--- branches/development/src/parallel/ForceMatrixDecomposition.hpp	2011/06/08 16:05:07	1576
+++ trunk/src/parallel/ForceMatrixDecomposition.hpp	2013/08/19 13:12:00	1929
@@ -35,8 +35,9 @@
  *                                                                      
  * [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).          
- * [4]  Vardeman & Gezelter, in progress (2009).                        
+ * [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).
  */
  
 #ifndef PARALLEL_FORCEMATRIXDECOMPOSITION_HPP
@@ -55,64 +56,61 @@ namespace OpenMD {
   
   class ForceMatrixDecomposition : public ForceDecomposition {
   public:
-    ForceMatrixDecomposition(SimInfo* info) : ForceDecomposition(info) {};
+    ForceMatrixDecomposition(SimInfo* info, InteractionManager* iMan);
 
     void distributeInitialData();
     void zeroWorkArrays();
     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();
-    vector<int> getSkipsForRowAtom(int atom1);
-    int getTopoDistance(int atom1, int atom2);
-    bool skipAtomPair(int atom1, int atom2);
+    int& getNAtomsInRow();
+    int getTopologicalDistance(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
-    InteractionData fillInteractionData(int atom1, int atom2);
-    void unpackInteractionData(InteractionData idat, int atom1, int atom2);
-    InteractionData fillSkipData(int atom1, int atom2);
+    void fillInteractionData(InteractionData &idat, int atom1, int atom2);
+    void unpackInteractionData(InteractionData &idat, int atom1, int atom2);
 
   private: 
     void createGtypeCutoffMap();
 
     int nLocal_;
     int nGroups_;
-    vector<int> identsLocal;
     vector<int> AtomLocalToGlobal;
     vector<int> cgLocalToGlobal;
-    vector<RealType> massFactorsLocal;
-    vector<vector<int> > skipsForLocalAtom;
-    vector<vector<int> > toposForLocalAtom;
-    vector<vector<int> > topoDistLocal;
     vector<RealType> groupCutoff;
     vector<int> groupToGtype;
 
 #ifdef IS_MPI    
-    DataStorage atomRowData;
-    DataStorage atomColData;
+    DataStorage atomRowData;    DataStorage atomColData;
     DataStorage cgRowData;
     DataStorage cgColData;
 
@@ -121,40 +119,50 @@ namespace OpenMD {
     int nGroupsInRow_;
     int nGroupsInCol_;
 
-    Communicator<Row, int>* AtomCommIntRow;
-    Communicator<Row, RealType>* AtomCommRealRow; 
-    Communicator<Row, Vector3d>* AtomCommVectorRow; 
-    Communicator<Row, Mat3x3d>*  AtomCommMatrixRow; 
-    Communicator<Row, potVec>* AtomCommPotRow;
+    Communicator<Row> rowComm;
+    Communicator<Column> colComm;
 
-    Communicator<Column, int>* AtomCommIntColumn;
-    Communicator<Column, RealType>* AtomCommRealColumn; 
-    Communicator<Column, Vector3d>* AtomCommVectorColumn; 
-    Communicator<Column, Mat3x3d>*  AtomCommMatrixColumn;
-    Communicator<Column, potVec>* AtomCommPotColumn; 
+    Plan<int>* AtomPlanIntRow;
+    Plan<RealType>* AtomPlanRealRow; 
+    Plan<Vector3d>* AtomPlanVectorRow; 
+    Plan<Mat3x3d>*  AtomPlanMatrixRow; 
+    Plan<potVec>* AtomPlanPotRow;
 
-    Communicator<Row, int>* cgCommIntRow;
-    Communicator<Row, Vector3d>* cgCommVectorRow; 
-    Communicator<Column, int>* cgCommIntColumn;
-    Communicator<Column, Vector3d>* cgCommVectorColumn; 
+    Plan<int>* AtomPlanIntColumn;
+    Plan<RealType>* AtomPlanRealColumn; 
+    Plan<Vector3d>* AtomPlanVectorColumn; 
+    Plan<Mat3x3d>*  AtomPlanMatrixColumn;
+    Plan<potVec>* AtomPlanPotColumn; 
 
+    Plan<int>* cgPlanIntRow;
+    Plan<Vector3d>* cgPlanVectorRow; 
+    Plan<int>* cgPlanIntColumn;
+    Plan<Vector3d>* cgPlanVectorColumn; 
+
     // work arrays for assembling potential energy
     vector<potVec> pot_row;
     vector<potVec> pot_col;
-    potVec pot_local;
 
+    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;
 
     vector<int> AtomRowToGlobal;
     vector<int> AtomColToGlobal;
 
+public:
     vector<int> cgRowToGlobal;
     vector<int> cgColToGlobal;
 
+private:
     vector<RealType> groupCutoffRow;
     vector<RealType> groupCutoffCol;
     vector<int> groupColToGtype;
@@ -168,10 +176,6 @@ namespace OpenMD {
 
     vector<RealType> massFactorsRow;
     vector<RealType> massFactorsCol;
-
-    vector<vector<int> > skipsForRowAtom;
-    vector<vector<int> > toposForRowAtom;
-    vector<vector<int> > topoDistRow;
 #endif
 
   };