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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 1568 by gezelter, Wed May 25 16:20:37 2011 UTC vs.
Revision 1571 by gezelter, Fri May 27 16:45:44 2011 UTC

# Line 74 | Line 74 | namespace OpenMD {
74      vector<int> getAtomsInGroupColumn(int cg2);
75      Vector3d getAtomToGroupVectorRow(int atom1, int cg1);
76      Vector3d getAtomToGroupVectorColumn(int atom2, int cg2);
77 <    RealType getMfactRow(int atom1);
78 <    RealType getMfactColumn(int atom2);
77 >    RealType getMassFactorRow(int atom1);
78 >    RealType getMassFactorColumn(int atom2);
79  
80      // spatial data
81      Vector3d getIntergroupVector(int cg1, int cg2);
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 124 | Line 133 | namespace OpenMD {
133  
134      vector<vector<RealType> > pot_row;
135      vector<vector<RealType> > pot_col;
136 +
137      vector<int> identsRow;
138      vector<int> identsCol;
139  
140 <    vector<int> AtomLocalToGlobal;
140 >    vector<AtomType*> atypesRow;
141 >    vector<AtomType*> atypesCol;
142 >
143      vector<int> AtomRowToGlobal;
144      vector<int> AtomColToGlobal;
145 <    vector<int> cgLocalToGlobal;
145 >
146      vector<int> cgRowToGlobal;
147      vector<int> cgColToGlobal;
148  
149      vector<vector<int> > cellListRow_;
150      vector<vector<int> > cellListCol_;
151 +
152 +    vector<vector<int> > groupListRow_;
153 +    vector<vector<int> > groupListCol_;
154 +
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
140 –    vector<RealType> pot_local;
162  
163    };
164  

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