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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 1569 by gezelter, Thu May 26 13:55:04 2011 UTC vs.
Revision 1571 by gezelter, Fri May 27 16:45:44 2011 UTC

# Line 82 | Line 82 | namespace OpenMD {
82      Vector3d getInteratomicVector(int atom1, int atom2);
83        
84      // atom bookkeeping
85 <    vector<int> getAtomList();
86 <    vector<int> getSkipsForAtom(int atom1);
85 >    int getNAtomsInRow();
86 >    vector<int> getSkipsForRowAtom(int atom1);
87 >    int getTopoDistance(int atom1, int atom2);
88      bool skipAtomPair(int atom1, int atom2);
89      void addForceToAtomRow(int atom1, Vector3d fg);
90      void addForceToAtomColumn(int atom2, Vector3d fg);
# Line 95 | Line 96 | namespace OpenMD {
96    private:
97      int nLocal_;
98      int nGroups_;
99 +    vector<int> identsLocal;
100      vector<int> AtomLocalToGlobal;
101      vector<int> cgLocalToGlobal;
102      vector<RealType> pot_local;
103      vector<RealType> massFactorsLocal;
104 +    vector<vector<int> > skipsForLocalAtom;
105 +    vector<vector<int> > toposForLocalAtom;
106 +    vector<vector<int> > topoDistLocal;
107  
108   #ifdef IS_MPI    
109      DataStorage atomRowData;
# Line 132 | Line 137 | namespace OpenMD {
137      vector<int> identsRow;
138      vector<int> identsCol;
139  
140 +    vector<AtomType*> atypesRow;
141 +    vector<AtomType*> atypesCol;
142 +
143      vector<int> AtomRowToGlobal;
144      vector<int> AtomColToGlobal;
145  
# Line 147 | Line 155 | namespace OpenMD {
155      vector<RealType> massFactorsRow;
156      vector<RealType> massFactorsCol;
157  
158 +    vector<vector<int> > skipsForRowAtom;
159 +    vector<vector<int> > toposForRowAtom;
160 +    vector<vector<int> > topoDistRow;
161   #endif
162  
163    };

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