--- branches/development/src/parallel/ForceMatrixDecomposition.hpp	2011/05/26 13:55:04	1569
+++ branches/development/src/parallel/ForceMatrixDecomposition.hpp	2011/05/27 16:45:44	1571
@@ -82,8 +82,9 @@ namespace OpenMD {
     Vector3d getInteratomicVector(int atom1, int atom2);
        
     // atom bookkeeping
-    vector<int> getAtomList();
-    vector<int> getSkipsForAtom(int atom1);
+    int getNAtomsInRow();
+    vector<int> getSkipsForRowAtom(int atom1);
+    int getTopoDistance(int atom1, int atom2);
     bool skipAtomPair(int atom1, int atom2);
     void addForceToAtomRow(int atom1, Vector3d fg);
     void addForceToAtomColumn(int atom2, Vector3d fg);
@@ -95,10 +96,14 @@ namespace OpenMD {
   private: 
     int nLocal_;
     int nGroups_;
+    vector<int> identsLocal;
     vector<int> AtomLocalToGlobal;
     vector<int> cgLocalToGlobal;
     vector<RealType> pot_local;
     vector<RealType> massFactorsLocal;
+    vector<vector<int> > skipsForLocalAtom;
+    vector<vector<int> > toposForLocalAtom;
+    vector<vector<int> > topoDistLocal;
 
 #ifdef IS_MPI    
     DataStorage atomRowData;
@@ -132,6 +137,9 @@ namespace OpenMD {
     vector<int> identsRow;
     vector<int> identsCol;
 
+    vector<AtomType*> atypesRow;
+    vector<AtomType*> atypesCol;
+
     vector<int> AtomRowToGlobal;
     vector<int> AtomColToGlobal;
 
@@ -147,6 +155,9 @@ namespace OpenMD {
     vector<RealType> massFactorsRow;
     vector<RealType> massFactorsCol;
 
+    vector<vector<int> > skipsForRowAtom;
+    vector<vector<int> > toposForRowAtom;
+    vector<vector<int> > topoDistRow;
 #endif
 
   };