--- branches/development/src/parallel/Decomposition.hpp	2011/04/10 15:16:39	1546
+++ branches/development/src/parallel/ForceDecomposition.hpp	2011/05/26 13:55:04	1569
@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
+ * Copyright (c) 2011 The University of Notre Dame. All Rights Reserved.
  *
  * The University of Notre Dame grants you ("Licensee") a
  * non-exclusive, royalty free, license to use, modify and
@@ -39,20 +39,23 @@
  * [4]  Vardeman & Gezelter, in progress (2009).                        
  */
  
-#ifndef PARALLEL_DECOMPOSITION_HPP
-#define PARALLEL_DECOMPOSITION_HPP
+#ifndef PARALLEL_FORCEDECOMPOSITION_HPP
+#define PARALLEL_FORCEDECOMPOSITION_HPP
 
 #include "brains/SimInfo.hpp"
+#include "brains/SnapshotManager.hpp"
 #include "nonbonded/NonBondedInteraction.hpp"
 
 using namespace std;
 namespace OpenMD {
   
   /**
-   * @class Decomposition 
-   * Decomposition is an interface for passing out and collecting information
-   * from many processors at various stages of the main non-bonded ForceLoop.
+   * @class ForceDecomposition 
    *
+   * ForceDecomposition is an interface for passing out and collecting
+   * information from many processors at various stages of the main
+   * non-bonded ForceLoop.
+   *
    * The pairwise force calculation has an outer-running loop (the "I"
    * loop) and an inner-running loop (the "J" loop).  In parallel
    * decompositions, these loop over different groups of atoms on
@@ -76,15 +79,15 @@ namespace OpenMD {
    *  end
    * collectData                        (parallel communication)
    *
-   * Decomposition provides the interface for ForceLoop to do the
+   * ForceDecomposition provides the interface for ForceLoop to do the
    * communication steps and to iterate using the correct set of atoms
    * and cutoff groups.
    */
-  class Decomposition {
+  class ForceDecomposition {
   public:
 
-    Decomposition(SimInfo* info) : info_(info) {}
-    virtual ~Decomposition() {}
+    ForceDecomposition(SimInfo* info);
+    virtual ~ForceDecomposition() {}
     
     virtual void distributeInitialData() = 0;
     virtual void distributeData() = 0;
@@ -93,20 +96,21 @@ namespace OpenMD {
     virtual void collectData() = 0;
 
     // neighbor list routines
-    virtual bool checkNeighborList() = 0;
+    virtual bool checkNeighborList();
     virtual vector<pair<int, int> >  buildNeighborList() = 0;
 
     // group bookkeeping
     virtual pair<int, int> getGroupTypes(int cg1, int cg2) = 0;
 
     // Group->atom bookkeeping
-    virtual vector<int> getAtomsInGroupI(int cg1) = 0;
-    virtual vector<int> getAtomsInGroupJ(int cg2) = 0;
-    virtual Vector3d getAtomToGroupVectorI(int atom1, int cg1) = 0;
-    virtual Vector3d getAtomToGroupVectorJ(int atom2, int cg2) = 0;
-    virtual RealType getMfactI(int atom1) = 0;
-    virtual RealType getMfactJ(int atom2) = 0;
+    virtual vector<int> getAtomsInGroupRow(int cg1) = 0; 
+    virtual vector<int> getAtomsInGroupColumn(int cg2) = 0;
 
+    virtual Vector3d getAtomToGroupVectorRow(int atom1, int cg1) = 0;
+    virtual Vector3d getAtomToGroupVectorColumn(int atom2, int cg2) = 0;
+    virtual RealType getMassFactorRow(int atom1) = 0;
+    virtual RealType getMassFactorColumn(int atom2) = 0;
+
     // spatial data
     virtual Vector3d getIntergroupVector(int cg1, int cg2) = 0;
     virtual Vector3d getInteratomicVector(int atom1, int atom2) = 0;
@@ -115,16 +119,21 @@ namespace OpenMD {
     virtual vector<int> getAtomList() = 0;
     virtual vector<int> getSkipsForAtom(int atom1) = 0;
     virtual bool skipAtomPair(int atom1, int atom2) = 0;
-    virtual void addForceToAtomI(int atom1, Vector3d fg) = 0;
-    virtual void addForceToAtomJ(int atom2, Vector3d fg) = 0;
+    virtual void addForceToAtomRow(int atom1, Vector3d fg) = 0;
+    virtual void addForceToAtomColumn(int atom2, Vector3d fg) = 0;
 
     // filling interaction blocks with pointers
     virtual InteractionData fillInteractionData(int atom1, int atom2) = 0;
     virtual InteractionData fillSkipData(int atom1, int atom2) = 0;
-    virtual SelfData fillSelfData(int atom1) = 0;
+    virtual SelfData fillSelfData(int atom1);
     
   protected:
     SimInfo* info_;   
+    SnapshotManager* sman_;    
+    Snapshot* snap_;
+    int storageLayout_;
+    RealType skinThickness_;   /**< Verlet neighbor list skin thickness */    
+
     map<pair<int, int>, int> topoDist; //< topoDist gives the
                                        //topological distance between
                                        //two atomic sites.  This
@@ -145,6 +154,13 @@ namespace OpenMD {
                                        //& column.  It will be up to
                                        //the specific decomposition
                                        //method to fill this.
+
+    vector<vector<int> > groupList_;
+    vector<Vector3i> cellOffsets_;
+    Vector3i nCells_;
+    vector<vector<int> > cellList_;
+    vector<Vector3d> saved_CG_positions_;
+
   };    
 }
 #endif