--- branches/development/src/parallel/ForceMatrixDecomposition.hpp	2011/04/27 18:38:15	1549
+++ branches/development/src/parallel/ForceMatrixDecomposition.hpp	2011/05/26 21:56:04	1570
@@ -42,11 +42,12 @@
 #ifndef PARALLEL_FORCEMATRIXDECOMPOSITION_HPP
 #define PARALLEL_FORCEMATRIXDECOMPOSITION_HPP
 
-#include "Parallel/ForceDecomposition.hpp"
+#include "parallel/ForceDecomposition.hpp"
 #include "math/SquareMatrix3.hpp"
+#include "brains/Snapshot.hpp"
 
 #ifdef IS_MPI
-#include "Parallel/Communicator.hpp"
+#include "parallel/Communicator.hpp"
 #endif
 
 using namespace std;
@@ -54,7 +55,8 @@ namespace OpenMD {
   
   class ForceMatrixDecomposition : public ForceDecomposition {
   public:
-    ForceMatrixDecomposition(SimInfo* info) : ForceDecomposition(info) {sman_ = info_->getSnapshotManager();}
+    ForceMatrixDecomposition(SimInfo* info) : ForceDecomposition(info) {};
+
     void distributeInitialData();
     void distributeData();
     void collectIntermediateData();
@@ -62,7 +64,6 @@ namespace OpenMD {
     void collectData();
 
     // neighbor list routines
-    bool checkNeighborList();
     vector<pair<int, int> >  buildNeighborList();
 
     // group bookkeeping
@@ -73,16 +74,17 @@ namespace OpenMD {
     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();
+    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);
@@ -90,11 +92,29 @@ namespace OpenMD {
     // filling interaction blocks with pointers
     InteractionData fillInteractionData(int atom1, int atom2);
     InteractionData fillSkipData(int atom1, int atom2);
-    SelfData fillSelfData(int atom1);
 
   private: 
-    SnapshotManager* sman_;    
+    int nLocal_;
+    int nGroups_;
+    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;
+    DataStorage atomColData;
+    DataStorage cgRowData;
+    DataStorage cgColData;
+
+    int nAtomsInRow_; 
+    int nAtomsInCol_;
+    int nGroupsInRow_;
+    int nGroupsInCol_;
+
     Communicator<Row, int>* AtomCommIntRow;
     Communicator<Row, RealType>* AtomCommRealRow; 
     Communicator<Row, Vector3d>* AtomCommVectorRow; 
@@ -112,17 +132,32 @@ namespace OpenMD {
 
     vector<vector<RealType> > pot_row;
     vector<vector<RealType> > pot_col;
+
     vector<int> identsRow;
     vector<int> identsCol;
 
-    vector<int> AtomLocalToGlobal;
     vector<int> AtomRowToGlobal;
     vector<int> AtomColToGlobal;
-    vector<int> cgLocalToGlobal;
+
     vector<int> cgRowToGlobal;
     vector<int> cgColToGlobal;
+
+    vector<vector<int> > cellListRow_;
+    vector<vector<int> > cellListCol_;
+
+    vector<vector<int> > groupListRow_;
+    vector<vector<int> > groupListCol_;
+
+    vector<RealType> massFactorsRow;
+    vector<RealType> massFactorsCol;
+
+    vector<vector<int> > skipsForRowAtom;
+    vector<vector<int> > toposForRowAtom;
+    vector<vector<int> > topoDistRow;
+
+
 #endif
-    vector<RealType> pot_local;
+
   };
 
 }