--- branches/development/src/parallel/ForceMatrixDecomposition.hpp	2011/11/22 20:38:56	1665
+++ trunk/src/parallel/ForceMatrixDecomposition.hpp	2013/08/19 13:51:04	1930
@@ -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).
  */
@@ -63,34 +63,37 @@ namespace OpenMD {
     void distributeData();
     void collectIntermediateData();
     void distributeIntermediateData();
+    void collectSelfData();
     void collectData();
 
     // neighbor list routines
-    vector<pair<int, int> >  buildNeighborList();
+    void buildNeighborList(vector<pair<int, int> >& neighborList);
 
     // group bookkeeping
-    groupCutoffs getGroupCutoffs(int cg1, int cg2);
+    void getGroupCutoffs(int &cg1, int &cg2, RealType &rcut, RealType &rcutsq, RealType &rlistsq);
+    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);
 
     // filling interaction blocks with pointers
     void fillInteractionData(InteractionData &idat, int atom1, int atom2);
@@ -141,9 +144,15 @@ 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;
 
@@ -168,6 +177,9 @@ namespace OpenMD {
 
     vector<RealType> massFactorsRow;
     vector<RealType> massFactorsCol;
+
+    vector<int> regionRow;
+    vector<int> regionCol;
 #endif
 
   };