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root/OpenMD/trunk/src/parallel/ForceMatrixDecomposition.hpp
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Comparing branches/development/src/parallel/ForceMatrixDecomposition.hpp (file contents):
Revision 1593 by gezelter, Fri Jul 15 21:35:14 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_FORCEMATRIXDECOMPOSITION_HPP
# Line 62 | Line 63 | namespace OpenMD {
63      void distributeData();
64      void collectIntermediateData();
65      void distributeIntermediateData();
66 +    void collectSelfData();
67      void collectData();
68  
69      // neighbor list routines
# Line 69 | Line 71 | namespace OpenMD {
71  
72      // group bookkeeping
73      groupCutoffs getGroupCutoffs(int cg1, int cg2);
74 +    Vector3d getGroupVelocityColumn(int cg2);
75  
76      // Group->atom bookkeeping
77      vector<int> getAtomsInGroupRow(int cg1);
# Line 86 | Line 89 | namespace OpenMD {
89      int getNAtomsInRow();
90      int getTopologicalDistance(int atom1, int atom2);
91      vector<int> getExcludesForAtom(int atom1);
92 <    bool skipAtomPair(int atom1, int atom2);
92 >    bool skipAtomPair(int atom1, int atom2, int cg1, int cg2);
93      bool excludeAtomPair(int atom1, int atom2);
94      void addForceToAtomRow(int atom1, Vector3d fg);
95      void addForceToAtomColumn(int atom2, Vector3d fg);
96 +    Vector3d getAtomVelocityColumn(int atom2);
97  
98      // filling interaction blocks with pointers
99      void fillInteractionData(InteractionData &idat, int atom1, int atom2);
# Line 106 | Line 110 | namespace OpenMD {
110      vector<int> groupToGtype;
111  
112   #ifdef IS_MPI    
113 <    DataStorage atomRowData;
110 <    DataStorage atomColData;
113 >    DataStorage atomRowData;    DataStorage atomColData;
114      DataStorage cgRowData;
115      DataStorage cgColData;
116  
# Line 149 | Line 152 | namespace OpenMD {
152      vector<int> AtomRowToGlobal;
153      vector<int> AtomColToGlobal;
154  
155 + public:
156      vector<int> cgRowToGlobal;
157      vector<int> cgColToGlobal;
158  
159 + private:
160      vector<RealType> groupCutoffRow;
161      vector<RealType> groupCutoffCol;
162      vector<int> groupColToGtype;

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