--- branches/development/src/parallel/ForceDecomposition.hpp	2011/03/18 19:31:52	1544
+++ branches/development/src/parallel/ForceMatrixDecomposition.hpp	2012/05/24 20:59:54	1723
@@ -36,71 +36,141 @@
  * [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).                        
+ * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
+ * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
  */
  
-#ifndef PARALLEL_FORCEDECOMPOSITION_HPP
-#define PARALLEL_FORCEDECOMPOSITION_HPP
+#ifndef PARALLEL_FORCEMATRIXDECOMPOSITION_HPP
+#define PARALLEL_FORCEMATRIXDECOMPOSITION_HPP
 
-#include "Parallel/Decomposition.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;
 namespace OpenMD {
   
-  class ForceDecomposition : public Decomposition {
+  class ForceMatrixDecomposition : public ForceDecomposition {
   public:
-    ForceDecomposition(SimInfo* info) : Decomposition(info) {sman_ = info_->getSnapshotManager();}
+    ForceMatrixDecomposition(SimInfo* info, InteractionManager* iMan);
+
     void distributeInitialData();
+    void zeroWorkArrays();
     void distributeData();
     void collectIntermediateData();
     void distributeIntermediateData();
     void collectData();
 
-    unsigned int getNcutoffGroupsI();
-    unsigned int getNcutoffGroupsJ();
+    // neighbor list routines
+    vector<pair<int, int> >  buildNeighborList();
 
-    vector<int> getAtomsInGroupI(int whichCGI);
-    vector<int> getAtomsInGroupJ(int whichCGJ);
+    // group bookkeeping
+    groupCutoffs getGroupCutoffs(int cg1, int cg2);
+    Vector3d getGroupVelocityColumn(int cg2);
 
-    AtomType* getAtomTypeI(int whichAtomI);
-    AtomType* getAtomTypeJ(int whichAtomJ);   
+    // Group->atom bookkeeping
+    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);
 
+    // spatial data
+    Vector3d getIntergroupVector(int cg1, int cg2);
+    Vector3d getInteratomicVector(int atom1, int atom2);
+       
+    // atom bookkeeping
+    int getNAtomsInRow();
+    int getTopologicalDistance(int atom1, int atom2);
+    vector<int> getExcludesForAtom(int atom1); 
+    bool skipAtomPair(int atom1, int atom2);
+    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);
+    void unpackInteractionData(InteractionData &idat, int atom1, int atom2);
+
   private: 
-    SnapshotManager* sman_;    
+    void createGtypeCutoffMap();
+
+    int nLocal_;
+    int nGroups_;
+    vector<int> AtomLocalToGlobal;
+    vector<int> cgLocalToGlobal;
+    vector<RealType> groupCutoff;
+    vector<int> groupToGtype;
+
 #ifdef IS_MPI    
-    Communicator<Row, int>* AtomCommIntI;
-    Communicator<Row, RealType>* AtomCommRealI; 
-    Communicator<Row, Vector3d>* AtomCommVectorI; 
-    Communicator<Row, Mat3x3d>*  AtomCommMatrixI; 
+    DataStorage atomRowData;    DataStorage atomColData;
+    DataStorage cgRowData;
+    DataStorage cgColData;
 
-    Communicator<Column, int>* AtomCommIntJ;
-    Communicator<Column, RealType>* AtomCommRealJ; 
-    Communicator<Column, Vector3d>* AtomCommVectorJ; 
-    Communicator<Column, Mat3x3d>*  AtomCommMatrixJ; 
+    int nAtomsInRow_; 
+    int nAtomsInCol_;
+    int nGroupsInRow_;
+    int nGroupsInCol_;
 
-    Communicator<Row, int>* cgCommIntI;
-    Communicator<Row, Vector3d>* cgCommVectorI; 
-    Communicator<Column, int>* cgCommIntJ;
-    Communicator<Column, Vector3d>* cgCommVectorJ; 
+    Communicator<Row> rowComm;
+    Communicator<Column> colComm;
 
-    vector<vector<RealType> > pot_row;
-    vector<vector<RealType> > pot_col;
-    vector<int> identRow;
-    vector<int> identCol;
+    Plan<int>* AtomPlanIntRow;
+    Plan<RealType>* AtomPlanRealRow; 
+    Plan<Vector3d>* AtomPlanVectorRow; 
+    Plan<Mat3x3d>*  AtomPlanMatrixRow; 
+    Plan<potVec>* AtomPlanPotRow;
 
-    vector<int> AtomLocalToGlobal;
+    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;
+
+    vector<int> identsRow;
+    vector<int> identsCol;
+
+    vector<AtomType*> atypesRow;
+    vector<AtomType*> atypesCol;
+
     vector<int> AtomRowToGlobal;
     vector<int> AtomColToGlobal;
-    vector<int> cgLocalToGlobal;
+
+public:
     vector<int> cgRowToGlobal;
     vector<int> cgColToGlobal;
+
+private:
+    vector<RealType> groupCutoffRow;
+    vector<RealType> groupCutoffCol;
+    vector<int> groupColToGtype;
+    vector<int> groupRowToGtype;
+
+    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;
+
   };
 
 }