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root/OpenMD/trunk/src/parallel/ForceMatrixDecomposition.hpp
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Comparing trunk/src/parallel/ForceMatrixDecomposition.hpp (file contents):
Revision 1929 by gezelter, Mon Aug 19 13:12:00 2013 UTC vs.
Revision 2062 by gezelter, Tue Mar 3 16:40:39 2015 UTC

# Line 67 | Line 67 | namespace OpenMD {
67      void collectData();
68  
69      // neighbor list routines
70 <    void buildNeighborList(vector<pair<int, int> >& neighborList);
70 >    void buildNeighborList(vector<int>& neighborList, vector<int>& point);
71  
72      // group bookkeeping
73 –    void getGroupCutoffs(int &cg1, int &cg2, RealType &rcut, RealType &rcutsq, RealType &rlistsq);
73      Vector3d& getGroupVelocityColumn(int cg2);
74  
75      // Group->atom bookkeeping
# Line 82 | Line 81 | namespace OpenMD {
81      RealType& getMassFactorColumn(int atom2);
82  
83      // spatial data
84 <    Vector3d getIntergroupVector(int cg1, int cg2);
85 <    Vector3d getInteratomicVector(int atom1, int atom2);
84 >    inline Vector3d getIntergroupVector(int cg1, int cg2);
85 >    inline Vector3d getInteratomicVector(int atom1, int atom2);
86        
87      // atom bookkeeping
88      int& getNAtomsInRow();
# Line 96 | Line 95 | namespace OpenMD {
95      Vector3d& getAtomVelocityColumn(int atom2);
96  
97      // filling interaction blocks with pointers
98 <    void fillInteractionData(InteractionData &idat, int atom1, int atom2);
98 >    void fillInteractionData(InteractionData &idat, int atom1, int atom2, bool newAtom1 = true);
99      void unpackInteractionData(InteractionData &idat, int atom1, int atom2);
100  
101 <  private:
103 <    void createGtypeCutoffMap();
104 <
101 >  private:    
102      int nLocal_;
103      int nGroups_;
104      vector<int> AtomLocalToGlobal;
# Line 110 | Line 107 | namespace OpenMD {
107      vector<int> groupToGtype;
108  
109   #ifdef IS_MPI    
110 <    DataStorage atomRowData;    DataStorage atomColData;
110 >    DataStorage atomRowData;
111 >    DataStorage atomColData;
112      DataStorage cgRowData;
113      DataStorage cgColData;
114  
# Line 163 | Line 161 | namespace OpenMD {
161      vector<int> cgColToGlobal;
162  
163   private:
166 –    vector<RealType> groupCutoffRow;
167 –    vector<RealType> groupCutoffCol;
168 –    vector<int> groupColToGtype;
169 –    vector<int> groupRowToGtype;
170 –
164      vector<vector<int> > cellListRow_;
165      vector<vector<int> > cellListCol_;
166  
# Line 176 | Line 169 | namespace OpenMD {
169  
170      vector<RealType> massFactorsRow;
171      vector<RealType> massFactorsCol;
172 +
173 +    vector<int> regionRow;
174 +    vector<int> regionCol;
175   #endif
176  
177    };

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