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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 1568 by gezelter, Wed May 25 16:20:37 2011 UTC vs.
Revision 1583 by gezelter, Thu Jun 16 22:00:08 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  
52   using namespace std;
53   namespace OpenMD {
54    
55 +  typedef tuple3<RealType, RealType, RealType> groupCutoffs;
56 +
57    /**
58     * @class ForceDecomposition
59     *
# Line 86 | 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;
98      virtual void distributeData() = 0;
99 +    virtual void zeroWorkArrays() = 0;
100      virtual void collectIntermediateData() = 0;
101      virtual void distributeIntermediateData() = 0;
102      virtual void collectData() = 0;
103 +    virtual potVec* getEmbeddingPotential() { return &embeddingPot; }
104 +    virtual potVec* getPairwisePotential() { return &pairwisePot; }
105  
106      // neighbor list routines
107      virtual bool checkNeighborList();
108      virtual vector<pair<int, int> >  buildNeighborList() = 0;
109  
110 +    // how to handle cutoffs:
111 +    void setCutoffPolicy(CutoffPolicy cp) {cutoffPolicy_ = cp;}
112 +    void setUserCutoff(RealType rcut) {userCutoff_ = rcut; userChoseCutoff_ = true; }
113 +
114      // group bookkeeping
115 <    virtual pair<int, int> getGroupTypes(int cg1, int cg2) = 0;
115 >    virtual groupCutoffs getGroupCutoffs(int cg1, int cg2) = 0;
116  
117      // Group->atom bookkeeping
118 <    virtual vector<int> getAtomsInGroupRow(int cg1) = 0;
118 >    virtual vector<int> getAtomsInGroupRow(int cg1) = 0;
119      virtual vector<int> getAtomsInGroupColumn(int cg2) = 0;
120 +
121      virtual Vector3d getAtomToGroupVectorRow(int atom1, int cg1) = 0;
122      virtual Vector3d getAtomToGroupVectorColumn(int atom2, int cg2) = 0;
123 <    virtual RealType getMfactRow(int atom1) = 0;
124 <    virtual RealType getMfactColumn(int atom2) = 0;
123 >    virtual RealType getMassFactorRow(int atom1) = 0;
124 >    virtual RealType getMassFactorColumn(int atom2) = 0;
125  
126      // spatial data
127      virtual Vector3d getIntergroupVector(int cg1, int cg2) = 0;
128      virtual Vector3d getInteratomicVector(int atom1, int atom2) = 0;
129        
130      // atom bookkeeping
131 <    virtual vector<int> getAtomList() = 0;
131 >    virtual int getNAtomsInRow() = 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 InteractionData fillSkipData(int atom1, int atom2) = 0;
141 <    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_;  
148      SnapshotManager* sman_;    
149      Snapshot* snap_;
150 +    ForceField* ff_;
151 +    InteractionManager* interactionMan_;
152 +
153      int storageLayout_;
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
160 <                                       //declaration is agnostic
161 <                                       //regarding the parallel
162 <                                       //decomposition.  The two
163 <                                       //indices could be local or row
164 <                                       //& column.  It will be up to
165 <                                       //the specific decomposition
166 <                                       //method to fill this.
167 <    map<pair<int, int>, bool> exclude; //< exclude is the set of pairs
168 <                                       //to leave out of non-bonded
169 <                                       //force evaluations.  This
170 <                                       //declaration is agnostic
171 <                                       //regarding the parallel
172 <                                       //decomposition.  The two
173 <                                       //indices could be local or row
174 <                                       //& column.  It will be up to
154 <                                       //the specific decomposition
155 <                                       //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_;
179  
180 +    bool userChoseCutoff_;
181 +    RealType userCutoff_;
182 +    CutoffPolicy cutoffPolicy_;
183 +
184 +    map<pair<int, int>, tuple3<RealType, RealType, RealType> > gTypeCutoffMap;
185 +
186    };    
187   }
188   #endif

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