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root/OpenMD/branches/devel_omp/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.
branches/devel_omp/src/parallel/ForceDecomposition.hpp (file contents), Revision 1608 by mciznick, Tue Aug 9 01:58:56 2011 UTC

# Line 48 | Line 48
48   #include "nonbonded/Cutoffs.hpp"
49   #include "nonbonded/InteractionManager.hpp"
50   #include "utils/Tuple.hpp"
51 + #include "primitives/Molecule.hpp"
52  
53   using namespace std;
54   namespace OpenMD {
# Line 91 | Line 92 | namespace OpenMD {
92    class ForceDecomposition {
93    public:
94  
95 <    ForceDecomposition(SimInfo* info);
95 >    ForceDecomposition(SimInfo* info, InteractionManager* iMan);
96      virtual ~ForceDecomposition() {}
97      
98      virtual void distributeInitialData() = 0;
# Line 100 | Line 101 | namespace OpenMD {
101      virtual void collectIntermediateData() = 0;
102      virtual void distributeIntermediateData() = 0;
103      virtual void collectData() = 0;
104 <    virtual potVec getLongRangePotential() { return longRangePot_; }
104 >    virtual potVec* getEmbeddingPotential() { return &embeddingPot; }
105 >    virtual potVec* getPairwisePotential() { return &pairwisePot; }
106  
107      // neighbor list routines
108      virtual bool checkNeighborList();
109      virtual vector<pair<int, int> >  buildNeighborList() = 0;
110 +    virtual vector<vector<CutoffGroup *> >  buildLayerBasedNeighborList() = 0;
111  
112      // how to handle cutoffs:
113      void setCutoffPolicy(CutoffPolicy cp) {cutoffPolicy_ = cp;}
# Line 124 | Line 127 | namespace OpenMD {
127  
128      // spatial data
129      virtual Vector3d getIntergroupVector(int cg1, int cg2) = 0;
130 +    virtual Vector3d getIntergroupVector(CutoffGroup *cg1, CutoffGroup *cg2) = 0;
131      virtual Vector3d getInteratomicVector(int atom1, int atom2) = 0;
132        
133      // atom bookkeeping
134      virtual int getNAtomsInRow() = 0;
135 <    virtual vector<int> getSkipsForRowAtom(int atom1) = 0;
135 >    virtual vector<int> getExcludesForAtom(int atom1) = 0;
136      virtual bool skipAtomPair(int atom1, int atom2) = 0;
137 +    virtual bool excludeAtomPair(int atom1, int atom2) = 0;
138 +    virtual int getTopologicalDistance(int atom1, int atom2) = 0;
139      virtual void addForceToAtomRow(int atom1, Vector3d fg) = 0;
140      virtual void addForceToAtomColumn(int atom2, Vector3d fg) = 0;
141  
142 +    virtual void addForceToAtomRowOMP(int atom1, Vector3d fg) = 0;
143 +    virtual void addForceToAtomColumnOMP(int atom2, Vector3d fg) = 0;
144 +
145 +
146      // filling interaction blocks with pointers
147 <    virtual InteractionData fillInteractionData(int atom1, int atom2) = 0;
148 <    virtual void unpackInteractionData(InteractionData idat, int atom1, int atom2) = 0;
149 <    virtual InteractionData fillSkipData(int atom1, int atom2) = 0;
150 <    virtual SelfData fillSelfData(int atom1);
147 >    virtual void fillInteractionData(InteractionData &idat, int atom1, int atom2) = 0;
148 >    virtual void fillInteractionDataOMP(InteractionDataPrv &idat, int atom1, int atom2) = 0;
149 >    virtual void unpackInteractionData(InteractionData &idat, int atom1, int atom2) = 0;
150 >
151 >    virtual void unpackInteractionDataOMP(InteractionDataPrv &idat, int atom1, int atom2) = 0;
152 >
153 >    virtual void fillSelfData(SelfData &sdat, int atom1);
154      
155    protected:
156      SimInfo* info_;  
# Line 150 | Line 163 | namespace OpenMD {
163      RealType skinThickness_;   /**< Verlet neighbor list skin thickness */    
164      RealType largestRcut_;
165  
166 <    map<pair<int, int>, int> topoDist; //< topoDist gives the
167 <                                       //topological distance between
168 <                                       //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.
166 >    vector<int> idents;
167 >    potVec pairwisePot;
168 >    potVec embeddingPot;
169  
170 +    /**
171 +     * The topological distance between two atomic sites is handled
172 +     * via two vector structures for speed.  These structures agnostic
173 +     * regarding the parallel decomposition.  The index for
174 +     * toposForAtom could be local or row, while the values could be
175 +     * local or column.  It will be up to the specific decomposition
176 +     * method to fill these.
177 +     */
178 +    vector<vector<int> > toposForAtom;
179 +    vector<vector<int> > topoDist;                                      
180 +    vector<vector<int> > excludesForAtom;
181      vector<vector<int> > groupList_;
182 +    vector<RealType> massFactors;
183 +    vector<AtomType*> atypesLocal;
184  
185      vector<Vector3i> cellOffsets_;
186 +    vector<Vector3i> cellAllOffsets_;
187      Vector3i nCells_;
188      vector<vector<int> > cellList_;
189      vector<Vector3d> saved_CG_positions_;
180 –    potVec longRangePot_;
190  
191      bool userChoseCutoff_;
192      RealType userCutoff_;

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