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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 1579 by gezelter, Thu Jun 9 20:26:29 2011 UTC vs.
Revision 1756 by gezelter, Mon Jun 18 18:23:20 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 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 void collectSelfData() = 0;
105 >    virtual potVec* getEmbeddingPotential() { return &embeddingPot; }
106 >    virtual potVec* getPairwisePotential() { return &pairwisePot; }
107  
108      // neighbor list routines
109      virtual bool checkNeighborList();
# Line 112 | Line 115 | namespace OpenMD {
115  
116      // group bookkeeping
117      virtual groupCutoffs getGroupCutoffs(int cg1, int cg2) = 0;
118 +    virtual Vector3d getGroupVelocityColumn(int atom2) = 0;
119  
120      // Group->atom bookkeeping
121      virtual vector<int> getAtomsInGroupRow(int cg1) = 0;
# Line 128 | Line 132 | namespace OpenMD {
132        
133      // atom bookkeeping
134      virtual int getNAtomsInRow() = 0;
135 <    virtual vector<int> getSkipsForAtom(int atom1) = 0;
136 <    virtual bool skipAtomPair(int atom1, int atom2) = 0;
135 >    virtual vector<int> getExcludesForAtom(int atom1) = 0;
136 >    virtual bool skipAtomPair(int atom1, int atom2, int cg1, int cg2) = 0;
137 >    virtual bool excludeAtomPair(int atom1, int atom2) = 0;
138 >    virtual int getTopologicalDistance(int atom1, int atom2) = 0;
139      virtual void addForceToAtomRow(int atom1, Vector3d fg) = 0;
140      virtual void addForceToAtomColumn(int atom2, Vector3d fg) = 0;
141 <    virtual int getTopologicalDistance(int atom1, int atom2) = 0;
141 >    virtual Vector3d getAtomVelocityColumn(int atom2) = 0;
142  
143      // filling interaction blocks with pointers
144 <    virtual InteractionData fillInteractionData(int atom1, int atom2) = 0;
145 <    virtual void unpackInteractionData(InteractionData idat, int atom1, int atom2) = 0;
146 <    virtual InteractionData fillSkipData(int atom1, int atom2) = 0;
147 <    virtual SelfData fillSelfData(int atom1);
144 >    virtual void fillInteractionData(InteractionData &idat, int atom1, int atom2) = 0;
145 >    virtual void unpackInteractionData(InteractionData &idat, int atom1, int atom2) = 0;
146 >
147 >    virtual void fillSelfData(SelfData &sdat, int atom1);
148 >
149 >    virtual void addToHeatFlux(Vector3d hf);
150 >    virtual void setHeatFlux(Vector3d hf);
151      
152    protected:
153      SimInfo* info_;  
# Line 148 | Line 157 | namespace OpenMD {
157      InteractionManager* interactionMan_;
158  
159      int storageLayout_;
160 +    bool needVelocities_;
161      RealType skinThickness_;   /**< Verlet neighbor list skin thickness */    
162      RealType largestRcut_;
163  
164 +    vector<int> idents;
165 +    potVec pairwisePot;
166 +    potVec embeddingPot;
167 +
168      /**
169       * The topological distance between two atomic sites is handled
170       * via two vector structures for speed.  These structures agnostic
# Line 160 | Line 174 | namespace OpenMD {
174       * method to fill these.
175       */
176      vector<vector<int> > toposForAtom;
177 <    vector<vector<int> > topoDist;
178 <                                      
165 <    vector<vector<int> > skipsForAtom;
166 <
177 >    vector<vector<int> > topoDist;                                      
178 >    vector<vector<int> > excludesForAtom;
179      vector<vector<int> > groupList_;
180 +    vector<RealType> massFactors;
181 +    vector<AtomType*> atypesLocal;
182  
183      vector<Vector3i> cellOffsets_;
184      Vector3i nCells_;
185      vector<vector<int> > cellList_;
186      vector<Vector3d> saved_CG_positions_;
173 –    potVec longRangePot_;
187  
188      bool userChoseCutoff_;
189      RealType userCutoff_;

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