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Comparing branches/development/src/parallel/ForceDecomposition.hpp (file contents):
Revision 1576 by gezelter, Wed Jun 8 16:05:07 2011 UTC vs.
Revision 1723 by gezelter, Thu May 24 20:59:54 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 91 | 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;
# Line 100 | Line 101 | namespace OpenMD {
101      virtual void collectIntermediateData() = 0;
102      virtual void distributeIntermediateData() = 0;
103      virtual void collectData() = 0;
104 <    virtual potVec getLongRangePotential() { return longRangePot_; }
104 >    virtual potVec* getEmbeddingPotential() { return &embeddingPot; }
105 >    virtual potVec* getPairwisePotential() { return &pairwisePot; }
106  
107      // neighbor list routines
108      virtual bool checkNeighborList();
# Line 112 | Line 114 | namespace OpenMD {
114  
115      // group bookkeeping
116      virtual groupCutoffs getGroupCutoffs(int cg1, int cg2) = 0;
117 +    virtual Vector3d getGroupVelocityColumn(int atom2) = 0;
118  
119      // Group->atom bookkeeping
120      virtual vector<int> getAtomsInGroupRow(int cg1) = 0;
# Line 128 | Line 131 | namespace OpenMD {
131        
132      // atom bookkeeping
133      virtual int getNAtomsInRow() = 0;
134 <    virtual vector<int> getSkipsForRowAtom(int atom1) = 0;
134 >    virtual vector<int> getExcludesForAtom(int atom1) = 0;
135      virtual bool skipAtomPair(int atom1, int atom2) = 0;
136 +    virtual bool excludeAtomPair(int atom1, int atom2) = 0;
137 +    virtual int getTopologicalDistance(int atom1, int atom2) = 0;
138      virtual void addForceToAtomRow(int atom1, Vector3d fg) = 0;
139      virtual void addForceToAtomColumn(int atom2, Vector3d fg) = 0;
140 +    virtual Vector3d getAtomVelocityColumn(int atom2) = 0;
141  
142      // filling interaction blocks with pointers
143 <    virtual InteractionData fillInteractionData(int atom1, int atom2) = 0;
144 <    virtual void unpackInteractionData(InteractionData idat, int atom1, int atom2) = 0;
145 <    virtual InteractionData fillSkipData(int atom1, int atom2) = 0;
146 <    virtual SelfData fillSelfData(int atom1);
143 >    virtual void fillInteractionData(InteractionData &idat, int atom1, int atom2) = 0;
144 >    virtual void unpackInteractionData(InteractionData &idat, int atom1, int atom2) = 0;
145 >
146 >    virtual void fillSelfData(SelfData &sdat, int atom1);
147 >
148 >    virtual void addToHeatFlux(Vector3d hf);
149 >    virtual void setHeatFlux(Vector3d hf);
150      
151    protected:
152      SimInfo* info_;  
# Line 147 | Line 156 | namespace OpenMD {
156      InteractionManager* interactionMan_;
157  
158      int storageLayout_;
159 +    bool needVelocities_;
160      RealType skinThickness_;   /**< Verlet neighbor list skin thickness */    
161      RealType largestRcut_;
162  
163 <    map<pair<int, int>, int> topoDist; //< topoDist gives the
164 <                                       //topological distance between
165 <                                       //two atomic sites.  This
156 <                                       //declaration is agnostic
157 <                                       //regarding the parallel
158 <                                       //decomposition.  The two
159 <                                       //indices could be local or row
160 <                                       //& column.  It will be up to
161 <                                       //the specific decomposition
162 <                                       //method to fill this.
163 <    map<pair<int, int>, bool> exclude; //< exclude is the set of pairs
164 <                                       //to leave out of non-bonded
165 <                                       //force evaluations.  This
166 <                                       //declaration is agnostic
167 <                                       //regarding the parallel
168 <                                       //decomposition.  The two
169 <                                       //indices could be local or row
170 <                                       //& column.  It will be up to
171 <                                       //the specific decomposition
172 <                                       //method to fill this.
163 >    vector<int> idents;
164 >    potVec pairwisePot;
165 >    potVec embeddingPot;
166  
167 +    /**
168 +     * The topological distance between two atomic sites is handled
169 +     * via two vector structures for speed.  These structures agnostic
170 +     * regarding the parallel decomposition.  The index for
171 +     * toposForAtom could be local or row, while the values could be
172 +     * local or column.  It will be up to the specific decomposition
173 +     * method to fill these.
174 +     */
175 +    vector<vector<int> > toposForAtom;
176 +    vector<vector<int> > topoDist;                                      
177 +    vector<vector<int> > excludesForAtom;
178      vector<vector<int> > groupList_;
179 +    vector<RealType> massFactors;
180 +    vector<AtomType*> atypesLocal;
181  
182      vector<Vector3i> cellOffsets_;
183      Vector3i nCells_;
184      vector<vector<int> > cellList_;
185      vector<Vector3d> saved_CG_positions_;
180 –    potVec longRangePot_;
186  
187      bool userChoseCutoff_;
188      RealType userCutoff_;

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