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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 1583 by gezelter, Thu Jun 16 22:00:08 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 83 | 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 100 | Line 105 | namespace OpenMD {
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();
# Line 113 | Line 120 | namespace OpenMD {
120  
121      // group bookkeeping
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 129 | Line 137 | namespace OpenMD {
137        
138      // atom bookkeeping
139      virtual int getNAtomsInRow() = 0;
140 <    virtual vector<int> getSkipsForAtom(int atom1) = 0;
141 <    virtual bool skipAtomPair(int atom1, int atom2) = 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 int getTopologicalDistance(int atom1, int atom2) = 0;
146 >    virtual Vector3d getAtomVelocityColumn(int atom2) = 0;
147  
148      // filling interaction blocks with pointers
149      virtual void fillInteractionData(InteractionData &idat, int atom1, int atom2) = 0;
150      virtual void unpackInteractionData(InteractionData &idat, int atom1, int atom2) = 0;
151  
142 –    virtual void fillSkipData(InteractionData &idat, int atom1, int atom2) = 0;
143 –    virtual void unpackSkipData(InteractionData &idat, int atom1, int atom2) = 0;
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_;  
# Line 151 | Line 162 | namespace OpenMD {
162      InteractionManager* interactionMan_;
163  
164      int storageLayout_;
165 +    bool needVelocities_;
166      RealType skinThickness_;   /**< Verlet neighbor list skin thickness */    
167      RealType largestRcut_;
168  
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
# Line 168 | Line 181 | namespace OpenMD {
181       */
182      vector<vector<int> > toposForAtom;
183      vector<vector<int> > topoDist;                                      
184 <    vector<vector<int> > skipsForAtom;
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_;

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