--- branches/development/src/parallel/ForceMatrixDecomposition.hpp	2012/05/24 20:59:54	1723
+++ trunk/src/parallel/ForceMatrixDecomposition.hpp	2015/03/03 17:02:20	2064
@@ -35,7 +35,7 @@
  *                                                                      
  * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
  * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
- * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
+ * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
  * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
  * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
  */
@@ -63,44 +63,42 @@ namespace OpenMD {
     void distributeData();
     void collectIntermediateData();
     void distributeIntermediateData();
+    void collectSelfData();
     void collectData();
 
     // neighbor list routines
-    vector<pair<int, int> >  buildNeighborList();
+    void buildNeighborList(vector<int>& neighborList, vector<int>& point);
 
     // group bookkeeping
-    groupCutoffs getGroupCutoffs(int cg1, int cg2);
-    Vector3d getGroupVelocityColumn(int cg2);
+    Vector3d& getGroupVelocityColumn(int cg2);
 
     // Group->atom bookkeeping
-    vector<int> getAtomsInGroupRow(int cg1);
-    vector<int> getAtomsInGroupColumn(int cg2);
+    vector<int>& getAtomsInGroupRow(int cg1);
+    vector<int>& getAtomsInGroupColumn(int cg2);
     Vector3d getAtomToGroupVectorRow(int atom1, int cg1);
     Vector3d getAtomToGroupVectorColumn(int atom2, int cg2);
-    RealType getMassFactorRow(int atom1);
-    RealType getMassFactorColumn(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
-    int getNAtomsInRow();
+    int& getNAtomsInRow();
     int getTopologicalDistance(int atom1, int atom2);
-    vector<int> getExcludesForAtom(int atom1); 
-    bool skipAtomPair(int atom1, int atom2);
+    vector<int>& getExcludesForAtom(int atom1); 
+    bool skipAtomPair(int atom1, int atom2, int cg1, int cg2);
     bool excludeAtomPair(int atom1, int atom2);
     void addForceToAtomRow(int atom1, Vector3d fg);
     void addForceToAtomColumn(int atom2, Vector3d fg);
-    Vector3d getAtomVelocityColumn(int atom2);
+    Vector3d& getAtomVelocityColumn(int atom2);
 
     // filling interaction blocks with pointers
-    void fillInteractionData(InteractionData &idat, int atom1, int atom2);
+    void fillInteractionData(InteractionData &idat, int atom1, int atom2, bool newAtom1 = true);
     void unpackInteractionData(InteractionData &idat, int atom1, int atom2);
 
-  private: 
-    void createGtypeCutoffMap();
-
+  private:     
     int nLocal_;
     int nGroups_;
     vector<int> AtomLocalToGlobal;
@@ -109,7 +107,8 @@ namespace OpenMD {
     vector<int> groupToGtype;
 
 #ifdef IS_MPI    
-    DataStorage atomRowData;    DataStorage atomColData;
+    DataStorage atomRowData;
+    DataStorage atomColData;
     DataStorage cgRowData;
     DataStorage cgColData;
 
@@ -142,9 +141,15 @@ namespace OpenMD {
     vector<potVec> pot_row;
     vector<potVec> pot_col;
 
+    vector<potVec> expot_row;
+    vector<potVec> expot_col;
+
     vector<int> identsRow;
     vector<int> identsCol;
 
+    vector<int> regionsRow;
+    vector<int> regionsCol;
+
     vector<AtomType*> atypesRow;
     vector<AtomType*> atypesCol;
 
@@ -156,11 +161,6 @@ namespace OpenMD {
     vector<int> cgColToGlobal;
 
 private:
-    vector<RealType> groupCutoffRow;
-    vector<RealType> groupCutoffCol;
-    vector<int> groupColToGtype;
-    vector<int> groupRowToGtype;
-
     vector<vector<int> > cellListRow_;
     vector<vector<int> > cellListCol_;
 
@@ -169,6 +169,9 @@ namespace OpenMD {
 
     vector<RealType> massFactorsRow;
     vector<RealType> massFactorsCol;
+
+    vector<int> regionRow;
+    vector<int> regionCol;
 #endif
 
   };