--- branches/development/src/parallel/ForceDecomposition.cpp	2011/03/18 19:31:52	1544
+++ trunk/src/parallel/ForceMatrixDecomposition.cpp	2015/03/03 16:40:39	2062
@@ -35,198 +35,1601 @@
  *                                                                      
  * [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/ForceDecomposition.hpp"
+#include "parallel/ForceMatrixDecomposition.hpp"
 #include "math/SquareMatrix3.hpp"
 #include "nonbonded/NonBondedInteraction.hpp"
 #include "brains/SnapshotManager.hpp"
+#include "brains/PairList.hpp"
 
 using namespace std;
 namespace OpenMD {
 
+  ForceMatrixDecomposition::ForceMatrixDecomposition(SimInfo* info, InteractionManager* iMan) : ForceDecomposition(info, iMan) {
+
+    // Row and colum scans must visit all surrounding cells
+    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) );
+  }
+
+
   /**
    * distributeInitialData is essentially a copy of the older fortran 
    * SimulationSetup
    */
-  
-  void ForceDecomposition::distributeInitialData() {
-#ifdef IS_MPI    
-    Snapshot* snap = sman_->getCurrentSnapshot();
-    int nLocal = snap->getNumberOfAtoms();
-    int nGroups = snap->getNumberOfCutoffGroups();
+  void ForceMatrixDecomposition::distributeInitialData() {
+    snap_ = sman_->getCurrentSnapshot();
+    storageLayout_ = sman_->getStorageLayout();
+    ff_ = info_->getForceField();
+    nLocal_ = snap_->getNumberOfAtoms();
+   
+    nGroups_ = info_->getNLocalCutoffGroups();
+    // gather the information for atomtype IDs (atids):
+    idents = info_->getIdentArray();
+    regions = info_->getRegions();
+    AtomLocalToGlobal = info_->getGlobalAtomIndices();
+    cgLocalToGlobal = info_->getGlobalGroupIndices();
+    vector<int> globalGroupMembership = info_->getGlobalGroupMembership();
 
-    AtomCommIntI = new Communicator<Row,int>(nLocal);
-    AtomCommRealI = new Communicator<Row,RealType>(nLocal);
-    AtomCommVectorI = new Communicator<Row,Vector3d>(nLocal);
-    AtomCommMatrixI = new Communicator<Row,Mat3x3d>(nLocal);
+    massFactors = info_->getMassFactors();
 
-    AtomCommIntJ = new Communicator<Column,int>(nLocal);
-    AtomCommRealJ = new Communicator<Column,RealType>(nLocal);
-    AtomCommVectorJ = new Communicator<Column,Vector3d>(nLocal);
-    AtomCommMatrixJ = new Communicator<Column,Mat3x3d>(nLocal);
+    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
+ 
+    MPI_Comm row = rowComm.getComm();
+    MPI_Comm col = colComm.getComm();
 
-    cgCommIntI = new Communicator<Row,int>(nGroups);
-    cgCommVectorI = new Communicator<Row,Vector3d>(nGroups);
-    cgCommIntJ = new Communicator<Column,int>(nGroups);
-    cgCommVectorJ = new Communicator<Column,Vector3d>(nGroups);
+    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_);
 
-    int nAtomsInRow = AtomCommIntI->getSize();
-    int nAtomsInCol = AtomCommIntJ->getSize();
-    int nGroupsInRow = cgCommIntI->getSize();
-    int nGroupsInCol = cgCommIntJ->getSize();
+    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_);
 
-    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));
+    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_);
+    atomColData.resize(nAtomsInCol_);
+    atomColData.setStorageLayout(storageLayout_);
+    cgRowData.resize(nGroupsInRow_);
+    cgRowData.setStorageLayout(DataStorage::dslPosition);
+    cgColData.resize(nGroupsInCol_);
+    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_);
     
-    vector<RealType> pot_local(N_INTERACTION_FAMILIES, 0.0);
+    AtomPlanIntRow->gather(idents, identsRow);
+    AtomPlanIntColumn->gather(idents, identsCol);
 
-    // gather the information for atomtype IDs (atids):
-    AtomCommIntI->gather(info_->getIdentArray(), identsRow);
-    AtomCommIntJ->gather(info_->getIdentArray(), identsCol);
+    regionsRow.resize(nAtomsInRow_);
+    regionsCol.resize(nAtomsInCol_);
+    
+    AtomPlanIntRow->gather(regions, regionsRow);
+    AtomPlanIntColumn->gather(regions, regionsCol);
+    
+    // allocate memory for the parallel objects
+    atypesRow.resize(nAtomsInRow_);
+    atypesCol.resize(nAtomsInCol_);
 
-    AtomLocalToGlobal = info_->getLocalToGlobalAtomIndex();
-    AtomCommIntI->gather(AtomLocalToGlobal, AtomRowToGlobal);
-    AtomCommIntJ->gather(AtomLocalToGlobal, AtomColToGlobal);
+    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]);         
 
-    cgLocalToGlobal = info_->getLocalToGlobalCutoffGroupIndex();
-    cgCommIntI->gather(cgLocalToGlobal, cgRowToGlobal);
-    cgCommIntJ->gather(cgLocalToGlobal, cgColToGlobal);
+    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);
 
-    // still need:
-    // topoDist
-    // exclude
+    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++) {
+      int gid = cgRowToGlobal[i];
+      for (int j = 0; j < nAtomsInRow_; j++) {
+        int aid = AtomRowToGlobal[j];
+        if (globalGroupMembership[aid] == gid)
+          groupListRow_[i].push_back(j);
+      }      
+    }
+
+    groupListCol_.clear();
+    groupListCol_.resize(nGroupsInCol_);
+    for (int i = 0; i < nGroupsInCol_; i++) {
+      int gid = cgColToGlobal[i];
+      for (int j = 0; j < nAtomsInCol_; j++) {
+        int aid = AtomColToGlobal[j];
+        if (globalGroupMembership[aid] == gid)
+          groupListCol_[i].push_back(j);
+      }      
+    }
+
+    excludesForAtom.clear();
+    excludesForAtom.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)) 
+          excludesForAtom[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);
+            }
+          }
+        }
+      }      
+    }
+
+#else
+    excludesForAtom.clear();
+    excludesForAtom.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];
+
+        if (excludes->hasPair(iglob, jglob)) 
+          excludesForAtom[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);
+            }
+          }
+        }
+      }      
+    }
 #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);
+        }
+      }      
+    }    
   }
     
+  int ForceMatrixDecomposition::getTopologicalDistance(int atom1, int atom2) {
+    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;
 
-  void ForceDecomposition::distributeData()  {
 #ifdef IS_MPI
-    Snapshot* snap = sman_->getCurrentSnapshot();
+    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));   
+
+    fill(expot_row.begin(), expot_row.end(), 
+         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
+
+    fill(expot_col.begin(), expot_col.end(), 
+         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));   
+
+    if (storageLayout_ & DataStorage::dslParticlePot) {    
+      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);
+    }
+
+    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);
+    }
+
+    if (storageLayout_ & DataStorage::dslSitePotential) {    
+      fill(atomRowData.sitePotential.begin(), 
+           atomRowData.sitePotential.end(), 0.0);
+      fill(atomColData.sitePotential.begin(), 
+           atomColData.sitePotential.end(), 0.0);
+    }
+
+#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);
+    }
+    
+    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);
+    }
+
+    if (storageLayout_ & DataStorage::dslElectricField) {      
+      fill(snap_->atomData.electricField.begin(), 
+           snap_->atomData.electricField.end(), V3Zero);
+    }
+    if (storageLayout_ & DataStorage::dslSitePotential) {      
+      fill(snap_->atomData.sitePotential.begin(), 
+           snap_->atomData.sitePotential.end(), 0.0);
+    }
+  }
+
+
+  void ForceMatrixDecomposition::distributeData()  {
+   
+#ifdef IS_MPI
+
+    snap_ = sman_->getCurrentSnapshot();
+    storageLayout_ = sman_->getStorageLayout();
+    
+    bool needsCG = true;
+    if(info_->getNCutoffGroups() != info_->getNAtoms())
+      needsCG = false;
+
     // gather up the atomic positions
-    AtomCommVectorI->gather(snap->atomData.position, 
-                            snap->atomIData.position);
-    AtomCommVectorJ->gather(snap->atomData.position, 
-                            snap->atomJData.position);
+    AtomPlanVectorRow->gather(snap_->atomData.position, 
+                              atomRowData.position);
+    AtomPlanVectorColumn->gather(snap_->atomData.position, 
+                                 atomColData.position);
     
     // gather up the cutoff group positions
-    cgCommVectorI->gather(snap->cgData.position, 
-                          snap->cgIData.position);
-    cgCommVectorJ->gather(snap->cgData.position, 
-                          snap->cgJData.position);
+
+    if (needsCG) {
+      cgPlanVectorRow->gather(snap_->cgData.position, 
+                              cgRowData.position);
+      
+      cgPlanVectorColumn->gather(snap_->cgData.position, 
+                                 cgColData.position);
+    }
+
+
+    if (needVelocities_) {
+      // gather up the atomic velocities
+      AtomPlanVectorColumn->gather(snap_->atomData.velocity, 
+                                   atomColData.velocity);
+
+      if (needsCG) {        
+        cgPlanVectorColumn->gather(snap_->cgData.velocity, 
+                                   cgColData.velocity);
+      }
+    }
+
     
     // if needed, gather the atomic rotation matrices
-    if (snap->atomData.getStorageLayout() & DataStorage::dslAmat) {
-      AtomCommMatrixI->gather(snap->atomData.aMat, 
-                              snap->atomIData.aMat);
-      AtomCommMatrixJ->gather(snap->atomData.aMat, 
-                              snap->atomJData.aMat);
+    if (storageLayout_ & DataStorage::dslAmat) {
+      AtomPlanMatrixRow->gather(snap_->atomData.aMat, 
+                                atomRowData.aMat);
+      AtomPlanMatrixColumn->gather(snap_->atomData.aMat, 
+                                   atomColData.aMat);
     }
-    
-    // if needed, gather the atomic eletrostatic frames
-    if (snap->atomData.getStorageLayout() & DataStorage::dslElectroFrame) {
-      AtomCommMatrixI->gather(snap->atomData.electroFrame, 
-                              snap->atomIData.electroFrame);
-      AtomCommMatrixJ->gather(snap->atomData.electroFrame, 
-                              snap->atomJData.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      
   }
   
-  void ForceDecomposition::collectIntermediateData() {
+  /* collects information obtained during the pre-pair loop onto local
+   * data structures.
+   */
+  void ForceMatrixDecomposition::collectIntermediateData() {
 #ifdef IS_MPI
-    Snapshot* snap = sman_->getCurrentSnapshot();
-    
-    if (snap->atomData.getStorageLayout() & DataStorage::dslDensity) {
 
-      AtomCommRealI->scatter(snap->atomIData.density, 
-                             snap->atomData.density);
+    snap_ = sman_->getCurrentSnapshot();
+    storageLayout_ = sman_->getStorageLayout();
 
-      int n = snap->atomData.density.size();
-      std::vector<RealType> rho_tmp(n, 0.0);
-      AtomCommRealJ->scatter(snap->atomJData.density, rho_tmp);
+    if (storageLayout_ & DataStorage::dslDensity) {
+      
+      AtomPlanRealRow->scatter(atomRowData.density, 
+                               snap_->atomData.density);
+      
+      int n = snap_->atomData.density.size();
+      vector<RealType> rho_tmp(n, 0.0);
+      AtomPlanRealColumn->scatter(atomColData.density, rho_tmp);
       for (int i = 0; i < n; i++)
-        snap->atomData.density[i] += rho_tmp[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
   }
-  
-  void ForceDecomposition::distributeIntermediateData() {
+
+  /*
+   * redistributes information obtained during the pre-pair loop out to 
+   * row and column-indexed data structures
+   */
+  void ForceMatrixDecomposition::distributeIntermediateData() {
 #ifdef IS_MPI
-    Snapshot* snap = sman_->getCurrentSnapshot();
-    if (snap->atomData.getStorageLayout() & DataStorage::dslFunctional) {
-      AtomCommRealI->gather(snap->atomData.functional, 
-                            snap->atomIData.functional);
-      AtomCommRealJ->gather(snap->atomData.functional, 
-                            snap->atomJData.functional);
+    snap_ = sman_->getCurrentSnapshot();
+    storageLayout_ = sman_->getStorageLayout();
+
+    if (storageLayout_ & DataStorage::dslFunctional) {
+      AtomPlanRealRow->gather(snap_->atomData.functional, 
+                              atomRowData.functional);
+      AtomPlanRealColumn->gather(snap_->atomData.functional, 
+                                 atomColData.functional);
     }
     
-    if (snap->atomData.getStorageLayout() & DataStorage::dslFunctionalDerivative) {
-      AtomCommRealI->gather(snap->atomData.functionalDerivative, 
-                            snap->atomIData.functionalDerivative);
-      AtomCommRealJ->gather(snap->atomData.functionalDerivative, 
-                            snap->atomJData.functionalDerivative);
+    if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
+      AtomPlanRealRow->gather(snap_->atomData.functionalDerivative, 
+                              atomRowData.functionalDerivative);
+      AtomPlanRealColumn->gather(snap_->atomData.functionalDerivative, 
+                                 atomColData.functionalDerivative);
     }
 #endif
   }
   
   
-  void ForceDecomposition::collectData() {
+  void ForceMatrixDecomposition::collectData() {
 #ifdef IS_MPI
-    Snapshot* snap = sman_->getCurrentSnapshot();
-    
-    int n = snap->atomData.force.size();
+    snap_ = sman_->getCurrentSnapshot();
+    storageLayout_ = sman_->getStorageLayout();
+
+    int n = snap_->atomData.force.size();
     vector<Vector3d> frc_tmp(n, V3Zero);
     
-    AtomCommVectorI->scatter(snap->atomIData.force, frc_tmp);
+    AtomPlanVectorRow->scatter(atomRowData.force, frc_tmp);
     for (int i = 0; i < n; i++) {
-      snap->atomData.force[i] += frc_tmp[i];
+      snap_->atomData.force[i] += frc_tmp[i];
       frc_tmp[i] = 0.0;
     }
     
-    AtomCommVectorJ->scatter(snap->atomJData.force, frc_tmp);
-    for (int i = 0; i < n; i++)
-      snap->atomData.force[i] += frc_tmp[i];
-    
-    
-    if (snap->atomData.getStorageLayout() & DataStorage::dslTorque) {
+    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);
 
-      AtomCommVectorI->scatter(snap->atomIData.torque, trq_tmp);
-      for (int i = 0; i < n; i++) {
-        snap->atomData.torque[i] += trq_tmp[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;
       }
       
-      AtomCommVectorJ->scatter(snap->atomJData.torque, trq_tmp);
-      for (int i = 0; i < n; i++)
-        snap->atomData.torque[i] += trq_tmp[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];
+            
+    }
     
-    int nLocal = snap->getNumberOfAtoms();
+    if (storageLayout_ & DataStorage::dslFlucQForce) {
 
-    vector<vector<RealType> > pot_temp(N_INTERACTION_FAMILIES, 
-                                       vector<RealType> (nLocal, 0.0));
+      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];
+    }
+
+    if (storageLayout_ & DataStorage::dslSitePotential) {
+
+      int nsp = snap_->atomData.sitePotential.size();
+      vector<RealType> sp_tmp(nsp, 0.0);
+
+      AtomPlanRealRow->scatter(atomRowData.sitePotential, sp_tmp);
+      for (int i = 0; i < nsp; i++) {
+        snap_->atomData.sitePotential[i] += sp_tmp[i];
+        sp_tmp[i] = 0.0;
+      }
+      
+      AtomPlanRealColumn->scatter(atomColData.sitePotential, sp_tmp);
+      for (int i = 0; i < nsp; i++)
+        snap_->atomData.sitePotential[i] += sp_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
+          
+    AtomPlanPotRow->scatter(pot_row, pot_temp);
+    AtomPlanPotRow->scatter(expot_row, expot_temp);
+
+    for (int ii = 0;  ii < pot_temp.size(); ii++ ) 
+      pairwisePot += pot_temp[ii];
+
+    for (int ii = 0;  ii < expot_temp.size(); ii++ ) 
+      excludedPot += expot_temp[ii];
+        
+    if (storageLayout_ & DataStorage::dslParticlePot) {
+      // This is the pairwise contribution to the particle pot.  The
+      // embedding contribution is added in each of the low level
+      // 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));
+      
+    AtomPlanPotColumn->scatter(pot_col, pot_temp);    
+    AtomPlanPotColumn->scatter(expot_col, expot_temp);    
     
-    for (int i = 0; i < N_INTERACTION_FAMILIES; i++) {
-      AtomCommRealI->scatter(pot_row[i], pot_temp[i]);
-      for (int ii = 0;  ii < pot_temp[i].size(); ii++ ) {
-        pot_local[i] += pot_temp[i][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);
+        }
       }
     }
+    
+    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_Allreduce(&ploc1, &ploc2, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
+      pairwisePot[ii] = ploc2;
+    }
+
+    for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
+      RealType ploc1 = excludedPot[ii];
+      RealType ploc2 = 0.0;
+      MPI_Allreduce(&ploc1, &ploc2, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
+      excludedPot[ii] = ploc2;
+    }
+
+    // Here be dragons.
+    MPI_Comm col = colComm.getComm();
+
+    MPI_Allreduce(MPI_IN_PLACE, 
+                  &snap_->frameData.conductiveHeatFlux[0], 3, 
+                  MPI_REALTYPE, MPI_SUM, col);
+
+
 #endif
+
   }
+
+  /** 
+   * Collects information obtained during the post-pair (and embedding
+   * functional) loops onto local data structures.
+   */
+  void ForceMatrixDecomposition::collectSelfData() {
+
+#ifdef IS_MPI
+    snap_ = sman_->getCurrentSnapshot();
+    storageLayout_ = sman_->getStorageLayout();
+
+    for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
+      RealType ploc1 = embeddingPot[ii];
+      RealType ploc2 = 0.0;
+      MPI_Allreduce(&ploc1, &ploc2, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
+      embeddingPot[ii] = ploc2;
+    }    
+    for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
+      RealType ploc1 = excludedSelfPot[ii];
+      RealType ploc2 = 0.0;
+      MPI_Allreduce(&ploc1, &ploc2, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
+      excludedSelfPot[ii] = ploc2;
+    }    
+#endif
+    
+  }
+
+  int& ForceMatrixDecomposition::getNAtomsInRow() {   
+#ifdef IS_MPI
+    return nAtomsInRow_;
+#else
+    return nLocal_;
+#endif
+  }
+
+  /**
+   * returns the list of atoms belonging to this group.  
+   */
+  vector<int>& ForceMatrixDecomposition::getAtomsInGroupRow(int cg1){
+#ifdef IS_MPI
+    return groupListRow_[cg1];
+#else 
+    return groupList_[cg1];
+#endif
+  }
+
+  vector<int>& ForceMatrixDecomposition::getAtomsInGroupColumn(int cg2){
+#ifdef IS_MPI
+    return groupListCol_[cg2];
+#else 
+    return groupList_[cg2];
+#endif
+  }
+  
+  inline Vector3d ForceMatrixDecomposition::getIntergroupVector(int cg1,
+                                                                int cg2){
+
+    Vector3d d;
+#ifdef IS_MPI
+    d = cgColData.position[cg2] - cgRowData.position[cg1];
+#else
+    d = snap_->cgData.position[cg2] - snap_->cgData.position[cg1];
+#endif
+    
+    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;
+    
+#ifdef IS_MPI
+    d = cgRowData.position[cg1] - atomRowData.position[atom1];
+#else
+    d = snap_->cgData.position[cg1] - snap_->atomData.position[atom1];
+#endif
+    if (usePeriodicBoundaryConditions_) {
+      snap_->wrapVector(d);
+    }
+    return d;    
+  }
+  
+  Vector3d ForceMatrixDecomposition::getAtomToGroupVectorColumn(int atom2,
+                                                                int cg2) {
+    Vector3d d;
+    
+#ifdef IS_MPI
+    d = cgColData.position[cg2] - atomColData.position[atom2];
+#else
+    d = snap_->cgData.position[cg2] - snap_->atomData.position[atom2];
+#endif
+    if (usePeriodicBoundaryConditions_) {
+      snap_->wrapVector(d);
+    }
+    return d;    
+  }
+
+  RealType& ForceMatrixDecomposition::getMassFactorRow(int atom1) {
+#ifdef IS_MPI
+    return massFactorsRow[atom1];
+#else
+    return massFactors[atom1];
+#endif
+  }
+
+  RealType& ForceMatrixDecomposition::getMassFactorColumn(int atom2) {
+#ifdef IS_MPI
+    return massFactorsCol[atom2];
+#else
+    return massFactors[atom2];
+#endif
+
+  }
+    
+  inline Vector3d ForceMatrixDecomposition::getInteratomicVector(int atom1,
+                                                                 int atom2){
+    Vector3d d;
+    
+#ifdef IS_MPI
+    d = atomColData.position[atom2] - atomRowData.position[atom1];
+#else
+    d = snap_->atomData.position[atom2] - snap_->atomData.position[atom1];
+#endif
+    if (usePeriodicBoundaryConditions_) {
+      snap_->wrapVector(d);
+    }
+    return d;    
+  }
+
+  vector<int>& ForceMatrixDecomposition::getExcludesForAtom(int atom1) {
+    return excludesForAtom[atom1];
+  }
+
+  /**
+   * We need to exclude some overcounted interactions that result from
+   * the parallel decomposition.
+   */
+  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   
+
+    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;
+    }
+#endif    
+
+#ifndef IS_MPI
+    if (group1 == group2) {
+      if (unique_id_1 < unique_id_2) return true;
+    }
+#endif
+    
+    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;
+  }
+
+
+  void ForceMatrixDecomposition::addForceToAtomRow(int atom1, Vector3d fg){
+#ifdef IS_MPI
+    atomRowData.force[atom1] += fg;
+#else
+    snap_->atomData.force[atom1] += fg;
+#endif
+  }
+
+  void ForceMatrixDecomposition::addForceToAtomColumn(int atom2, Vector3d fg){
+#ifdef IS_MPI
+    atomColData.force[atom2] += fg;
+#else
+    snap_->atomData.force[atom2] += fg;
+#endif
+  }
+
+    // filling interaction blocks with pointers
+  void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat, 
+                                                     int atom1, int atom2,
+                                                     bool newAtom1) {
+
+    idat.excluded = excludeAtomPair(atom1, atom2);
+
+    if (newAtom1) {
+      
+#ifdef IS_MPI
+      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::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]);
+      }
+      
+      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]);
+      }
+      
+      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.atid1 = idents[atom1];
+      idat.atid2 = idents[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::dslTorque) {
+        idat.t1 = &(snap_->atomData.torque[atom1]);
+        idat.t2 = &(snap_->atomData.torque[atom2]);
+      }
+      
+      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]);
+      }
+      
+      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]);
+      }
+      
+      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
+      
+    } else {
+      // atom1 is not new, so don't bother updating properties of that atom:
+#ifdef IS_MPI
+    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.A2 = &(atomColData.aMat[atom2]);
+    }
+    
+    if (storageLayout_ & DataStorage::dslTorque) {
+      idat.t2 = &(atomColData.torque[atom2]);
+    }
+
+    if (storageLayout_ & DataStorage::dslDipole) {
+      idat.dipole2 = &(atomColData.dipole[atom2]);
+    }
+
+    if (storageLayout_ & DataStorage::dslQuadrupole) {
+      idat.quadrupole2 = &(atomColData.quadrupole[atom2]);
+    }
+
+    if (storageLayout_ & DataStorage::dslDensity) {
+      idat.rho2 = &(atomColData.density[atom2]);
+    }
+
+    if (storageLayout_ & DataStorage::dslFunctional) {
+      idat.frho2 = &(atomColData.functional[atom2]);
+    }
+
+    if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
+      idat.dfrho2 = &(atomColData.functionalDerivative[atom2]);
+    }
+
+    if (storageLayout_ & DataStorage::dslParticlePot) {
+      idat.particlePot2 = &(atomColData.particlePot[atom2]);
+    }
+
+    if (storageLayout_ & DataStorage::dslSkippedCharge) {              
+      idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
+    }
+
+    if (storageLayout_ & DataStorage::dslFlucQPosition) {
+      idat.flucQ2 = &(atomColData.flucQPos[atom2]);
+    }
+
+#else   
+    idat.atid2 = idents[atom2];
+
+    if (regions[atom1] >= 0 && regions[atom2] >= 0) {
+      idat.sameRegion = (regions[atom1] == regions[atom2]);
+    } else {
+      idat.sameRegion = false;
+    }
+
+    if (storageLayout_ & DataStorage::dslAmat) {
+      idat.A2 = &(snap_->atomData.aMat[atom2]);
+    }
+
+    if (storageLayout_ & DataStorage::dslTorque) {
+      idat.t2 = &(snap_->atomData.torque[atom2]);
+    }
+
+    if (storageLayout_ & DataStorage::dslDipole) {
+      idat.dipole2 = &(snap_->atomData.dipole[atom2]);
+    }
+
+    if (storageLayout_ & DataStorage::dslQuadrupole) {
+      idat.quadrupole2 = &(snap_->atomData.quadrupole[atom2]);
+    }
+
+    if (storageLayout_ & DataStorage::dslDensity) {     
+      idat.rho2 = &(snap_->atomData.density[atom2]);
+    }
+
+    if (storageLayout_ & DataStorage::dslFunctional) {
+      idat.frho2 = &(snap_->atomData.functional[atom2]);
+    }
+
+    if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
+      idat.dfrho2 = &(snap_->atomData.functionalDerivative[atom2]);
+    }
+
+    if (storageLayout_ & DataStorage::dslParticlePot) {
+      idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
+    }
+
+    if (storageLayout_ & DataStorage::dslSkippedCharge) {
+      idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
+    }
+
+    if (storageLayout_ & DataStorage::dslFlucQPosition) {              
+      idat.flucQ2 = &(snap_->atomData.flucQPos[atom2]);
+    }
+
+#endif
+    }
+  }
   
+  void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat,
+                                                       int atom1, int atom2) {  
+#ifdef IS_MPI
+    pot_row[atom1] += RealType(0.5) *  *(idat.pot);
+    pot_col[atom2] += RealType(0.5) *  *(idat.pot);
+    expot_row[atom1] += RealType(0.5) *  *(idat.excludedPot);
+    expot_col[atom2] += RealType(0.5) *  *(idat.excludedPot);
+
+    atomRowData.force[atom1] += *(idat.f1);
+    atomColData.force[atom2] -= *(idat.f1);
+
+    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);
+    }
+
+    if (storageLayout_ & DataStorage::dslSitePotential) {              
+      atomRowData.sitePotential[atom1] += *(idat.sPot1);
+      atomColData.sitePotential[atom2] += *(idat.sPot2);
+    }
+
+#else
+    pairwisePot += *(idat.pot);
+    excludedPot += *(idat.excludedPot);
+
+    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::dslFlucQForce) {              
+      snap_->atomData.flucQFrc[atom1] -= *(idat.dVdFQ1);
+      snap_->atomData.flucQFrc[atom2] -= *(idat.dVdFQ2);
+    }
+
+    if (storageLayout_ & DataStorage::dslElectricField) {              
+      snap_->atomData.electricField[atom1] += *(idat.eField1);
+      snap_->atomData.electricField[atom2] += *(idat.eField2);
+    }
+
+    if (storageLayout_ & DataStorage::dslSitePotential) {              
+      snap_->atomData.sitePotential[atom1] += *(idat.sPot1);
+      snap_->atomData.sitePotential[atom2] += *(idat.sPot2);
+    }
+
+#endif
+    
+  }
+
+  /*
+   * buildNeighborList
+   *
+   * Constructs the Verlet neighbor list for a force-matrix
+   * decomposition.  In this case, each processor is responsible for
+   * row-site interactions with column-sites. 
+   *
+   * neighborList is returned as a packed array of neighboring
+   * column-ordered CutoffGroups.  The starting position in
+   * neighborList for each row-ordered CutoffGroup is given by the
+   * returned vector point.
+   */
+  void ForceMatrixDecomposition::buildNeighborList(vector<int>& neighborList,
+                                                   vector<int>& point) {
+    neighborList.clear();
+    point.clear();
+    int len = 0;
+    
+    bool doAllPairs = false;
+
+    Snapshot* snap_ = sman_->getCurrentSnapshot();
+    Mat3x3d box;
+    Mat3x3d invBox;
+
+    Vector3d rs, scaled, dr;
+    Vector3i whichCell;
+    int cellIndex;
+
+#ifdef IS_MPI
+    cellListRow_.clear();
+    cellListCol_.clear();
+    point.resize(nGroupsInRow_+1);
+#else
+    cellList_.clear();
+    point.resize(nGroups_+1);
+#endif
+    
+    if (!usePeriodicBoundaryConditions_) {
+      box = snap_->getBoundingBox();
+      invBox = snap_->getInvBoundingBox();
+    } else {
+      box = snap_->getHmat();
+      invBox = snap_->getInvHmat();
+    }
+    
+    Vector3d A = box.getColumn(0);
+    Vector3d B = box.getColumn(1);
+    Vector3d C = box.getColumn(2);
+
+    // Required for triclinic cells
+    Vector3d AxB = cross(A, B);
+    Vector3d BxC = cross(B, C);
+    Vector3d CxA = cross(C, A);
+
+    // unit vectors perpendicular to the faces of the triclinic cell:
+    AxB.normalize();
+    BxC.normalize();
+    CxA.normalize();
+
+    // A set of perpendicular lengths in triclinic cells:
+    RealType Wa = abs(dot(A, BxC));
+    RealType Wb = abs(dot(B, CxA));
+    RealType Wc = abs(dot(C, AxB));
+    
+    nCells_.x() = int( Wa / rList_ );
+    nCells_.y() = int( Wb / rList_ );
+    nCells_.z() = int( Wc / 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
+    
+    if (!doAllPairs) {
+      
+#ifdef IS_MPI
+      
+      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);
+      }
+      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);
+      }
+            
+#else
+      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);
+      }
+
+#endif
+
+#ifdef IS_MPI
+      for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
+        rs = cgRowData.position[j1];
+#else
+
+      for (int j1 = 0; j1 < nGroups_; j1++) {
+        rs = snap_->cgData.position[j1];
+#endif
+        point[j1] = len;
+        
+        // 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:
+        int m1 = Vlinear(whichCell, nCells_);
+
+        for (vector<Vector3i>::iterator os = cellOffsets_.begin();
+             os != cellOffsets_.end(); ++os) {
+              
+          Vector3i m2v = whichCell + (*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_);                                      
+#ifdef IS_MPI
+          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)] - rs;
+            if (usePeriodicBoundaryConditions_) {
+              snap_->wrapVector(dr);
+            }
+            if (dr.lengthSquare() < rListSq_) {
+              neighborList.push_back( (*j2) );
+              ++len;
+            }                 
+          }        
+#else
+          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.
+            
+            if ( (*j2) >= j1 ) {
+              
+              dr = snap_->cgData.position[(*j2)] - rs;
+              if (usePeriodicBoundaryConditions_) {
+                snap_->wrapVector(dr);
+              }
+              if ( dr.lengthSquare() < rListSq_) {
+                neighborList.push_back( (*j2) );
+                ++len;
+              }
+            }
+          }                
+#endif
+        }
+      }      
+    } else {
+      // branch to do all cutoff group pairs
+#ifdef IS_MPI
+      for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
+        point[j1] = len;
+        rs = cgRowData.position[j1];
+        for (int j2 = 0; j2 < nGroupsInCol_; j2++) {    
+          dr = cgColData.position[j2] - rs;
+          if (usePeriodicBoundaryConditions_) {
+            snap_->wrapVector(dr);
+          }
+          if (dr.lengthSquare() < rListSq_) {
+            neighborList.push_back( j2 );
+            ++len;
+          }
+        }
+      }      
+#else
+      // include all groups here.
+      for (int j1 = 0; j1 < nGroups_; j1++) {
+        point[j1] = len;
+        rs = snap_->cgData.position[j1];
+        // include self group interactions j2 == j1
+        for (int j2 = j1; j2 < nGroups_; j2++) {
+          dr = snap_->cgData.position[j2] - rs;
+          if (usePeriodicBoundaryConditions_) {
+            snap_->wrapVector(dr);
+          }
+          if (dr.lengthSquare() < rListSq_) {
+            neighborList.push_back( j2 );
+            ++len;
+          }
+        }    
+      }
+#endif
+    }
+
+#ifdef IS_MPI
+    point[nGroupsInRow_] = len;
+#else
+    point[nGroups_] = len;
+#endif
+  
+    // save the local cutoff group positions for the check that is
+    // done on each loop:
+    saved_CG_positions_.clear();
+    saved_CG_positions_.reserve(nGroups_);
+    for (int i = 0; i < nGroups_; i++)
+      saved_CG_positions_.push_back(snap_->cgData.position[i]);
+  }
 } //end namespace OpenMD