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root/OpenMD/trunk/src/parallel/ForceDecomposition.hpp
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Comparing branches/development/src/parallel/ForceDecomposition.hpp (file contents):
Revision 1576 by gezelter, Wed Jun 8 16:05:07 2011 UTC vs.
Revision 1583 by gezelter, Thu Jun 16 22:00:08 2011 UTC

# Line 91 | Line 91 | namespace OpenMD {
91    class ForceDecomposition {
92    public:
93  
94 <    ForceDecomposition(SimInfo* info);
94 >    ForceDecomposition(SimInfo* info, InteractionManager* iMan);
95      virtual ~ForceDecomposition() {}
96      
97      virtual void distributeInitialData() = 0;
# Line 100 | Line 100 | namespace OpenMD {
100      virtual void collectIntermediateData() = 0;
101      virtual void distributeIntermediateData() = 0;
102      virtual void collectData() = 0;
103 <    virtual potVec getLongRangePotential() { return longRangePot_; }
103 >    virtual potVec* getEmbeddingPotential() { return &embeddingPot; }
104 >    virtual potVec* getPairwisePotential() { return &pairwisePot; }
105  
106      // neighbor list routines
107      virtual bool checkNeighborList();
# Line 128 | Line 129 | namespace OpenMD {
129        
130      // atom bookkeeping
131      virtual int getNAtomsInRow() = 0;
132 <    virtual vector<int> getSkipsForRowAtom(int atom1) = 0;
132 >    virtual vector<int> getSkipsForAtom(int atom1) = 0;
133      virtual bool skipAtomPair(int atom1, int atom2) = 0;
134      virtual void addForceToAtomRow(int atom1, Vector3d fg) = 0;
135      virtual void addForceToAtomColumn(int atom2, Vector3d fg) = 0;
136 +    virtual int getTopologicalDistance(int atom1, int atom2) = 0;
137  
138      // filling interaction blocks with pointers
139 <    virtual InteractionData fillInteractionData(int atom1, int atom2) = 0;
140 <    virtual void unpackInteractionData(InteractionData idat, int atom1, int atom2) = 0;
141 <    virtual InteractionData fillSkipData(int atom1, int atom2) = 0;
142 <    virtual SelfData fillSelfData(int atom1);
139 >    virtual void fillInteractionData(InteractionData &idat, int atom1, int atom2) = 0;
140 >    virtual void unpackInteractionData(InteractionData &idat, int atom1, int atom2) = 0;
141 >
142 >    virtual void fillSkipData(InteractionData &idat, int atom1, int atom2) = 0;
143 >    virtual void unpackSkipData(InteractionData &idat, int atom1, int atom2) = 0;
144 >    virtual void fillSelfData(SelfData &sdat, int atom1);
145      
146    protected:
147      SimInfo* info_;  
# Line 150 | Line 154 | namespace OpenMD {
154      RealType skinThickness_;   /**< Verlet neighbor list skin thickness */    
155      RealType largestRcut_;
156  
157 <    map<pair<int, int>, int> topoDist; //< topoDist gives the
158 <                                       //topological distance between
159 <                                       //two atomic sites.  This
156 <                                       //declaration is agnostic
157 <                                       //regarding the parallel
158 <                                       //decomposition.  The two
159 <                                       //indices could be local or row
160 <                                       //& column.  It will be up to
161 <                                       //the specific decomposition
162 <                                       //method to fill this.
163 <    map<pair<int, int>, bool> exclude; //< exclude is the set of pairs
164 <                                       //to leave out of non-bonded
165 <                                       //force evaluations.  This
166 <                                       //declaration is agnostic
167 <                                       //regarding the parallel
168 <                                       //decomposition.  The two
169 <                                       //indices could be local or row
170 <                                       //& column.  It will be up to
171 <                                       //the specific decomposition
172 <                                       //method to fill this.
157 >    vector<int> idents;
158 >    potVec pairwisePot;
159 >    potVec embeddingPot;
160  
161 +    /**
162 +     * The topological distance between two atomic sites is handled
163 +     * via two vector structures for speed.  These structures agnostic
164 +     * regarding the parallel decomposition.  The index for
165 +     * toposForAtom could be local or row, while the values could be
166 +     * local or column.  It will be up to the specific decomposition
167 +     * method to fill these.
168 +     */
169 +    vector<vector<int> > toposForAtom;
170 +    vector<vector<int> > topoDist;                                      
171 +    vector<vector<int> > skipsForAtom;
172      vector<vector<int> > groupList_;
173 +    vector<RealType> massFactors;
174  
175      vector<Vector3i> cellOffsets_;
176      Vector3i nCells_;
177      vector<vector<int> > cellList_;
178      vector<Vector3d> saved_CG_positions_;
180 –    potVec longRangePot_;
179  
180      bool userChoseCutoff_;
181      RealType userCutoff_;

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