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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 1587 by gezelter, Fri Jul 8 20:25:32 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 void collectSelfData() = 0;
105      virtual potVec* getEmbeddingPotential() { return &embeddingPot; }
106      virtual potVec* getPairwisePotential() { return &pairwisePot; }
107  
# Line 113 | 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 130 | Line 133 | namespace OpenMD {
133      // atom bookkeeping
134      virtual int getNAtomsInRow() = 0;
135      virtual vector<int> getExcludesForAtom(int atom1) = 0;
136 <    virtual bool skipAtomPair(int atom1, int atom2) = 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 Vector3d getAtomVelocityColumn(int atom2) = 0;
142  
139 –
143      // filling interaction blocks with pointers
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 151 | 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  
# Line 171 | Line 178 | namespace OpenMD {
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_;

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