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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 1549 by gezelter, Wed Apr 27 18:38:15 2011 UTC vs.
trunk/src/parallel/ForceDecomposition.hpp (file contents), Revision 1896 by gezelter, Tue Jul 2 20:02:31 2013 UTC

# Line 35 | Line 35
35   *                                                                      
36   * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).            
37   * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
38 < * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
39 < * [4]  Vardeman & Gezelter, in progress (2009).                        
38 > * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
39 > * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40 > * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
42  
43   #ifndef PARALLEL_FORCEDECOMPOSITION_HPP
44   #define PARALLEL_FORCEDECOMPOSITION_HPP
45  
46   #include "brains/SimInfo.hpp"
47 + #include "brains/SnapshotManager.hpp"
48   #include "nonbonded/NonBondedInteraction.hpp"
49 + #include "nonbonded/Cutoffs.hpp"
50 + #include "nonbonded/InteractionManager.hpp"
51 + #include "utils/Tuple.hpp"
52  
53   using namespace std;
54   namespace OpenMD {
55    
56 +  typedef tuple3<RealType, RealType, RealType> groupCutoffs;
57 +
58    /**
59     * @class ForceDecomposition
60     *
# Line 77 | Line 84 | namespace OpenMD {
84     *  |  endif
85     *  end
86     * collectData                        (parallel communication)
87 +   * loop over i
88 +   * | localComputation
89 +   * end
90 +   * collectSelfData                    (parallel communication)
91     *
92     * ForceDecomposition provides the interface for ForceLoop to do the
93     * communication steps and to iterate using the correct set of atoms
# Line 85 | Line 96 | namespace OpenMD {
96    class ForceDecomposition {
97    public:
98  
99 <    ForceDecomposition(SimInfo* info) : info_(info) {}
99 >    ForceDecomposition(SimInfo* info, InteractionManager* iMan);
100      virtual ~ForceDecomposition() {}
101      
102      virtual void distributeInitialData() = 0;
103      virtual void distributeData() = 0;
104 +    virtual void zeroWorkArrays() = 0;
105      virtual void collectIntermediateData() = 0;
106      virtual void distributeIntermediateData() = 0;
107      virtual void collectData() = 0;
108 +    virtual void collectSelfData() = 0;
109 +    virtual potVec* getEmbeddingPotential() { return &embeddingPot; }
110 +    virtual potVec* getPairwisePotential() { return &pairwisePot; }
111 +    virtual potVec* getExcludedPotential() { return &excludedPot; }
112 +    virtual potVec* getExcludedSelfPotential() { return &excludedSelfPot; }
113  
114      // neighbor list routines
115 <    virtual bool checkNeighborList() = 0;
116 <    virtual vector<pair<int, int> >  buildNeighborList() = 0;
115 >    virtual bool checkNeighborList();
116 >    virtual void buildNeighborList(vector<pair<int, int> >& neighborList) = 0;
117  
118 +    // how to handle cutoffs:
119 +    void setCutoffPolicy(CutoffPolicy cp) {cutoffPolicy_ = cp;}
120 +    void setUserCutoff(RealType rcut) {userCutoff_ = rcut; userChoseCutoff_ = true; }
121 +
122      // group bookkeeping
123 <    virtual pair<int, int> getGroupTypes(int cg1, int cg2) = 0;
123 >    virtual void getGroupCutoffs(int &cg1, int &cg2, RealType &rcut, RealType &rcutsq, RealType &rlistsq) = 0;
124 >    virtual Vector3d& getGroupVelocityColumn(int atom2) = 0;
125  
126      // Group->atom bookkeeping
127 <    virtual vector<int> getAtomsInGroupRow(int cg1) = 0;
128 <    virtual vector<int> getAtomsInGroupColumn(int cg2) = 0;
127 >    virtual vector<int>& getAtomsInGroupRow(int cg1) = 0;
128 >    virtual vector<int>& getAtomsInGroupColumn(int cg2) = 0;
129 >
130      virtual Vector3d getAtomToGroupVectorRow(int atom1, int cg1) = 0;
131      virtual Vector3d getAtomToGroupVectorColumn(int atom2, int cg2) = 0;
132 <    virtual RealType getMfactRow(int atom1) = 0;
133 <    virtual RealType getMfactColumn(int atom2) = 0;
132 >    virtual RealType& getMassFactorRow(int atom1) = 0;
133 >    virtual RealType& getMassFactorColumn(int atom2) = 0;
134  
135      // spatial data
136      virtual Vector3d getIntergroupVector(int cg1, int cg2) = 0;
137      virtual Vector3d getInteratomicVector(int atom1, int atom2) = 0;
138        
139      // atom bookkeeping
140 <    virtual vector<int> getAtomList() = 0;
141 <    virtual vector<int> getSkipsForAtom(int atom1) = 0;
142 <    virtual bool skipAtomPair(int atom1, int atom2) = 0;
140 >    virtual int& getNAtomsInRow() = 0;
141 >    virtual vector<int>& getExcludesForAtom(int atom1) = 0;
142 >    virtual bool skipAtomPair(int atom1, int atom2, int cg1, int cg2) = 0;
143 >    virtual bool excludeAtomPair(int atom1, int atom2) = 0;
144 >    virtual int getTopologicalDistance(int atom1, int atom2) = 0;
145      virtual void addForceToAtomRow(int atom1, Vector3d fg) = 0;
146      virtual void addForceToAtomColumn(int atom2, Vector3d fg) = 0;
147 +    virtual Vector3d& getAtomVelocityColumn(int atom2) = 0;
148  
149      // filling interaction blocks with pointers
150 <    virtual InteractionData fillInteractionData(int atom1, int atom2) = 0;
151 <    virtual InteractionData fillSkipData(int atom1, int atom2) = 0;
152 <    virtual SelfData fillSelfData(int atom1) = 0;
150 >    virtual void fillInteractionData(InteractionData &idat, int atom1, int atom2) = 0;
151 >    virtual void unpackInteractionData(InteractionData &idat, int atom1, int atom2) = 0;
152 >
153 >    virtual void fillSelfData(SelfData &sdat, int atom1);
154 >
155 >    virtual void addToHeatFlux(Vector3d hf);
156 >    virtual void setHeatFlux(Vector3d hf);
157      
158    protected:
159      SimInfo* info_;  
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
179 <                                       //method to fill this.
160 >    SnapshotManager* sman_;    
161 >    Snapshot* snap_;
162 >    ForceField* ff_;
163 >    InteractionManager* interactionMan_;
164 >
165 >    int storageLayout_;
166 >    bool needVelocities_;
167 >    bool usePeriodicBoundaryConditions_;
168 >    RealType skinThickness_;   /**< Verlet neighbor list skin thickness */    
169 >    RealType largestRcut_;
170 >
171 >    vector<int> idents;
172 >    potVec pairwisePot;
173 >    potVec embeddingPot;
174 >    potVec excludedPot;
175 >    potVec excludedSelfPot;
176 >
177 >    /**
178 >     * The topological distance between two atomic sites is handled
179 >     * via two vector structures for speed.  These structures agnostic
180 >     * regarding the parallel decomposition.  The index for
181 >     * toposForAtom could be local or row, while the values could be
182 >     * local or column.  It will be up to the specific decomposition
183 >     * method to fill these.
184 >     */
185 >    vector<vector<int> > toposForAtom;
186 >    vector<vector<int> > topoDist;                                      
187 >    vector<vector<int> > excludesForAtom;
188 >    vector<vector<int> > groupList_;
189 >    vector<RealType> massFactors;
190 >    vector<AtomType*> atypesLocal;
191 >
192 >    vector<Vector3i> cellOffsets_;
193 >    Vector3i nCells_;
194 >    vector<vector<int> > cellList_;
195 >    vector<Vector3d> saved_CG_positions_;
196 >
197 >    bool userChoseCutoff_;
198 >    RealType userCutoff_;
199 >    CutoffPolicy cutoffPolicy_;
200 >
201 >    //map<pair<int, int>, tuple3<RealType, RealType, RealType> > gTypeCutoffMap;
202 >    vector<vector<RealType> > GrCut;
203 >    vector<vector<RealType> > GrCutSq;
204 >    vector<vector<RealType> > GrlistSq;
205 >
206    };    
207   }
208   #endif

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