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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 1579 by gezelter, Thu Jun 9 20:26:29 2011 UTC vs.
branches/devel_omp/src/parallel/ForceDecomposition.hpp (file contents), Revision 1614 by mciznick, Tue Aug 23 20:55:51 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 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> getSkipsForAtom(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;
135 –    virtual int getTopologicalDistance(int atom1, int atom2) = 0;
141  
142      // filling interaction blocks with pointers
143 <    virtual InteractionData fillInteractionData(int atom1, int atom2) = 0;
144 <    virtual void unpackInteractionData(InteractionData idat, int atom1, int atom2) = 0;
145 <    virtual InteractionData fillSkipData(int atom1, int atom2) = 0;
146 <    virtual SelfData fillSelfData(int atom1);
143 >    virtual void fillInteractionData(InteractionData &idat, int atom1, int atom2) = 0;
144 >    virtual void fillInteractionDataOMP(InteractionDataPrv &idat, int atom1, int atom2) = 0;
145 >    virtual void unpackInteractionData(InteractionData &idat, int atom1, int atom2) = 0;
146 >
147 >    virtual void unpackInteractionDataOMP(InteractionDataPrv &idat, int atom1, int atom2) = 0;
148 >
149 >    virtual void fillSelfData(SelfData &sdat, int atom1);
150      
151    protected:
152      SimInfo* info_;  
# Line 151 | Line 159 | namespace OpenMD {
159      RealType skinThickness_;   /**< Verlet neighbor list skin thickness */    
160      RealType largestRcut_;
161  
162 +    vector<int> idents;
163 +    potVec pairwisePot;
164 +    potVec embeddingPot;
165 +
166      /**
167       * The topological distance between two atomic sites is handled
168       * via two vector structures for speed.  These structures agnostic
# Line 160 | Line 172 | namespace OpenMD {
172       * method to fill these.
173       */
174      vector<vector<int> > toposForAtom;
175 <    vector<vector<int> > topoDist;
176 <                                      
165 <    vector<vector<int> > skipsForAtom;
166 <
175 >    vector<vector<int> > topoDist;                                      
176 >    vector<vector<int> > excludesForAtom;
177      vector<vector<int> > groupList_;
178 +    vector<RealType> massFactors;
179 +    vector<AtomType*> atypesLocal;
180  
181      vector<Vector3i> cellOffsets_;
182 +    vector<Vector3i> cellAllOffsets_;
183      Vector3i nCells_;
184      vector<vector<int> > cellList_;
185      vector<Vector3d> saved_CG_positions_;
173 –    potVec longRangePot_;
186  
187      bool userChoseCutoff_;
188      RealType userCutoff_;

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