData.functional);
-      AtomCommRealColumn->gather(snap_->atomData.functional, 
+      AtomPlanRealColumn->gather(snap_->atomData.functional, 
                                  atomColData.functional);
     }
     
     if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
-      AtomCommRealRow->gather(snap_->atomData.functionalDerivative, 
+      AtomPlanRealRow->gather(snap_->atomData.functionalDerivative, 
                               atomRowData.functionalDerivative);
-      AtomCommRealColumn->gather(snap_->atomData.functionalDerivative, 
+      AtomPlanRealColumn->gather(snap_->atomData.functionalDerivative, 
                                  atomColData.functionalDerivative);
     }
 #endif
@@ -569,58 +755,219 @@ namespace OpenMD {
     int n = snap_->atomData.force.size();
     vector<Vector3d> frc_tmp(n, V3Zero);
     
-    AtomCommVectorRow->scatter(atomRowData.force, frc_tmp);
+    AtomPlanVectorRow->scatter(atomRowData.force, frc_tmp);
     for (int i = 0; i < n; i++) {
       snap_->atomData.force[i] += frc_tmp[i];
       frc_tmp[i] = 0.0;
     }
     
-    AtomCommVectorColumn->scatter(atomColData.force, frc_tmp);
-    for (int i = 0; i < n; i++)
+    AtomPlanVectorColumn->scatter(atomColData.force, frc_tmp);
+    for (int i = 0; i < n; i++) {
       snap_->atomData.force[i] += frc_tmp[i];
-    
-    
+    }
+        
     if (storageLayout_ & DataStorage::dslTorque) {
 
-      int nt = snap_->atomData.force.size();
+      int nt = snap_->atomData.torque.size();
       vector<Vector3d> trq_tmp(nt, V3Zero);
 
-      AtomCommVectorRow->scatter(atomRowData.torque, trq_tmp);
-      for (int i = 0; i < n; i++) {
+      AtomPlanVectorRow->scatter(atomRowData.torque, trq_tmp);
+      for (int i = 0; i < nt; i++) {
         snap_->atomData.torque[i] += trq_tmp[i];
         trq_tmp[i] = 0.0;
       }
       
-      AtomCommVectorColumn->scatter(atomColData.torque, trq_tmp);
-      for (int i = 0; i < n; i++)
+      AtomPlanVectorColumn->scatter(atomColData.torque, trq_tmp);
+      for (int i = 0; i < nt; i++)
         snap_->atomData.torque[i] += trq_tmp[i];
     }
+
+    if (storageLayout_ & DataStorage::dslSkippedCharge) {
+
+      int ns = snap_->atomData.skippedCharge.size();
+      vector<RealType> skch_tmp(ns, 0.0);
+
+      AtomPlanRealRow->scatter(atomRowData.skippedCharge, skch_tmp);
+      for (int i = 0; i < ns; i++) {
+        snap_->atomData.skippedCharge[i] += skch_tmp[i];
+        skch_tmp[i] = 0.0;
+      }
+      
+      AtomPlanRealColumn->scatter(atomColData.skippedCharge, skch_tmp);
+      for (int i = 0; i < ns; i++) 
+        snap_->atomData.skippedCharge[i] += skch_tmp[i];
+            
+    }
     
+    if (storageLayout_ & DataStorage::dslFlucQForce) {
+
+      int nq = snap_->atomData.flucQFrc.size();
+      vector<RealType> fqfrc_tmp(nq, 0.0);
+
+      AtomPlanRealRow->scatter(atomRowData.flucQFrc, fqfrc_tmp);
+      for (int i = 0; i < nq; i++) {
+        snap_->atomData.flucQFrc[i] += fqfrc_tmp[i];
+        fqfrc_tmp[i] = 0.0;
+      }
+      
+      AtomPlanRealColumn->scatter(atomColData.flucQFrc, fqfrc_tmp);
+      for (int i = 0; i < nq; i++) 
+        snap_->atomData.flucQFrc[i] += fqfrc_tmp[i];
+            
+    }
+
+    if (storageLayout_ & DataStorage::dslElectricField) {
+
+      int nef = snap_->atomData.electricField.size();
+      vector<Vector3d> efield_tmp(nef, V3Zero);
+
+      AtomPlanVectorRow->scatter(atomRowData.electricField, efield_tmp);
+      for (int i = 0; i < nef; i++) {
+        snap_->atomData.electricField[i] += efield_tmp[i];
+        efield_tmp[i] = 0.0;
+      }
+      
+      AtomPlanVectorColumn->scatter(atomColData.electricField, efield_tmp);
+      for (int i = 0; i < nef; i++)
+        snap_->atomData.electricField[i] += efield_tmp[i];
+    }
+
+
     nLocal_ = snap_->getNumberOfAtoms();
 
     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
           
-    AtomCommPotRow->scatter(pot_row, pot_temp);
+    AtomPlanPotRow->scatter(pot_row, pot_temp);
+    AtomPlanPotRow->scatter(expot_row, expot_temp);
 
-    for (int ii = 0;  ii < pot_temp.size(); ii++ )
-      pot_local += pot_temp[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
+      // embedding contribution is added in each of the low level
+      // non-bonded routines.  In single processor, this is done in
+      // unpackInteractionData, not in collectData.
+      for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
+        for (int i = 0; i < nLocal_; i++) {
+          // factor of two is because the total potential terms are divided
+          // by 2 in parallel due to row/ column scatter       
+          snap_->atomData.particlePot[i] += 2.0 * pot_temp[i](ii);
+        }
+      }
+    }
+
     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));
       
-    AtomCommPotColumn->scatter(pot_col, pot_temp);    
+    AtomPlanPotColumn->scatter(pot_col, pot_temp);    
+    AtomPlanPotColumn->scatter(expot_col, expot_temp);    
     
     for (int ii = 0;  ii < pot_temp.size(); ii++ )
-      pot_local += pot_temp[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
+      // non-bonded routines.  In single processor, this is done in
+      // unpackInteractionData, not in collectData.
+      for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
+        for (int i = 0; i < nLocal_; i++) {
+          // factor of two is because the total potential terms are divided
+          // by 2 in parallel due to row/ column scatter       
+          snap_->atomData.particlePot[i] += 2.0 * pot_temp[i](ii);
+        }
+      }
+    }
     
+    if (storageLayout_ & DataStorage::dslParticlePot) {
+      int npp = snap_->atomData.particlePot.size();
+      vector<RealType> ppot_temp(npp, 0.0);
+
+      // This is the direct or embedding contribution to the particle
+      // pot.
+      
+      AtomPlanRealRow->scatter(atomRowData.particlePot, ppot_temp);
+      for (int i = 0; i < npp; i++) {
+        snap_->atomData.particlePot[i] += ppot_temp[i];
+      }
+
+      fill(ppot_temp.begin(), ppot_temp.end(), 0.0);
+      
+      AtomPlanRealColumn->scatter(atomColData.particlePot, ppot_temp);
+      for (int i = 0; i < npp; i++) {
+        snap_->atomData.particlePot[i] += ppot_temp[i];
+      }
+    }
+
+    for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
+      RealType ploc1 = pairwisePot[ii];
+      RealType ploc2 = 0.0;
+      MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
+      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();
+
+    col.Allreduce(MPI::IN_PLACE, 
+                  &snap_->frameData.conductiveHeatFlux[0], 3, 
+                  MPI::REALTYPE, MPI::SUM);
+
+
 #endif
+
   }
 
-  int ForceMatrixDecomposition::getNAtomsInRow() {   
+  /** 
+   * Collects information obtained during the post-pair (and embedding
+   * functional) loops onto local data structures.
+   */
+  void ForceMatrixDecomposition::collectSelfData() {
+    snap_ = sman_->getCurrentSnapshot();
+    storageLayout_ = sman_->getStorageLayout();
+
 #ifdef IS_MPI
+    for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
+      RealType ploc1 = embeddingPot[ii];
+      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
+    
+  }
+
+
+
+  int& ForceMatrixDecomposition::getNAtomsInRow() {   
+#ifdef IS_MPI
     return nAtomsInRow_;
 #else
     return nLocal_;
@@ -630,7 +977,7 @@ namespace OpenMD {
   /**
    * returns the list of atoms belonging to this group.  
    */
-  vector<int> ForceMatrixDecomposition::getAtomsInGroupRow(int cg1){
+  vector<int>& ForceMatrixDecomposition::getAtomsInGroupRow(int cg1){
 #ifdef IS_MPI
     return groupListRow_[cg1];
 #else 
@@ -638,7 +985,7 @@ namespace OpenMD {
 #endif
   }
 
-  vector<int> ForceMatrixDecomposition::getAtomsInGroupColumn(int cg2){
+  vector<int>& ForceMatrixDecomposition::getAtomsInGroupColumn(int cg2){
 #ifdef IS_MPI
     return groupListCol_[cg2];
 #else 
@@ -655,11 +1002,29 @@ namespace OpenMD {
     d = snap_->cgData.position[cg2] - snap_->cgData.position[cg1];
 #endif
     
-    snap_->wrapVector(d);
+    if (usePeriodicBoundaryConditions_) {
+      snap_->wrapVector(d);
+    }
     return d;    
   }
 
+  Vector3d& ForceMatrixDecomposition::getGroupVelocityColumn(int cg2){
+#ifdef IS_MPI
+    return cgColData.velocity[cg2];
+#else
+    return snap_->cgData.velocity[cg2];
+#endif
+  }
 
+  Vector3d& ForceMatrixDecomposition::getAtomVelocityColumn(int atom2){
+#ifdef IS_MPI
+    return atomColData.velocity[atom2];
+#else
+    return snap_->atomData.velocity[atom2];
+#endif
+  }
+
+
   Vector3d ForceMatrixDecomposition::getAtomToGroupVectorRow(int atom1, int cg1){
 
     Vector3d d;
@@ -669,8 +1034,9 @@ namespace OpenMD {
 #else
     d = snap_->cgData.position[cg1] - snap_->atomData.position[atom1];
 #endif
-
-    snap_->wrapVector(d);
+    if (usePeriodicBoundaryConditions_) {
+      snap_->wrapVector(d);
+    }
     return d;    
   }
   
@@ -682,12 +1048,13 @@ namespace OpenMD {
 #else
     d = snap_->cgData.position[cg2] - snap_->atomData.position[atom2];
 #endif
-    
-    snap_->wrapVector(d);
+    if (usePeriodicBoundaryConditions_) {
+      snap_->wrapVector(d);
+    }
     return d;    
   }
 
-  RealType ForceMatrixDecomposition::getMassFactorRow(int atom1) {
+  RealType& ForceMatrixDecomposition::getMassFactorRow(int atom1) {
 #ifdef IS_MPI
     return massFactorsRow[atom1];
 #else
@@ -695,7 +1062,7 @@ namespace OpenMD {
 #endif
   }
 
-  RealType ForceMatrixDecomposition::getMassFactorColumn(int atom2) {
+  RealType& ForceMatrixDecomposition::getMassFactorColumn(int atom2) {
 #ifdef IS_MPI
     return massFactorsCol[atom2];
 #else
@@ -712,50 +1079,76 @@ namespace OpenMD {
 #else
     d = snap_->atomData.position[atom2] - snap_->atomData.position[atom1];
 #endif
-
-    snap_->wrapVector(d);
+    if (usePeriodicBoundaryConditions_) {
+      snap_->wrapVector(d);
+    }
     return d;    
   }
 
-  vector<int> ForceMatrixDecomposition::getSkipsForAtom(int atom1) {
-    return skipsForAtom[atom1];
+  vector<int>& ForceMatrixDecomposition::getExcludesForAtom(int atom1) {
+    return excludesForAtom[atom1];
   }
 
   /**
-   * There are a number of reasons to skip a pair or a
-   * particle. Mostly we do this to exclude atoms who are involved in
-   * short range interactions (bonds, bends, torsions), but we also
-   * need to exclude some overcounted interactions that result from
+   * We need to exclude some overcounted interactions that result from
    * the parallel decomposition.
    */
-  bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
+  bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2, int cg1, int cg2) {
     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];
+#else
+    unique_id_1 = AtomLocalToGlobal[atom1];
+    unique_id_2 = AtomLocalToGlobal[atom2];
+    int group1 = cgLocalToGlobal[cg1];
+    int group2 = cgLocalToGlobal[cg2];
+#endif   
 
-    // this situation should only arise in MPI simulations
     if (unique_id_1 == unique_id_2) return true;
-    
+
+#ifdef IS_MPI
     // this prevents us from doing the pair on multiple processors
     if (unique_id_1 < unique_id_2) {
       if ((unique_id_1 + unique_id_2) % 2 == 0) return true;
     } else {
-      if ((unique_id_1 + unique_id_2) % 2 == 1) return true; 
+      if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
     }
-#else
-    // in the normal loop, the atom numbers are unique
-    unique_id_1 = atom1;
-    unique_id_2 = atom2;
+#endif    
+
+#ifndef IS_MPI
+    if (group1 == group2) {
+      if (unique_id_1 < unique_id_2) return true;
+    }
 #endif
     
-    for (vector<int>::iterator i = skipsForAtom[atom1].begin();
-         i != skipsForAtom[atom1].end(); ++i) {
-      if ( (*i) == unique_id_2 ) return true;
-    }    
+    return false;
+  }
 
+  /**
+   * We need to handle the interactions for atoms who are involved in
+   * the same rigid body as well as some short range interactions
+   * (bonds, bends, torsions) differently from other interactions.
+   * We'll still visit the pairwise routines, but with a flag that
+   * tells those routines to exclude the pair from direct long range
+   * interactions.  Some indirect interactions (notably reaction
+   * field) must still be handled for these pairs.
+   */
+  bool ForceMatrixDecomposition::excludeAtomPair(int atom1, int atom2) {
+
+    // excludesForAtom was constructed to use row/column indices in the MPI
+    // version, and to use local IDs in the non-MPI version:
+    
+    for (vector<int>::iterator i = excludesForAtom[atom1].begin();
+         i != excludesForAtom[atom1].end(); ++i) {
+      if ( (*i) == atom2 ) return true;
+    }
+
+    return false;
   }
 
 
@@ -776,28 +1169,42 @@ namespace OpenMD {
   }
 
     // filling interaction blocks with pointers
-  void ForceMatrixDecomposition::fillInteractionData(InteractionData idat, 
-                                                     int atom1, int atom2) {    
+  void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat, 
+                                                     int atom1, int atom2) {
+
+    idat.excluded = excludeAtomPair(atom1, atom2);
+   
 #ifdef IS_MPI
-    
-    idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]), 
-                             ff_->getAtomType(identsCol[atom2]) );
-    
+    //idat.atypes = make_pair( atypesRow[atom1], atypesCol[atom2]);
+    idat.atid1 = identsRow[atom1];
+    idat.atid2 = identsCol[atom2];
+
+    if (regionsRow[atom1] >= 0 && regionsCol[atom2] >= 0) {
+      idat.sameRegion = (regionsRow[atom1] == regionsCol[atom2]);
+    } else {
+      idat.sameRegion = false;
+    }
+
     if (storageLayout_ & DataStorage::dslAmat) {
       idat.A1 = &(atomRowData.aMat[atom1]);
       idat.A2 = &(atomColData.aMat[atom2]);
     }
     
-    if (storageLayout_ & DataStorage::dslElectroFrame) {
-      idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
-      idat.eFrame2 = &(atomColData.electroFrame[atom2]);
-    }
-
     if (storageLayout_ & DataStorage::dslTorque) {
       idat.t1 = &(atomRowData.torque[atom1]);
       idat.t2 = &(atomColData.torque[atom2]);
     }
 
+    if (storageLayout_ & DataStorage::dslDipole) {
+      idat.dipole1 = &(atomRowData.dipole[atom1]);
+      idat.dipole2 = &(atomColData.dipole[atom2]);
+    }
+
+    if (storageLayout_ & DataStorage::dslQuadrupole) {
+      idat.quadrupole1 = &(atomRowData.quadrupole[atom1]);
+      idat.quadrupole2 = &(atomColData.quadrupole[atom2]);
+    }
+
     if (storageLayout_ & DataStorage::dslDensity) {
       idat.rho1 = &(atomRowData.density[atom1]);
       idat.rho2 = &(atomColData.density[atom2]);
@@ -818,27 +1225,49 @@ namespace OpenMD {
       idat.particlePot2 = &(atomColData.particlePot[atom2]);
     }
 
+    if (storageLayout_ & DataStorage::dslSkippedCharge) {              
+      idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]);
+      idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
+    }
+
+    if (storageLayout_ & DataStorage::dslFlucQPosition) {              
+      idat.flucQ1 = &(atomRowData.flucQPos[atom1]);
+      idat.flucQ2 = &(atomColData.flucQPos[atom2]);
+    }
+
 #else
+    
+    //idat.atypes = make_pair( atypesLocal[atom1], atypesLocal[atom2]);
+    idat.atid1 = idents[atom1];
+    idat.atid2 = idents[atom2];
 
-    idat.atypes = make_pair( ff_->getAtomType(identsLocal[atom1]), 
-                             ff_->getAtomType(identsLocal[atom2]) );
+    if (regions[atom1] >= 0 && regions[atom2] >= 0) {
+      idat.sameRegion = (regions[atom1] == regions[atom2]);
+    } else {
+      idat.sameRegion = false;
+    }
 
     if (storageLayout_ & DataStorage::dslAmat) {
       idat.A1 = &(snap_->atomData.aMat[atom1]);
       idat.A2 = &(snap_->atomData.aMat[atom2]);
     }
 
-    if (storageLayout_ & DataStorage::dslElectroFrame) {
-      idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
-      idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
-    }
-
     if (storageLayout_ & DataStorage::dslTorque) {
       idat.t1 = &(snap_->atomData.torque[atom1]);
       idat.t2 = &(snap_->atomData.torque[atom2]);
     }
 
-    if (storageLayout_ & DataStorage::dslDensity) {
+    if (storageLayout_ & DataStorage::dslDipole) {
+      idat.dipole1 = &(snap_->atomData.dipole[atom1]);
+      idat.dipole2 = &(snap_->atomData.dipole[atom2]);
+    }
+
+    if (storageLayout_ & DataStorage::dslQuadrupole) {
+      idat.quadrupole1 = &(snap_->atomData.quadrupole[atom1]);
+      idat.quadrupole2 = &(snap_->atomData.quadrupole[atom2]);
+    }
+
+    if (storageLayout_ & DataStorage::dslDensity) {     
       idat.rho1 = &(snap_->atomData.density[atom1]);
       idat.rho2 = &(snap_->atomData.density[atom2]);
     }
@@ -858,54 +1287,68 @@ namespace OpenMD {
       idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
     }
 
+    if (storageLayout_ & DataStorage::dslSkippedCharge) {
+      idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
+      idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
+    }
+
+    if (storageLayout_ & DataStorage::dslFlucQPosition) {              
+      idat.flucQ1 = &(snap_->atomData.flucQPos[atom1]);
+      idat.flucQ2 = &(snap_->atomData.flucQPos[atom2]);
+    }
+
 #endif
   }
 
   
-  void ForceMatrixDecomposition::unpackInteractionData(InteractionData idat, int atom1, int atom2) {    
+  void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) {    
 #ifdef IS_MPI
-    pot_row[atom1] += 0.5 *  *(idat.pot);
-    pot_col[atom2] += 0.5 *  *(idat.pot);
+    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);
-#else
-    longRangePot_ += *(idat.pot);
-    
-    snap_->atomData.force[atom1] += *(idat.f1);
-    snap_->atomData.force[atom2] -= *(idat.f1);
-#endif
 
-  }
+    if (storageLayout_ & DataStorage::dslFlucQForce) {              
+      atomRowData.flucQFrc[atom1] -= *(idat.dVdFQ1);
+      atomColData.flucQFrc[atom2] -= *(idat.dVdFQ2);
+    }
 
+    if (storageLayout_ & DataStorage::dslElectricField) {              
+      atomRowData.electricField[atom1] += *(idat.eField1);
+      atomColData.electricField[atom2] += *(idat.eField2);
+    }
 
-  void ForceMatrixDecomposition::fillSkipData(InteractionData idat,
-                                              int atom1, int atom2) {
-#ifdef IS_MPI
-    idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]), 
-                             ff_->getAtomType(identsCol[atom2]) );
+#else
+    pairwisePot += *(idat.pot);
+    excludedPot += *(idat.excludedPot);
 
-    if (storageLayout_ & DataStorage::dslElectroFrame) {
-      idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
-      idat.eFrame2 = &(atomColData.electroFrame[atom2]);
+    snap_->atomData.force[atom1] += *(idat.f1);
+    snap_->atomData.force[atom2] -= *(idat.f1);
+
+    if (idat.doParticlePot) {
+      // This is the pairwise contribution to the particle pot.  The
+      // embedding contribution is added in each of the low level
+      // non-bonded routines.  In parallel, this calculation is done
+      // in collectData, not in unpackInteractionData.
+      snap_->atomData.particlePot[atom1] += *(idat.vpair) * *(idat.sw);
+      snap_->atomData.particlePot[atom2] += *(idat.vpair) * *(idat.sw);
     }
-    if (storageLayout_ & DataStorage::dslTorque) {
-      idat.t1 = &(atomRowData.torque[atom1]);
-      idat.t2 = &(atomColData.torque[atom2]);
+    
+    if (storageLayout_ & DataStorage::dslFlucQForce) {              
+      snap_->atomData.flucQFrc[atom1] -= *(idat.dVdFQ1);
+      snap_->atomData.flucQFrc[atom2] -= *(idat.dVdFQ2);
     }
-#else
-    idat.atypes = make_pair( ff_->getAtomType(identsLocal[atom1]), 
-                             ff_->getAtomType(identsLocal[atom2]) );
 
-    if (storageLayout_ & DataStorage::dslElectroFrame) {
-      idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
-      idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
+    if (storageLayout_ & DataStorage::dslElectricField) {              
+      snap_->atomData.electricField[atom1] += *(idat.eField1);
+      snap_->atomData.electricField[atom2] += *(idat.eField2);
     }
-    if (storageLayout_ & DataStorage::dslTorque) {
-      idat.t1 = &(snap_->atomData.torque[atom1]);
-      idat.t2 = &(snap_->atomData.torque[atom2]);
-    }
-#endif    
+
+#endif
+    
   }
 
   /*
@@ -914,204 +1357,273 @@ namespace OpenMD {
    * first element of pair is row-indexed CutoffGroup
    * second element of pair is column-indexed CutoffGroup
    */
-  vector<pair<int, int> > ForceMatrixDecomposition::buildNeighborList() {
-      
-    vector<pair<int, int> > neighborList;
+  void ForceMatrixDecomposition::buildNeighborList(vector<pair<int,int> >& neighborList) {
+    
+    neighborList.clear();
     groupCutoffs cuts;
-#ifdef IS_MPI
-    cellListRow_.clear();
-    cellListCol_.clear();
-#else
-    cellList_.clear();
-#endif
+    bool doAllPairs = false;
 
     RealType rList_ = (largestRcut_ + skinThickness_);
-    RealType rl2 = rList_ * rList_;
+    RealType rcut, rcutsq, rlistsq;
     Snapshot* snap_ = sman_->getCurrentSnapshot();
-    Mat3x3d Hmat = snap_->getHmat();
-    Vector3d Hx = Hmat.getColumn(0);
-    Vector3d Hy = Hmat.getColumn(1);
-    Vector3d Hz = Hmat.getColumn(2);
+    Mat3x3d box;
+    Mat3x3d invBox;
 
-    nCells_.x() = (int) ( Hx.length() )/ rList_;
-    nCells_.y() = (int) ( Hy.length() )/ rList_;
-    nCells_.z() = (int) ( Hz.length() )/ rList_;
-
-    Mat3x3d invHmat = snap_->getInvHmat();
     Vector3d rs, scaled, dr;
     Vector3i whichCell;
     int cellIndex;
-    int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
 
-    cerr << "flag1\n";
 #ifdef IS_MPI
+    cellListRow_.clear();
+    cellListCol_.clear();
+#else
+    cellList_.clear();
+#endif
+    
+    if (!usePeriodicBoundaryConditions_) {
+      box = snap_->getBoundingBox();
+      invBox = snap_->getInvBoundingBox();
+    } else {
+      box = snap_->getHmat();
+      invBox = snap_->getInvHmat();
+    }
+    
+    Vector3d boxX = box.getColumn(0);
+    Vector3d boxY = box.getColumn(1);
+    Vector3d boxZ = box.getColumn(2);
+    
+    nCells_.x() = int( boxX.length() / rList_ );
+    nCells_.y() = int( boxY.length() / rList_ );
+    nCells_.z() = int( boxZ.length() / rList_ );
+    
+    // handle small boxes where the cell offsets can end up repeating cells
+    
+    if (nCells_.x() < 3) doAllPairs = true;
+    if (nCells_.y() < 3) doAllPairs = true;
+    if (nCells_.z() < 3) doAllPairs = true;
+    
+    int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
+    
+#ifdef IS_MPI
     cellListRow_.resize(nCtot);
     cellListCol_.resize(nCtot);
 #else
     cellList_.resize(nCtot);
 #endif
-    cerr << "flag2\n";
+    
+    if (!doAllPairs) {
 #ifdef IS_MPI
-    for (int i = 0; i < nGroupsInRow_; i++) {
-      rs = cgRowData.position[i];
-
-      // scaled positions relative to the box vectors
-      scaled = invHmat * rs;
-
-      // wrap the vector back into the unit box by subtracting integer box 
-      // numbers
-      for (int j = 0; j < 3; j++) {
-        scaled[j] -= roundMe(scaled[j]);
-        scaled[j] += 0.5;
+      
+      for (int i = 0; i < nGroupsInRow_; i++) {
+        rs = cgRowData.position[i];
+        
+        // scaled positions relative to the box vectors
+        scaled = invBox * rs;
+        
+        // wrap the vector back into the unit box by subtracting integer box 
+        // numbers
+        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.
+        whichCell.x() = nCells_.x() * scaled.x();
+        whichCell.y() = nCells_.y() * scaled.y();
+        whichCell.z() = nCells_.z() * scaled.z();
+        
+        // find single index of this cell:
+        cellIndex = Vlinear(whichCell, nCells_);
+        
+        // add this cutoff group to the list of groups in this cell;
+        cellListRow_[cellIndex].push_back(i);
       }
-     
-      // find xyz-indices of cell that cutoffGroup is in.
-      whichCell.x() = nCells_.x() * scaled.x();
-      whichCell.y() = nCells_.y() * scaled.y();
-      whichCell.z() = nCells_.z() * scaled.z();
-
-      // find single index of this cell:
-      cellIndex = Vlinear(whichCell, nCells_);
-
-      // add this cutoff group to the list of groups in this cell;
-      cellListRow_[cellIndex].push_back(i);
-    }
-
-    for (int i = 0; i < nGroupsInCol_; i++) {
-      rs = cgColData.position[i];
-
-      // scaled positions relative to the box vectors
-      scaled = invHmat * rs;
-
-      // wrap the vector back into the unit box by subtracting integer box 
-      // numbers
-      for (int j = 0; j < 3; j++) {
-        scaled[j] -= roundMe(scaled[j]);
-        scaled[j] += 0.5;
+      for (int i = 0; i < nGroupsInCol_; i++) {
+        rs = cgColData.position[i];
+        
+        // scaled positions relative to the box vectors
+        scaled = invBox * rs;
+        
+        // wrap the vector back into the unit box by subtracting integer box 
+        // numbers
+        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.
+        whichCell.x() = nCells_.x() * scaled.x();
+        whichCell.y() = nCells_.y() * scaled.y();
+        whichCell.z() = nCells_.z() * scaled.z();
+        
+        // find single index of this cell:
+        cellIndex = Vlinear(whichCell, nCells_);
+        
+        // add this cutoff group to the list of groups in this cell;
+        cellListCol_[cellIndex].push_back(i);
       }
-
-      // find xyz-indices of cell that cutoffGroup is in.
-      whichCell.x() = nCells_.x() * scaled.x();
-      whichCell.y() = nCells_.y() * scaled.y();
-      whichCell.z() = nCells_.z() * scaled.z();
-
-      // find single index of this cell:
-      cellIndex = Vlinear(whichCell, nCells_);
-
-      // add this cutoff group to the list of groups in this cell;
-      cellListCol_[cellIndex].push_back(i);
-    }
+      
 #else
-    for (int i = 0; i < nGroups_; i++) {
-      rs = snap_->cgData.position[i];
-
-      // scaled positions relative to the box vectors
-      scaled = invHmat * rs;
-
-      // wrap the vector back into the unit box by subtracting integer box 
-      // numbers
-      for (int j = 0; j < 3; j++) {
-        scaled[j] -= roundMe(scaled[j]);
-        scaled[j] += 0.5;
+      for (int i = 0; i < nGroups_; i++) {
+        rs = snap_->cgData.position[i];
+        
+        // scaled positions relative to the box vectors
+        scaled = invBox * rs;
+        
+        // wrap the vector back into the unit box by subtracting integer box 
+        // numbers
+        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.
+        whichCell.x() = int(nCells_.x() * scaled.x());
+        whichCell.y() = int(nCells_.y() * scaled.y());
+        whichCell.z() = int(nCells_.z() * scaled.z());
+        
+        // find single index of this cell:
+        cellIndex = Vlinear(whichCell, nCells_);
+        
+        // add this cutoff group to the list of groups in this cell;
+        cellList_[cellIndex].push_back(i);
       }
 
-      // find xyz-indices of cell that cutoffGroup is in.
-      whichCell.x() = nCells_.x() * scaled.x();
-      whichCell.y() = nCells_.y() * scaled.y();
-      whichCell.z() = nCells_.z() * scaled.z();
-
-      // find single index of this cell:
-      cellIndex = Vlinear(whichCell, nCells_);      
-
-      // add this cutoff group to the list of groups in this cell;
-      cellList_[cellIndex].push_back(i);
-    }
 #endif
 
-    for (int m1z = 0; m1z < nCells_.z(); m1z++) {
-      for (int m1y = 0; m1y < nCells_.y(); m1y++) {
-        for (int m1x = 0; m1x < nCells_.x(); m1x++) {
-          Vector3i m1v(m1x, m1y, m1z);
-          int m1 = Vlinear(m1v, nCells_);
-
-          for (vector<Vector3i>::iterator os = cellOffsets_.begin();
-               os != cellOffsets_.end(); ++os) {
+      for (int m1z = 0; m1z < nCells_.z(); m1z++) {
+        for (int m1y = 0; m1y < nCells_.y(); m1y++) {
+          for (int m1x = 0; m1x < nCells_.x(); m1x++) {
+            Vector3i m1v(m1x, m1y, m1z);
+            int m1 = Vlinear(m1v, nCells_);
             
-            Vector3i m2v = m1v + (*os);
-            
-            if (m2v.x() >= nCells_.x()) {
-              m2v.x() = 0;           
-            } else if (m2v.x() < 0) {
-              m2v.x() = nCells_.x() - 1; 
-            }
-            
-            if (m2v.y() >= nCells_.y()) {
-              m2v.y() = 0;           
-            } else if (m2v.y() < 0) {
-              m2v.y() = nCells_.y() - 1; 
-            }
-            
-            if (m2v.z() >= nCells_.z()) {
-              m2v.z() = 0;           
-            } else if (m2v.z() < 0) {
-              m2v.z() = nCells_.z() - 1; 
-            }
-            
-            int m2 = Vlinear (m2v, nCells_);
+            for (vector<Vector3i>::iterator os = cellOffsets_.begin();
+                 os != cellOffsets_.end(); ++os) {
+              
+              Vector3i m2v = m1v + (*os);
+             
 
-#ifdef IS_MPI
-            for (vector<int>::iterator j1 = cellListRow_[m1].begin(); 
-                 j1 != cellListRow_[m1].end(); ++j1) {
-              for (vector<int>::iterator j2 = cellListCol_[m2].begin(); 
-                   j2 != cellListCol_[m2].end(); ++j2) {
-                               
-                // Always do this if we're in different cells or if
-                // we're in the same cell and the global index of the
-                // j2 cutoff group is less than the j1 cutoff group
+              if (m2v.x() >= nCells_.x()) {
+                m2v.x() = 0;           
+              } else if (m2v.x() < 0) {
+                m2v.x() = nCells_.x() - 1; 
+              }
+              
+              if (m2v.y() >= nCells_.y()) {
+                m2v.y() = 0;           
+              } else if (m2v.y() < 0) {
+                m2v.y() = nCells_.y() - 1; 
+              }
+              
+              if (m2v.z() >= nCells_.z()) {
+                m2v.z() = 0;           
+              } else if (m2v.z() < 0) {
+                m2v.z() = nCells_.z() - 1; 
+              }
 
-                if (m2 != m1 || cgColToGlobal[(*j2)] < cgRowToGlobal[(*j1)]) {
+              int m2 = Vlinear (m2v, nCells_);
+              
+#ifdef IS_MPI
+              for (vector<int>::iterator j1 = cellListRow_[m1].begin(); 
+                   j1 != cellListRow_[m1].end(); ++j1) {
+                for (vector<int>::iterator j2 = cellListCol_[m2].begin(); 
+                     j2 != cellListCol_[m2].end(); ++j2) {
+                  
+                  // In parallel, we need to visit *all* pairs of row
+                  // & column indicies and will divide labor in the
+                  // force evaluation later.
                   dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
-                  snap_->wrapVector(dr);
-                  cuts = getGroupCutoffs( (*j1), (*j2) );
-                  if (dr.lengthSquare() < cuts.third) {
-                    neighborList.push_back(make_pair((*j1), (*j2)));
+                  if (usePeriodicBoundaryConditions_) {
+                    snap_->wrapVector(dr);
                   }
+                  getGroupCutoffs( (*j1), (*j2), rcut, rcutsq, rlistsq );
+                  if (dr.lengthSquare() < rlistsq) {
+                    neighborList.push_back(make_pair((*j1), (*j2)));
+                  }                  
                 }
               }
-            }
 #else
+              for (vector<int>::iterator j1 = cellList_[m1].begin(); 
+                   j1 != cellList_[m1].end(); ++j1) {
+                for (vector<int>::iterator j2 = cellList_[m2].begin(); 
+                     j2 != cellList_[m2].end(); ++j2) {
+     
+                  // Always do this if we're in different cells or if
+                  // we're in the same cell and the global index of
+                  // the j2 cutoff group is greater than or equal to
+                  // the j1 cutoff group.  Note that Rappaport's code
+                  // has a "less than" conditional here, but that
+                  // deals with atom-by-atom computation.  OpenMD
+                  // allows atoms within a single cutoff group to
+                  // interact with each other.
 
-            for (vector<int>::iterator j1 = cellList_[m1].begin(); 
-                 j1 != cellList_[m1].end(); ++j1) {
-              for (vector<int>::iterator j2 = cellList_[m2].begin(); 
-                   j2 != cellList_[m2].end(); ++j2) {
+                  if (m2 != m1 || (*j2) >= (*j1) ) {
 
-                // Always do this if we're in different cells or if
-                // we're in the same cell and the global index of the
-                // j2 cutoff group is less than the j1 cutoff group
-
-                if (m2 != m1 || (*j2) < (*j1)) {
-                  dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
-                  snap_->wrapVector(dr);
-                  cuts = getGroupCutoffs( (*j1), (*j2) );
-                  if (dr.lengthSquare() < cuts.third) {
-                    neighborList.push_back(make_pair((*j1), (*j2)));
+                    dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
+                    if (usePeriodicBoundaryConditions_) {
+                      snap_->wrapVector(dr);
+                    }
+                    getGroupCutoffs( (*j1), (*j2), rcut, rcutsq, rlistsq );
+                    if (dr.lengthSquare() < rlistsq) {
+                      neighborList.push_back(make_pair((*j1), (*j2)));
+                    }
                   }
                 }
               }
-            }
 #endif
+            }
           }
         }
       }
+    } else {
+      // branch to do all cutoff group pairs
+#ifdef IS_MPI
+      for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
+        for (int j2 = 0; j2 < nGroupsInCol_; j2++) {    
+          dr = cgColData.position[j2] - cgRowData.position[j1];
+          if (usePeriodicBoundaryConditions_) {
+            snap_->wrapVector(dr);
+          }
+          getGroupCutoffs( j1, j2, rcut, rcutsq, rlistsq);
+          if (dr.lengthSquare() < rlistsq) {
+            neighborList.push_back(make_pair(j1, j2));
+          }
+        }
+      }      
+#else
+      // include all groups here.
+      for (int j1 = 0; j1 < nGroups_; j1++) {
+        // include self group interactions j2 == j1
+        for (int j2 = j1; j2 < nGroups_; j2++) {
+          dr = snap_->cgData.position[j2] - snap_->cgData.position[j1];
+          if (usePeriodicBoundaryConditions_) {
+            snap_->wrapVector(dr);
+          }
+          getGroupCutoffs( j1, j2, rcut, rcutsq, rlistsq );
+          if (dr.lengthSquare() < rlistsq) {
+            neighborList.push_back(make_pair(j1, j2));
+          }
+        }    
+      }
+#endif
     }
-    
+      
     // save the local cutoff group positions for the check that is
     // done on each loop:
     saved_CG_positions_.clear();
     for (int i = 0; i < nGroups_; i++)
       saved_CG_positions_.push_back(snap_->cgData.position[i]);
-    
-    return neighborList;
   }
 } //end namespace OpenMD