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root/OpenMD/branches/devel_omp/src/parallel/ForceDecomposition.hpp
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branches/development/src/parallel/ForceDecomposition.hpp (file contents), Revision 1568 by gezelter, Wed May 25 16:20:37 2011 UTC vs.
branches/devel_omp/src/parallel/ForceDecomposition.hpp (file contents), Revision 1598 by mciznick, Wed Jul 27 14:26:53 2011 UTC

# Line 45 | Line 45
45   #include "brains/SimInfo.hpp"
46   #include "brains/SnapshotManager.hpp"
47   #include "nonbonded/NonBondedInteraction.hpp"
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 {
55    
56 +  typedef tuple3<RealType, RealType, RealType> groupCutoffs;
57 +
58    /**
59     * @class ForceDecomposition
60     *
# Line 86 | 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;
99      virtual void distributeData() = 0;
100 +    virtual void zeroWorkArrays() = 0;
101      virtual void collectIntermediateData() = 0;
102      virtual void distributeIntermediateData() = 0;
103      virtual void collectData() = 0;
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;}
114 +    void setUserCutoff(RealType rcut) {userCutoff_ = rcut; userChoseCutoff_ = true; }
115 +
116      // group bookkeeping
117 <    virtual pair<int, int> getGroupTypes(int cg1, int cg2) = 0;
117 >    virtual groupCutoffs getGroupCutoffs(int cg1, int cg2) = 0;
118  
119      // Group->atom bookkeeping
120 <    virtual vector<int> getAtomsInGroupRow(int cg1) = 0;
120 >    virtual vector<int> getAtomsInGroupRow(int cg1) = 0;
121      virtual vector<int> getAtomsInGroupColumn(int cg2) = 0;
122 +
123      virtual Vector3d getAtomToGroupVectorRow(int atom1, int cg1) = 0;
124      virtual Vector3d getAtomToGroupVectorColumn(int atom2, int cg2) = 0;
125 <    virtual RealType getMfactRow(int atom1) = 0;
126 <    virtual RealType getMfactColumn(int atom2) = 0;
125 >    virtual RealType getMassFactorRow(int atom1) = 0;
126 >    virtual RealType getMassFactorColumn(int atom2) = 0;
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 vector<int> getAtomList() = 0;
135 <    virtual vector<int> getSkipsForAtom(int atom1) = 0;
134 >    virtual int getNAtomsInRow() = 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 +
143      // filling interaction blocks with pointers
144 <    virtual InteractionData fillInteractionData(int atom1, int atom2) = 0;
145 <    virtual InteractionData fillSkipData(int atom1, int atom2) = 0;
146 <    virtual SelfData fillSelfData(int atom1);
144 >    virtual void fillInteractionData(InteractionData &idat, int atom1, int atom2) = 0;
145 >    virtual void unpackInteractionData(InteractionData &idat, int atom1, int atom2) = 0;
146 >
147 >    virtual void fillSelfData(SelfData &sdat, int atom1);
148      
149    protected:
150      SimInfo* info_;  
151      SnapshotManager* sman_;    
152      Snapshot* snap_;
153 +    ForceField* ff_;
154 +    InteractionManager* interactionMan_;
155 +
156      int storageLayout_;
157      RealType skinThickness_;   /**< Verlet neighbor list skin thickness */    
158 +    RealType largestRcut_;
159  
160 <    map<pair<int, int>, int> topoDist; //< topoDist gives the
161 <                                       //topological distance between
162 <                                       //two atomic sites.  This
163 <                                       //declaration is agnostic
164 <                                       //regarding the parallel
165 <                                       //decomposition.  The two
166 <                                       //indices could be local or row
167 <                                       //& column.  It will be up to
168 <                                       //the specific decomposition
169 <                                       //method to fill this.
170 <    map<pair<int, int>, bool> exclude; //< exclude is the set of pairs
171 <                                       //to leave out of non-bonded
172 <                                       //force evaluations.  This
173 <                                       //declaration is agnostic
174 <                                       //regarding the parallel
175 <                                       //decomposition.  The two
176 <                                       //indices could be local or row
177 <                                       //& column.  It will be up to
178 <                                       //the specific decomposition
155 <                                       //method to fill this.
160 >    vector<int> idents;
161 >    potVec pairwisePot;
162 >    potVec embeddingPot;
163 >
164 >    /**
165 >     * The topological distance between two atomic sites is handled
166 >     * via two vector structures for speed.  These structures agnostic
167 >     * regarding the parallel decomposition.  The index for
168 >     * toposForAtom could be local or row, while the values could be
169 >     * local or column.  It will be up to the specific decomposition
170 >     * method to fill these.
171 >     */
172 >    vector<vector<int> > toposForAtom;
173 >    vector<vector<int> > topoDist;                                      
174 >    vector<vector<int> > excludesForAtom;
175 >    vector<vector<int> > groupList_;
176 >    vector<RealType> massFactors;
177 >    vector<AtomType*> atypesLocal;
178 >
179      vector<Vector3i> cellOffsets_;
180 +    vector<Vector3i> cellAllOffsets_;
181      Vector3i nCells_;
182      vector<vector<int> > cellList_;
183      vector<Vector3d> saved_CG_positions_;
184  
185 +    bool userChoseCutoff_;
186 +    RealType userCutoff_;
187 +    CutoffPolicy cutoffPolicy_;
188 +
189 +    map<pair<int, int>, tuple3<RealType, RealType, RealType> > gTypeCutoffMap;
190 +
191    };    
192   }
193   #endif

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