--- branches/development/src/parallel/ForceMatrixDecomposition.hpp	2011/06/03 21:39:49	1575
+++ branches/development/src/parallel/ForceMatrixDecomposition.hpp	2011/06/16 22:00:08	1583
@@ -55,7 +55,7 @@ namespace OpenMD {
   
   class ForceMatrixDecomposition : public ForceDecomposition {
   public:
-    ForceMatrixDecomposition(SimInfo* info) : ForceDecomposition(info) {};
+    ForceMatrixDecomposition(SimInfo* info, InteractionManager* iMan) : ForceDecomposition(info, iMan) {};
 
     void distributeInitialData();
     void zeroWorkArrays();
@@ -68,7 +68,7 @@ namespace OpenMD {
     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);
@@ -84,27 +84,27 @@ namespace OpenMD {
        
     // atom bookkeeping
     int getNAtomsInRow();
-    vector<int> getSkipsForRowAtom(int atom1);
-    int getTopoDistance(int atom1, int atom2);
+    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);
+    void fillInteractionData(InteractionData &idat, int atom1, int atom2);
+    void unpackInteractionData(InteractionData &idat, int atom1, int atom2);
+    void fillSkipData(InteractionData &idat, int atom1, int atom2);
+    void unpackSkipData(InteractionData &idat, int atom1, int atom2);
 
   private: 
+    void createGtypeCutoffMap();
+
     int nLocal_;
     int nGroups_;
-    vector<int> identsLocal;
     vector<int> AtomLocalToGlobal;
     vector<int> cgLocalToGlobal;
-    vector<RealType> massFactorsLocal;
-    vector<vector<int> > skipsForLocalAtom;
-    vector<vector<int> > toposForLocalAtom;
-    vector<vector<int> > topoDistLocal;
+    vector<RealType> groupCutoff;
+    vector<int> groupToGtype;
 
 #ifdef IS_MPI    
     DataStorage atomRowData;
@@ -137,7 +137,6 @@ namespace OpenMD {
     // work arrays for assembling potential energy
     vector<potVec> pot_row;
     vector<potVec> pot_col;
-    potVec pot_local;
 
     vector<int> identsRow;
     vector<int> identsCol;
@@ -151,6 +150,11 @@ namespace OpenMD {
     vector<int> cgRowToGlobal;
     vector<int> cgColToGlobal;
 
+    vector<RealType> groupCutoffRow;
+    vector<RealType> groupCutoffCol;
+    vector<int> groupColToGtype;
+    vector<int> groupRowToGtype;
+
     vector<vector<int> > cellListRow_;
     vector<vector<int> > cellListCol_;
 
@@ -159,10 +163,6 @@ namespace OpenMD {
 
     vector<RealType> massFactorsRow;
     vector<RealType> massFactorsCol;
-
-    vector<vector<int> > skipsForRowAtom;
-    vector<vector<int> > toposForRowAtom;
-    vector<vector<int> > topoDistRow;
 #endif
 
   };