--- branches/development/src/parallel/ForceMatrixDecomposition.cpp	2011/05/27 16:45:44	1571
+++ branches/development/src/parallel/ForceMatrixDecomposition.cpp	2011/06/21 06:34:35	1586
@@ -57,19 +57,20 @@ namespace OpenMD {
     storageLayout_ = sman_->getStorageLayout();
     ff_ = info_->getForceField();
     nLocal_ = snap_->getNumberOfAtoms();
-    nGroups_ = snap_->getNumberOfCutoffGroups();
 
+    nGroups_ = info_->getNLocalCutoffGroups();
     // gather the information for atomtype IDs (atids):
-    identsLocal = info_->getIdentArray();
+    idents = info_->getIdentArray();
     AtomLocalToGlobal = info_->getGlobalAtomIndices();
     cgLocalToGlobal = info_->getGlobalGroupIndices();
     vector<int> globalGroupMembership = info_->getGlobalGroupMembership();
-    vector<RealType> massFactorsLocal = info_->getMassFactors();
+
+    massFactors = info_->getMassFactors();
+
     PairList excludes = info_->getExcludedInteractions();
     PairList oneTwo = info_->getOneTwoInteractions();
     PairList oneThree = info_->getOneThreeInteractions();
     PairList oneFour = info_->getOneFourInteractions();
-    vector<RealType> pot_local(N_INTERACTION_FAMILIES, 0.0);
 
 #ifdef IS_MPI
  
@@ -77,11 +78,13 @@ namespace OpenMD {
     AtomCommRealRow = new Communicator<Row,RealType>(nLocal_);
     AtomCommVectorRow = new Communicator<Row,Vector3d>(nLocal_);
     AtomCommMatrixRow = new Communicator<Row,Mat3x3d>(nLocal_);
+    AtomCommPotRow = new Communicator<Row,potVec>(nLocal_);
 
     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_);
 
     cgCommIntRow = new Communicator<Row,int>(nGroups_);
     cgCommVectorRow = new Communicator<Row,Vector3d>(nGroups_);
@@ -102,29 +105,24 @@ namespace OpenMD {
     cgRowData.setStorageLayout(DataStorage::dslPosition);
     cgColData.resize(nGroupsInCol_);
     cgColData.setStorageLayout(DataStorage::dslPosition);
+        
+    identsRow.resize(nAtomsInRow_);
+    identsCol.resize(nAtomsInCol_);
     
-    vector<vector<RealType> > pot_row(N_INTERACTION_FAMILIES, 
-                                      vector<RealType> (nAtomsInRow_, 0.0));
-    vector<vector<RealType> > pot_col(N_INTERACTION_FAMILIES,
-                                      vector<RealType> (nAtomsInCol_, 0.0));
+    AtomCommIntRow->gather(idents, identsRow);
+    AtomCommIntColumn->gather(idents, identsCol);
     
-    identsRow.reserve(nAtomsInRow_);
-    identsCol.reserve(nAtomsInCol_);
-    
-    AtomCommIntRow->gather(identsLocal, identsRow);
-    AtomCommIntColumn->gather(identsLocal, identsCol);
-    
     AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
     AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
     
     cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
     cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
 
-    AtomCommRealRow->gather(massFactorsLocal, massFactorsRow);
-    AtomCommRealColumn->gather(massFactorsLocal, massFactorsCol);
+    AtomCommRealRow->gather(massFactors, massFactorsRow);
+    AtomCommRealColumn->gather(massFactors, massFactorsCol);
 
     groupListRow_.clear();
-    groupListRow_.reserve(nGroupsInRow_);
+    groupListRow_.resize(nGroupsInRow_);
     for (int i = 0; i < nGroupsInRow_; i++) {
       int gid = cgRowToGlobal[i];
       for (int j = 0; j < nAtomsInRow_; j++) {
@@ -135,7 +133,7 @@ namespace OpenMD {
     }
 
     groupListCol_.clear();
-    groupListCol_.reserve(nGroupsInCol_);
+    groupListCol_.resize(nGroupsInCol_);
     for (int i = 0; i < nGroupsInCol_; i++) {
       int gid = cgColToGlobal[i];
       for (int j = 0; j < nAtomsInCol_; j++) {
@@ -145,93 +143,350 @@ namespace OpenMD {
       }      
     }
 
-    skipsForRowAtom.clear();
-    skipsForRowAtom.reserve(nAtomsInRow_);
+    skipsForAtom.clear();
+    skipsForAtom.resize(nAtomsInRow_);
+    toposForAtom.clear();
+    toposForAtom.resize(nAtomsInRow_);
+    topoDist.clear();
+    topoDist.resize(nAtomsInRow_);
     for (int i = 0; i < nAtomsInRow_; i++) {
       int iglob = AtomRowToGlobal[i];
-      for (int j = 0; j < nAtomsInCol_; j++) {
-        int jglob = AtomColToGlobal[j];        
-        if (excludes.hasPair(iglob, jglob)) 
-          skipsForRowAtom[i].push_back(j);       
-      }      
-    }
 
-    toposForRowAtom.clear();
-    toposForRowAtom.reserve(nAtomsInRow_);
-    for (int i = 0; i < nAtomsInRow_; i++) {
-      int iglob = AtomRowToGlobal[i];
-      int nTopos = 0;
       for (int j = 0; j < nAtomsInCol_; j++) {
-        int jglob = AtomColToGlobal[j];        
+        int jglob = AtomColToGlobal[j];
+
+        if (excludes.hasPair(iglob, jglob)) 
+          skipsForAtom[i].push_back(j);       
+        
         if (oneTwo.hasPair(iglob, jglob)) {
-          toposForRowAtom[i].push_back(j);
-          topoDistRow[i][nTopos] = 1;
-          nTopos++;
+          toposForAtom[i].push_back(j);
+          topoDist[i].push_back(1);
+        } else {
+          if (oneThree.hasPair(iglob, jglob)) {
+            toposForAtom[i].push_back(j);
+            topoDist[i].push_back(2);
+          } else {
+            if (oneFour.hasPair(iglob, jglob)) {
+              toposForAtom[i].push_back(j);
+              topoDist[i].push_back(3);
+            }
+          }
         }
-        if (oneThree.hasPair(iglob, jglob)) {
-          toposForRowAtom[i].push_back(j);
-          topoDistRow[i][nTopos] = 2;
-          nTopos++;
-        }
-        if (oneFour.hasPair(iglob, jglob)) {
-          toposForRowAtom[i].push_back(j);
-          topoDistRow[i][nTopos] = 3;
-          nTopos++;
-        }
       }      
     }
 
 #endif
 
     groupList_.clear();
-    groupList_.reserve(nGroups_);
+    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)
+        if (globalGroupMembership[aid] == gid) {
           groupList_[i].push_back(j);
+        }
       }      
     }
 
-    skipsForLocalAtom.clear();
-    skipsForLocalAtom.reserve(nLocal_);
+    skipsForAtom.clear();
+    skipsForAtom.resize(nLocal_);
+    toposForAtom.clear();
+    toposForAtom.resize(nLocal_);
+    topoDist.clear();
+    topoDist.resize(nLocal_);
 
     for (int i = 0; i < nLocal_; i++) {
       int iglob = AtomLocalToGlobal[i];
+
       for (int j = 0; j < nLocal_; j++) {
-        int jglob = AtomLocalToGlobal[j];        
+        int jglob = AtomLocalToGlobal[j];
+
         if (excludes.hasPair(iglob, jglob)) 
-          skipsForLocalAtom[i].push_back(j);       
+          skipsForAtom[i].push_back(j);              
+        
+        if (oneTwo.hasPair(iglob, jglob)) {
+          toposForAtom[i].push_back(j);
+          topoDist[i].push_back(1);
+        } else {
+          if (oneThree.hasPair(iglob, jglob)) {
+            toposForAtom[i].push_back(j);
+            topoDist[i].push_back(2);
+          } else {
+            if (oneFour.hasPair(iglob, jglob)) {
+              toposForAtom[i].push_back(j);
+              topoDist[i].push_back(3);
+            }
+          }
+        }
       }      
     }
+    
+    createGtypeCutoffMap();
+  }
+   
+  void ForceMatrixDecomposition::createGtypeCutoffMap() {
+    
+    RealType tol = 1e-6;
+    RealType rc;
+    int atid;
+    set<AtomType*> atypes = info_->getSimulatedAtomTypes();
+    vector<RealType> atypeCutoff;
+    atypeCutoff.resize( atypes.size() );
+      
+    for (set<AtomType*>::iterator at = atypes.begin(); 
+         at != atypes.end(); ++at){
+      atid = (*at)->getIdent();
 
-    toposForLocalAtom.clear();
-    toposForLocalAtom.reserve(nLocal_);
-    for (int i = 0; i < nLocal_; i++) {
-      int iglob = AtomLocalToGlobal[i];
-      int nTopos = 0;
-      for (int j = 0; j < nLocal_; j++) {
-        int jglob = AtomLocalToGlobal[j];        
-        if (oneTwo.hasPair(iglob, jglob)) {
-          toposForLocalAtom[i].push_back(j);
-          topoDistLocal[i][nTopos] = 1;
-          nTopos++;
-        }
-        if (oneThree.hasPair(iglob, jglob)) {
-          toposForLocalAtom[i].push_back(j);
-          topoDistLocal[i][nTopos] = 2;
-          nTopos++;
-        }
-        if (oneFour.hasPair(iglob, jglob)) {
-          toposForLocalAtom[i].push_back(j);
-          topoDistLocal[i][nTopos] = 3;
-          nTopos++;
+      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
+    vector<RealType> groupCutoffRow(nGroupsInRow_, 0.0);
+    groupRowToGtype.resize(nGroupsInRow_);
+    for (int cg1 = 0; cg1 < nGroupsInRow_; cg1++) {
+      vector<int> atomListRow = getAtomsInGroupRow(cg1);
+      for (vector<int>::iterator ia = atomListRow.begin(); 
+           ia != atomListRow.end(); ++ia) {            
+        int atom1 = (*ia);
+        atid = identsRow[atom1];
+        if (atypeCutoff[atid] > groupCutoffRow[cg1]) {
+          groupCutoffRow[cg1] = atypeCutoff[atid];
         }
+      }
+
+      bool gTypeFound = false;
+      for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
+        if (abs(groupCutoffRow[cg1] - gTypeCutoffs[gt]) < tol) {
+          groupRowToGtype[cg1] = gt;
+          gTypeFound = true;
+        } 
+      }
+      if (!gTypeFound) {
+        gTypeCutoffs.push_back( groupCutoffRow[cg1] );
+        groupRowToGtype[cg1] = gTypeCutoffs.size() - 1;
+      }
+      
+    }
+    vector<RealType> groupCutoffCol(nGroupsInCol_, 0.0);
+    groupColToGtype.resize(nGroupsInCol_);
+    for (int cg2 = 0; cg2 < nGroupsInCol_; cg2++) {
+      vector<int> atomListCol = getAtomsInGroupColumn(cg2);
+      for (vector<int>::iterator jb = atomListCol.begin(); 
+           jb != atomListCol.end(); ++jb) {            
+        int atom2 = (*jb);
+        atid = identsCol[atom2];
+        if (atypeCutoff[atid] > groupCutoffCol[cg2]) {
+          groupCutoffCol[cg2] = atypeCutoff[atid];
+        }
+      }
+      bool gTypeFound = false;
+      for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
+        if (abs(groupCutoffCol[cg2] - gTypeCutoffs[gt]) < tol) {
+          groupColToGtype[cg2] = gt;
+          gTypeFound = true;
+        } 
+      }
+      if (!gTypeFound) {
+        gTypeCutoffs.push_back( groupCutoffCol[cg2] );
+        groupColToGtype[cg2] = gTypeCutoffs.size() - 1;
+      }
+    }
+#else
+
+    vector<RealType> groupCutoff(nGroups_, 0.0);
+    groupToGtype.resize(nGroups_);
+
+    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 = idents[atom1];
+        if (atypeCutoff[atid] > groupCutoff[cg1]) {
+          groupCutoff[cg1] = atypeCutoff[atid];
+        }
+      }
+
+      bool gTypeFound = false;
+      for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
+        if (abs(groupCutoff[cg1] - gTypeCutoffs[gt]) < tol) {
+          groupToGtype[cg1] = gt;
+          gTypeFound = true;
+        } 
+      }
+      if (!gTypeFound) {
+        gTypeCutoffs.push_back( groupCutoff[cg1] );
+        groupToGtype[cg1] = gTypeCutoffs.size() - 1;
       }      
     }
+#endif
+
+    // Now we find the maximum group cutoff value present in the simulation
+
+    RealType groupMax = *max_element(gTypeCutoffs.begin(), gTypeCutoffs.end());
+
+#ifdef IS_MPI
+    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++) {       
+        RealType thisRcut;
+        switch(cutoffPolicy_) {
+        case TRADITIONAL:
+          thisRcut = tradRcut;
+          break;
+        case MIX:
+          thisRcut = 0.5 * (gTypeCutoffs[i] + gTypeCutoffs[j]);
+          break;
+        case MAX:
+          thisRcut = max(gTypeCutoffs[i], gTypeCutoffs[j]);
+          break;
+        default:
+          sprintf(painCave.errMsg,
+                  "ForceMatrixDecomposition::createGtypeCutoffMap " 
+                  "hit an unknown cutoff policy!\n");
+          painCave.severity = OPENMD_ERROR;
+          painCave.isFatal = 1;
+          simError();
+          break;
+        }
+
+        pair<int,int> key = make_pair(i,j);
+        gTypeCutoffMap[key].first = thisRcut;
+
+        if (thisRcut > largestRcut_) largestRcut_ = thisRcut;
+
+        gTypeCutoffMap[key].second = thisRcut*thisRcut;
+        
+        gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2);
+
+        // sanity check
+        
+        if (userChoseCutoff_) {
+          if (abs(gTypeCutoffMap[key].first - userCutoff_) > 0.0001) {
+            sprintf(painCave.errMsg,
+                    "ForceMatrixDecomposition::createGtypeCutoffMap " 
+                    "user-specified rCut (%lf) does not match computed group Cutoff\n", userCutoff_);
+            painCave.severity = OPENMD_ERROR;
+            painCave.isFatal = 1;
+            simError();            
+          }
+        }
+      }
+    }
   }
-   
+
+
+  groupCutoffs ForceMatrixDecomposition::getGroupCutoffs(int cg1, int cg2) {
+    int i, j;   
+#ifdef IS_MPI
+    i = groupRowToGtype[cg1];
+    j = groupColToGtype[cg2];
+#else
+    i = groupToGtype[cg1];
+    j = groupToGtype[cg2];
+#endif    
+    return gTypeCutoffMap[make_pair(i,j)];
+  }
+
+  int ForceMatrixDecomposition::getTopologicalDistance(int atom1, int atom2) {
+    for (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;
+
+#ifdef IS_MPI
+    if (storageLayout_ & DataStorage::dslForce) {
+      fill(atomRowData.force.begin(), atomRowData.force.end(), V3Zero);
+      fill(atomColData.force.begin(), atomColData.force.end(), V3Zero);
+    }
+
+    if (storageLayout_ & DataStorage::dslTorque) {
+      fill(atomRowData.torque.begin(), atomRowData.torque.end(), V3Zero);
+      fill(atomColData.torque.begin(), atomColData.torque.end(), V3Zero);
+    }
+    
+    fill(pot_row.begin(), pot_row.end(), 
+         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
+
+    fill(pot_col.begin(), pot_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);
+    }
+
+    if (storageLayout_ & DataStorage::dslDensity) {      
+      fill(atomRowData.density.begin(), atomRowData.density.end(), 0.0);
+      fill(atomColData.density.begin(), atomColData.density.end(), 0.0);
+    }
+
+    if (storageLayout_ & DataStorage::dslFunctional) {   
+      fill(atomRowData.functional.begin(), atomRowData.functional.end(), 0.0);
+      fill(atomColData.functional.begin(), atomColData.functional.end(), 0.0);
+    }
+
+    if (storageLayout_ & DataStorage::dslFunctionalDerivative) {      
+      fill(atomRowData.functionalDerivative.begin(), 
+           atomRowData.functionalDerivative.end(), 0.0);
+      fill(atomColData.functionalDerivative.begin(), 
+           atomColData.functionalDerivative.end(), 0.0);
+    }
+
+    if (storageLayout_ & DataStorage::dslSkippedCharge) {      
+      fill(atomRowData.skippedCharge.begin(), atomRowData.skippedCharge.end(), 0.0);
+      fill(atomColData.skippedCharge.begin(), atomColData.skippedCharge.end(), 0.0);
+    }
+
+#else
+    
+    if (storageLayout_ & DataStorage::dslParticlePot) {      
+      fill(snap_->atomData.particlePot.begin(), 
+           snap_->atomData.particlePot.end(), 0.0);
+    }
+    
+    if (storageLayout_ & DataStorage::dslDensity) {      
+      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);
+    }
+    if (storageLayout_ & DataStorage::dslSkippedCharge) {      
+      fill(snap_->atomData.skippedCharge.begin(), 
+           snap_->atomData.skippedCharge.end(), 0.0);
+    }
+#endif
+    
+  }
+
+
   void ForceMatrixDecomposition::distributeData()  {
     snap_ = sman_->getCurrentSnapshot();
     storageLayout_ = sman_->getStorageLayout();
@@ -267,6 +522,9 @@ namespace OpenMD {
 #endif      
   }
   
+  /* collects information obtained during the pre-pair loop onto local
+   * data structures.
+   */
   void ForceMatrixDecomposition::collectIntermediateData() {
     snap_ = sman_->getCurrentSnapshot();
     storageLayout_ = sman_->getStorageLayout();
@@ -278,14 +536,18 @@ namespace OpenMD {
                                snap_->atomData.density);
       
       int n = snap_->atomData.density.size();
-      std::vector<RealType> rho_tmp(n, 0.0);
+      vector<RealType> rho_tmp(n, 0.0);
       AtomCommRealColumn->scatter(atomColData.density, rho_tmp);
       for (int i = 0; i < n; i++)
         snap_->atomData.density[i] += rho_tmp[i];
     }
 #endif
   }
-  
+
+  /*
+   * redistributes information obtained during the pre-pair loop out to 
+   * row and column-indexed data structures
+   */
   void ForceMatrixDecomposition::distributeIntermediateData() {
     snap_ = sman_->getCurrentSnapshot();
     storageLayout_ = sman_->getStorageLayout();
@@ -343,16 +605,25 @@ namespace OpenMD {
     
     nLocal_ = snap_->getNumberOfAtoms();
 
-    vector<vector<RealType> > pot_temp(N_INTERACTION_FAMILIES, 
-                                       vector<RealType> (nLocal_, 0.0));
+    vector<potVec> pot_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);
+
+    for (int ii = 0;  ii < pot_temp.size(); ii++ )
+      pairwisePot += pot_temp[ii];
     
-    for (int i = 0; i < N_INTERACTION_FAMILIES; i++) {
-      AtomCommRealRow->scatter(pot_row[i], pot_temp[i]);
-      for (int ii = 0;  ii < pot_temp[i].size(); ii++ ) {
-        pot_local[i] += pot_temp[i][ii];
-      }
-    }
+    fill(pot_temp.begin(), pot_temp.end(), 
+         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
+      
+    AtomCommPotColumn->scatter(pot_col, pot_temp);    
+    
+    for (int ii = 0;  ii < pot_temp.size(); ii++ )
+      pairwisePot += pot_temp[ii];    
 #endif
+
   }
 
   int ForceMatrixDecomposition::getNAtomsInRow() {   
@@ -427,7 +698,7 @@ namespace OpenMD {
 #ifdef IS_MPI
     return massFactorsRow[atom1];
 #else
-    return massFactorsLocal[atom1];
+    return massFactors[atom1];
 #endif
   }
 
@@ -435,7 +706,7 @@ namespace OpenMD {
 #ifdef IS_MPI
     return massFactorsCol[atom2];
 #else
-    return massFactorsLocal[atom2];
+    return massFactors[atom2];
 #endif
 
   }
@@ -453,20 +724,16 @@ namespace OpenMD {
     return d;    
   }
 
-  vector<int> ForceMatrixDecomposition::getSkipsForRowAtom(int atom1) {
-#ifdef IS_MPI
-    return skipsForRowAtom[atom1];
-#else
-    return skipsForLocalAtom[atom1];
-#endif
+  vector<int> ForceMatrixDecomposition::getSkipsForAtom(int atom1) {
+    return skipsForAtom[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 the
-   * parallel decomposition. 
+   * 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
+   * the parallel decomposition.
    */
   bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
     int unique_id_1, unique_id_2;
@@ -491,35 +758,15 @@ namespace OpenMD {
     unique_id_2 = atom2;
 #endif
     
-#ifdef IS_MPI
-    for (vector<int>::iterator i = skipsForRowAtom[atom1].begin();
-         i != skipsForRowAtom[atom1].end(); ++i) {
+    for (vector<int>::iterator i = skipsForAtom[atom1].begin();
+         i != skipsForAtom[atom1].end(); ++i) {
       if ( (*i) == unique_id_2 ) return true;
-    }    
-#else
-    for (vector<int>::iterator i = skipsForLocalAtom[atom1].begin();
-         i != skipsForLocalAtom[atom1].end(); ++i) {
-      if ( (*i) == unique_id_2 ) return true;
-    }    
-#endif
-  }
-
-  int ForceMatrixDecomposition::getTopoDistance(int atom1, int atom2) {
-    
-#ifdef IS_MPI
-    for (int i = 0; i < toposForRowAtom[atom1].size(); i++) {
-      if ( toposForRowAtom[atom1][i] == atom2 ) return topoDistRow[atom1][i];
     }
-#else
-    for (int i = 0; i < toposForLocalAtom[atom1].size(); i++) {
-      if ( toposForLocalAtom[atom1][i] == atom2 ) return topoDistLocal[atom1][i];
-    }
-#endif
 
-    // zero is default for unconnected (i.e. normal) pair interactions
-    return 0;
+    return false;
   }
 
+
   void ForceMatrixDecomposition::addForceToAtomRow(int atom1, Vector3d fg){
 #ifdef IS_MPI
     atomRowData.force[atom1] += fg;
@@ -537,14 +784,13 @@ namespace OpenMD {
   }
 
     // filling interaction blocks with pointers
-  InteractionData ForceMatrixDecomposition::fillInteractionData(int atom1, int atom2) {    
-    InteractionData idat;
-
+  void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat, 
+                                                     int atom1, int atom2) {    
 #ifdef IS_MPI
     
     idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]), 
                              ff_->getAtomType(identsCol[atom2]) );
-
+    
     if (storageLayout_ & DataStorage::dslAmat) {
       idat.A1 = &(atomRowData.aMat[atom1]);
       idat.A2 = &(atomColData.aMat[atom2]);
@@ -565,15 +811,25 @@ namespace OpenMD {
       idat.rho2 = &(atomColData.density[atom2]);
     }
 
+    if (storageLayout_ & DataStorage::dslFunctional) {
+      idat.frho1 = &(atomRowData.functional[atom1]);
+      idat.frho2 = &(atomColData.functional[atom2]);
+    }
+
     if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
       idat.dfrho1 = &(atomRowData.functionalDerivative[atom1]);
       idat.dfrho2 = &(atomColData.functionalDerivative[atom2]);
     }
 
+    if (storageLayout_ & DataStorage::dslParticlePot) {
+      idat.particlePot1 = &(atomRowData.particlePot[atom1]);
+      idat.particlePot2 = &(atomColData.particlePot[atom2]);
+    }
+
 #else
 
-    idat.atypes = make_pair( ff_->getAtomType(identsLocal[atom1]), 
-                             ff_->getAtomType(identsLocal[atom2]) );
+    idat.atypes = make_pair( ff_->getAtomType(idents[atom1]), 
+                             ff_->getAtomType(idents[atom2]) );
 
     if (storageLayout_ & DataStorage::dslAmat) {
       idat.A1 = &(snap_->atomData.aMat[atom1]);
@@ -590,22 +846,49 @@ namespace OpenMD {
       idat.t2 = &(snap_->atomData.torque[atom2]);
     }
 
-    if (storageLayout_ & DataStorage::dslDensity) {
+    if (storageLayout_ & DataStorage::dslDensity) {     
       idat.rho1 = &(snap_->atomData.density[atom1]);
       idat.rho2 = &(snap_->atomData.density[atom2]);
     }
 
+    if (storageLayout_ & DataStorage::dslFunctional) {
+      idat.frho1 = &(snap_->atomData.functional[atom1]);
+      idat.frho2 = &(snap_->atomData.functional[atom2]);
+    }
+
     if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
       idat.dfrho1 = &(snap_->atomData.functionalDerivative[atom1]);
       idat.dfrho2 = &(snap_->atomData.functionalDerivative[atom2]);
     }
+
+    if (storageLayout_ & DataStorage::dslParticlePot) {
+      idat.particlePot1 = &(snap_->atomData.particlePot[atom1]);
+      idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
+    }
+
 #endif
-    return idat;
   }
 
-  InteractionData ForceMatrixDecomposition::fillSkipData(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);
 
-    InteractionData idat;
+    atomRowData.force[atom1] += *(idat.f1);
+    atomColData.force[atom2] -= *(idat.f1);
+#else
+    pairwisePot += *(idat.pot);
+
+    snap_->atomData.force[atom1] += *(idat.f1);
+    snap_->atomData.force[atom2] -= *(idat.f1);
+#endif
+    
+  }
+
+
+  void ForceMatrixDecomposition::fillSkipData(InteractionData &idat,
+                                              int atom1, int atom2) {
 #ifdef IS_MPI
     idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]), 
                              ff_->getAtomType(identsCol[atom2]) );
@@ -614,33 +897,49 @@ namespace OpenMD {
       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::dslForce) {
-      idat.t1 = &(atomRowData.force[atom1]);
-      idat.t2 = &(atomColData.force[atom2]);
+
+    if (storageLayout_ & DataStorage::dslSkippedCharge) {
+      idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]);
+      idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
     }
 #else
-    idat.atypes = make_pair( ff_->getAtomType(identsLocal[atom1]), 
-                             ff_->getAtomType(identsLocal[atom2]) );
+    idat.atypes = make_pair( ff_->getAtomType(idents[atom1]), 
+                             ff_->getAtomType(idents[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::dslForce) {
-      idat.t1 = &(snap_->atomData.force[atom1]);
-      idat.t2 = &(snap_->atomData.force[atom2]);
+
+    if (storageLayout_ & DataStorage::dslSkippedCharge) {
+      idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
+      idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
     }
 #endif    
   }
 
+
+  void ForceMatrixDecomposition::unpackSkipData(InteractionData &idat, int atom1, int atom2) {    
+#ifdef IS_MPI
+    pot_row[atom1] += 0.5 *  *(idat.pot);
+    pot_col[atom2] += 0.5 *  *(idat.pot);
+#else
+    pairwisePot += *(idat.pot);   
+#endif
+
+  }
+
+
   /*
    * buildNeighborList
    *
@@ -650,6 +949,7 @@ namespace OpenMD {
   vector<pair<int, int> > ForceMatrixDecomposition::buildNeighborList() {
       
     vector<pair<int, int> > neighborList;
+    groupCutoffs cuts;
 #ifdef IS_MPI
     cellListRow_.clear();
     cellListCol_.clear();
@@ -657,10 +957,7 @@ namespace OpenMD {
     cellList_.clear();
 #endif
 
-    // dangerous to not do error checking.
-    RealType rCut_;
- 
-    RealType rList_ = (rCut_ + skinThickness_);
+    RealType rList_ = (largestRcut_ + skinThickness_);
     RealType rl2 = rList_ * rList_;
     Snapshot* snap_ = sman_->getCurrentSnapshot();
     Mat3x3d Hmat = snap_->getHmat();
@@ -676,16 +973,28 @@ namespace OpenMD {
     Vector3d rs, scaled, dr;
     Vector3i whichCell;
     int cellIndex;
+    int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
 
 #ifdef IS_MPI
+    cellListRow_.resize(nCtot);
+    cellListCol_.resize(nCtot);
+#else
+    cellList_.resize(nCtot);
+#endif
+
+#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++) 
+      for (int j = 0; j < 3; j++) {
         scaled[j] -= roundMe(scaled[j]);
+        scaled[j] += 0.5;
+      }
      
       // find xyz-indices of cell that cutoffGroup is in.
       whichCell.x() = nCells_.x() * scaled.x();
@@ -694,18 +1003,23 @@ namespace OpenMD {
 
       // 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++) 
+      for (int j = 0; j < 3; j++) {
         scaled[j] -= roundMe(scaled[j]);
+        scaled[j] += 0.5;
+      }
 
       // find xyz-indices of cell that cutoffGroup is in.
       whichCell.x() = nCells_.x() * scaled.x();
@@ -714,18 +1028,23 @@ namespace OpenMD {
 
       // 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++) 
+      for (int j = 0; j < 3; j++) {
         scaled[j] -= roundMe(scaled[j]);
+        scaled[j] += 0.5;
+      }
 
       // find xyz-indices of cell that cutoffGroup is in.
       whichCell.x() = nCells_.x() * scaled.x();
@@ -733,14 +1052,13 @@ namespace OpenMD {
       whichCell.z() = nCells_.z() * scaled.z();
 
       // find single index of this cell:
-      cellIndex = Vlinear(whichCell, nCells_);
+      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++) {
@@ -785,18 +1103,20 @@ namespace OpenMD {
                 if (m2 != m1 || cgColToGlobal[(*j2)] < cgRowToGlobal[(*j1)]) {
                   dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
                   snap_->wrapVector(dr);
-                  if (dr.lengthSquare() < rl2) {
+                  cuts = getGroupCutoffs( (*j1), (*j2) );
+                  if (dr.lengthSquare() < cuts.third) {
                     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 less than the j1 cutoff group
@@ -804,7 +1124,8 @@ namespace OpenMD {
                 if (m2 != m1 || (*j2) < (*j1)) {
                   dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
                   snap_->wrapVector(dr);
-                  if (dr.lengthSquare() < rl2) {
+                  cuts = getGroupCutoffs( (*j1), (*j2) );
+                  if (dr.lengthSquare() < cuts.third) {
                     neighborList.push_back(make_pair((*j1), (*j2)));
                   }
                 }
@@ -815,13 +1136,13 @@ namespace OpenMD {
         }
       }
     }
-
+    
     // 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