--- branches/development/src/parallel/ForceMatrixDecomposition.hpp	2011/04/28 18:38:21	1551
+++ branches/development/src/parallel/ForceMatrixDecomposition.hpp	2011/05/26 13:55:04	1569
@@ -42,12 +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;
@@ -55,7 +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();
@@ -63,7 +64,6 @@ namespace OpenMD {
     void collectData();
 
     // neighbor list routines
-    bool checkNeighborList();
     vector<pair<int, int> >  buildNeighborList();
 
     // group bookkeeping
@@ -74,8 +74,8 @@ 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);
@@ -91,19 +91,26 @@ 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_;    
-    Snapshot* snap_;
-    int storageLayout_;
-#ifdef IS_MPI    
+    int nLocal_;
+    int nGroups_;
+    vector<int> AtomLocalToGlobal;
+    vector<int> cgLocalToGlobal;
+    vector<RealType> pot_local;
+    vector<RealType> massFactorsLocal;
 
+#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; 
@@ -121,17 +128,27 @@ 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;
+
 #endif
-    vector<RealType> pot_local;
+
   };
 
 }