--- branches/development/src/parallel/ForceMatrixDecomposition.hpp	2011/05/24 21:24:45	1567
+++ branches/development/src/parallel/ForceMatrixDecomposition.hpp	2011/06/09 20:26:29	1579
@@ -55,52 +55,57 @@ namespace OpenMD {
   
   class ForceMatrixDecomposition : public ForceDecomposition {
   public:
-    ForceMatrixDecomposition(SimInfo* info) : ForceDecomposition(info) {sman_ = info_->getSnapshotManager();}
+    ForceMatrixDecomposition(SimInfo* info, InteractionManager* iMan) : ForceDecomposition(info, iMan) {};
+
     void distributeInitialData();
+    void zeroWorkArrays();
     void distributeData();
     void collectIntermediateData();
     void distributeIntermediateData();
     void collectData();
 
     // neighbor list routines
-    bool checkNeighborList();
     vector<pair<int, int> >  buildNeighborList();
 
     // group bookkeeping
-    pair<int, int> getGroupTypes(int cg1, int cg2);
+    groupCutoffs getGroupCutoffs(int cg1, int cg2);
 
     // Group->atom bookkeeping
     vector<int> getAtomsInGroupRow(int cg1);
     vector<int> getAtomsInGroupColumn(int cg2);
     Vector3d getAtomToGroupVectorRow(int atom1, int cg1);
     Vector3d getAtomToGroupVectorColumn(int atom2, int cg2);
-    RealType getMfactRow(int atom1);
-    RealType getMfactColumn(int atom2);
+    RealType getMassFactorRow(int atom1);
+    RealType getMassFactorColumn(int atom2);
 
     // spatial data
     Vector3d getIntergroupVector(int cg1, int cg2);
     Vector3d getInteratomicVector(int atom1, int atom2);
        
     // atom bookkeeping
-    vector<int> getAtomList();
-    vector<int> getSkipsForAtom(int atom1);
+    int getNAtomsInRow();
+    int getTopologicalDistance(int atom1, int atom2);
+    vector<int> getSkipsForAtom(int atom1); 
     bool skipAtomPair(int atom1, int atom2);
     void addForceToAtomRow(int atom1, Vector3d fg);
     void addForceToAtomColumn(int atom2, Vector3d fg);
 
     // filling interaction blocks with pointers
     InteractionData fillInteractionData(int atom1, int atom2);
+    void unpackInteractionData(InteractionData idat, int atom1, int atom2);
     InteractionData fillSkipData(int atom1, int atom2);
-    SelfData fillSelfData(int atom1);
 
   private: 
-    SnapshotManager* sman_;    
-    Snapshot* snap_;
-    int storageLayout_;
-    vector<Vector3i> Cells;
+    void createGtypeCutoffMap();
 
     int nLocal_;
     int nGroups_;
+    vector<int> identsLocal;
+    vector<int> AtomLocalToGlobal;
+    vector<int> cgLocalToGlobal;
+    vector<RealType> massFactorsLocal;
+    vector<RealType> groupCutoff;
+    vector<int> groupToGtype;
 
 #ifdef IS_MPI    
     DataStorage atomRowData;
@@ -117,35 +122,50 @@ namespace OpenMD {
     Communicator<Row, RealType>* AtomCommRealRow; 
     Communicator<Row, Vector3d>* AtomCommVectorRow; 
     Communicator<Row, Mat3x3d>*  AtomCommMatrixRow; 
+    Communicator<Row, potVec>* AtomCommPotRow;
 
     Communicator<Column, int>* AtomCommIntColumn;
     Communicator<Column, RealType>* AtomCommRealColumn; 
     Communicator<Column, Vector3d>* AtomCommVectorColumn; 
-    Communicator<Column, Mat3x3d>*  AtomCommMatrixColumn; 
+    Communicator<Column, Mat3x3d>*  AtomCommMatrixColumn;
+    Communicator<Column, potVec>* AtomCommPotColumn; 
 
     Communicator<Row, int>* cgCommIntRow;
     Communicator<Row, Vector3d>* cgCommVectorRow; 
     Communicator<Column, int>* cgCommIntColumn;
     Communicator<Column, Vector3d>* cgCommVectorColumn; 
 
-    vector<vector<RealType> > pot_row;
-    vector<vector<RealType> > pot_col;
+    // work arrays for assembling potential energy
+    vector<potVec> pot_row;
+    vector<potVec> pot_col;
+    potVec pot_local;
+
     vector<int> identsRow;
     vector<int> identsCol;
 
-    vector<int> AtomLocalToGlobal;
+    vector<AtomType*> atypesRow;
+    vector<AtomType*> atypesCol;
+
     vector<int> AtomRowToGlobal;
     vector<int> AtomColToGlobal;
-    vector<int> cgLocalToGlobal;
+
     vector<int> cgRowToGlobal;
     vector<int> cgColToGlobal;
 
-    vector<vector<int> > CellListRow;
-    vector<vector<int> > CellListCol;
-#else 
-    vector<vector<int> > CellList;
+    vector<RealType> groupCutoffRow;
+    vector<RealType> groupCutoffCol;
+    vector<int> groupColToGtype;
+    vector<int> groupRowToGtype;
+
+    vector<vector<int> > cellListRow_;
+    vector<vector<int> > cellListCol_;
+
+    vector<vector<int> > groupListRow_;
+    vector<vector<int> > groupListCol_;
+
+    vector<RealType> massFactorsRow;
+    vector<RealType> massFactorsCol;
 #endif
-    vector<RealType> pot_local;
 
   };