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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 1665 by gezelter, Tue Nov 22 20:38:56 2011 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 129 | Line 130 | namespace OpenMD {
130        
131      // atom bookkeeping
132      virtual int getNAtomsInRow() = 0;
133 <    virtual vector<int> getSkipsForAtom(int atom1) = 0;
133 >    virtual vector<int> getExcludesForAtom(int atom1) = 0;
134      virtual bool skipAtomPair(int atom1, int atom2) = 0;
135 +    virtual bool excludeAtomPair(int atom1, int atom2) = 0;
136 +    virtual int getTopologicalDistance(int atom1, int atom2) = 0;
137      virtual void addForceToAtomRow(int atom1, Vector3d fg) = 0;
138      virtual void addForceToAtomColumn(int atom2, Vector3d fg) = 0;
136 –    virtual int getTopologicalDistance(int atom1, int atom2) = 0;
139  
140 +
141      // filling interaction blocks with pointers
142      virtual void fillInteractionData(InteractionData &idat, int atom1, int atom2) = 0;
143      virtual void unpackInteractionData(InteractionData &idat, int atom1, int atom2) = 0;
144  
142 –    virtual void fillSkipData(InteractionData &idat, int atom1, int atom2) = 0;
143 –    virtual void unpackSkipData(InteractionData &idat, int atom1, int atom2) = 0;
145      virtual void fillSelfData(SelfData &sdat, int atom1);
146      
147    protected:
# Line 168 | Line 169 | namespace OpenMD {
169       */
170      vector<vector<int> > toposForAtom;
171      vector<vector<int> > topoDist;                                      
172 <    vector<vector<int> > skipsForAtom;
172 >    vector<vector<int> > excludesForAtom;
173      vector<vector<int> > groupList_;
174      vector<RealType> massFactors;
175 +    vector<AtomType*> atypesLocal;
176  
177      vector<Vector3i> cellOffsets_;
178      Vector3i nCells_;

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