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root/OpenMD/trunk/src/parallel/ForceMatrixDecomposition.hpp
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Comparing trunk/src/parallel/ForceMatrixDecomposition.hpp (file contents):
Revision 1879 by gezelter, Sun Jun 16 15:15:42 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 <    vector<pair<int, int> >  buildNeighborList();
70 >    void buildNeighborList(vector<int>& neighborList, vector<int>& point);
71  
72      // group bookkeeping
73 <    groupCutoffs getGroupCutoffs(int cg1, int cg2);
74 <    Vector3d getGroupVelocityColumn(int cg2);
73 >    Vector3d& getGroupVelocityColumn(int cg2);
74  
75      // Group->atom bookkeeping
76 <    vector<int> getAtomsInGroupRow(int cg1);
77 <    vector<int> getAtomsInGroupColumn(int cg2);
76 >    vector<int>& getAtomsInGroupRow(int cg1);
77 >    vector<int>& getAtomsInGroupColumn(int cg2);
78      Vector3d getAtomToGroupVectorRow(int atom1, int cg1);
79      Vector3d getAtomToGroupVectorColumn(int atom2, int cg2);
80 <    RealType getMassFactorRow(int atom1);
81 <    RealType getMassFactorColumn(int atom2);
80 >    RealType& getMassFactorRow(int atom1);
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();
88 >    int& getNAtomsInRow();
89      int getTopologicalDistance(int atom1, int atom2);
90 <    vector<int> getExcludesForAtom(int atom1);
90 >    vector<int>& getExcludesForAtom(int atom1);
91      bool skipAtomPair(int atom1, int atom2, int cg1, int cg2);
92      bool excludeAtomPair(int atom1, int atom2);
93      void addForceToAtomRow(int atom1, Vector3d fg);
94      void addForceToAtomColumn(int atom2, Vector3d fg);
95 <    Vector3d getAtomVelocityColumn(int atom2);
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 149 | Line 147 | namespace OpenMD {
147      vector<int> identsRow;
148      vector<int> identsCol;
149  
150 +    vector<int> regionsRow;
151 +    vector<int> regionsCol;
152 +
153      vector<AtomType*> atypesRow;
154      vector<AtomType*> atypesCol;
155  
# Line 160 | Line 161 | namespace OpenMD {
161      vector<int> cgColToGlobal;
162  
163   private:
163 –    vector<RealType> groupCutoffRow;
164 –    vector<RealType> groupCutoffCol;
165 –    vector<int> groupColToGtype;
166 –    vector<int> groupRowToGtype;
167 –
164      vector<vector<int> > cellListRow_;
165      vector<vector<int> > cellListCol_;
166  
# Line 173 | 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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