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Comparing branches/development/src/parallel/ForceDecomposition.hpp (file contents):
Revision 1569 by gezelter, Thu May 26 13:55:04 2011 UTC vs.
Revision 1760 by gezelter, Thu Jun 21 19:26:46 2012 UTC

# Line 36 | Line 36
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).                        
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
# Line 45 | Line 46
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 78 | 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 86 | Line 96 | namespace OpenMD {
96    class ForceDecomposition {
97    public:
98  
99 <    ForceDecomposition(SimInfo* 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  
113      // neighbor list routines
114      virtual bool checkNeighborList();
115      virtual vector<pair<int, int> >  buildNeighborList() = 0;
116  
117 +    // how to handle cutoffs:
118 +    void setCutoffPolicy(CutoffPolicy cp) {cutoffPolicy_ = cp;}
119 +    void setUserCutoff(RealType rcut) {userCutoff_ = rcut; userChoseCutoff_ = true; }
120 +
121      // group bookkeeping
122 <    virtual pair<int, int> getGroupTypes(int cg1, int cg2) = 0;
122 >    virtual groupCutoffs getGroupCutoffs(int cg1, int cg2) = 0;
123 >    virtual Vector3d getGroupVelocityColumn(int atom2) = 0;
124  
125      // Group->atom bookkeeping
126      virtual vector<int> getAtomsInGroupRow(int cg1) = 0;
# Line 116 | Line 136 | namespace OpenMD {
136      virtual Vector3d getInteratomicVector(int atom1, int atom2) = 0;
137        
138      // atom bookkeeping
139 <    virtual vector<int> getAtomList() = 0;
140 <    virtual vector<int> getSkipsForAtom(int atom1) = 0;
141 <    virtual bool skipAtomPair(int atom1, int atom2) = 0;
139 >    virtual int getNAtomsInRow() = 0;
140 >    virtual vector<int> getExcludesForAtom(int atom1) = 0;
141 >    virtual bool skipAtomPair(int atom1, int atom2, int cg1, int cg2) = 0;
142 >    virtual bool excludeAtomPair(int atom1, int atom2) = 0;
143 >    virtual int getTopologicalDistance(int atom1, int atom2) = 0;
144      virtual void addForceToAtomRow(int atom1, Vector3d fg) = 0;
145      virtual void addForceToAtomColumn(int atom2, Vector3d fg) = 0;
146 +    virtual Vector3d getAtomVelocityColumn(int atom2) = 0;
147  
148      // filling interaction blocks with pointers
149 <    virtual InteractionData fillInteractionData(int atom1, int atom2) = 0;
150 <    virtual InteractionData fillSkipData(int atom1, int atom2) = 0;
151 <    virtual SelfData fillSelfData(int atom1);
149 >    virtual void fillInteractionData(InteractionData &idat, int atom1, int atom2) = 0;
150 >    virtual void unpackInteractionData(InteractionData &idat, int atom1, int atom2) = 0;
151 >
152 >    virtual void fillSelfData(SelfData &sdat, int atom1);
153 >
154 >    virtual void addToHeatFlux(Vector3d hf);
155 >    virtual void setHeatFlux(Vector3d hf);
156      
157    protected:
158      SimInfo* info_;  
159      SnapshotManager* sman_;    
160      Snapshot* snap_;
161 +    ForceField* ff_;
162 +    InteractionManager* interactionMan_;
163 +
164      int storageLayout_;
165 +    bool needVelocities_;
166      RealType skinThickness_;   /**< Verlet neighbor list skin thickness */    
167 +    RealType largestRcut_;
168  
169 <    map<pair<int, int>, int> topoDist; //< topoDist gives the
170 <                                       //topological distance between
171 <                                       //two atomic sites.  This
172 <                                       //declaration is agnostic
141 <                                       //regarding the parallel
142 <                                       //decomposition.  The two
143 <                                       //indices could be local or row
144 <                                       //& column.  It will be up to
145 <                                       //the specific decomposition
146 <                                       //method to fill this.
147 <    map<pair<int, int>, bool> exclude; //< exclude is the set of pairs
148 <                                       //to leave out of non-bonded
149 <                                       //force evaluations.  This
150 <                                       //declaration is agnostic
151 <                                       //regarding the parallel
152 <                                       //decomposition.  The two
153 <                                       //indices could be local or row
154 <                                       //& column.  It will be up to
155 <                                       //the specific decomposition
156 <                                       //method to fill this.
169 >    vector<int> idents;
170 >    potVec pairwisePot;
171 >    potVec embeddingPot;
172 >    potVec excludedPot;
173  
174 +    /**
175 +     * The topological distance between two atomic sites is handled
176 +     * via two vector structures for speed.  These structures agnostic
177 +     * regarding the parallel decomposition.  The index for
178 +     * toposForAtom could be local or row, while the values could be
179 +     * local or column.  It will be up to the specific decomposition
180 +     * method to fill these.
181 +     */
182 +    vector<vector<int> > toposForAtom;
183 +    vector<vector<int> > topoDist;                                      
184 +    vector<vector<int> > excludesForAtom;
185      vector<vector<int> > groupList_;
186 +    vector<RealType> massFactors;
187 +    vector<AtomType*> atypesLocal;
188 +
189      vector<Vector3i> cellOffsets_;
190      Vector3i nCells_;
191      vector<vector<int> > cellList_;
192      vector<Vector3d> saved_CG_positions_;
193  
194 +    bool userChoseCutoff_;
195 +    RealType userCutoff_;
196 +    CutoffPolicy cutoffPolicy_;
197 +
198 +    map<pair<int, int>, tuple3<RealType, RealType, RealType> > gTypeCutoffMap;
199 +
200    };    
201   }
202   #endif

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