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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 1570 by gezelter, Thu May 26 21:56:04 2011 UTC vs.
Revision 1583 by gezelter, Thu Jun 16 22:00:08 2011 UTC

# Line 55 | Line 55 | namespace OpenMD {
55    
56    class ForceMatrixDecomposition : public ForceDecomposition {
57    public:
58 <    ForceMatrixDecomposition(SimInfo* info) : ForceDecomposition(info) {};
58 >    ForceMatrixDecomposition(SimInfo* info, InteractionManager* iMan) : ForceDecomposition(info, iMan) {};
59  
60      void distributeInitialData();
61 +    void zeroWorkArrays();
62      void distributeData();
63      void collectIntermediateData();
64      void distributeIntermediateData();
# Line 67 | Line 68 | namespace OpenMD {
68      vector<pair<int, int> >  buildNeighborList();
69  
70      // group bookkeeping
71 <    pair<int, int> getGroupTypes(int cg1, int cg2);
71 >    groupCutoffs getGroupCutoffs(int cg1, int cg2);
72  
73      // Group->atom bookkeeping
74      vector<int> getAtomsInGroupRow(int cg1);
# Line 83 | Line 84 | namespace OpenMD {
84        
85      // atom bookkeeping
86      int getNAtomsInRow();
87 <    vector<int> getSkipsForRowAtom(int atom1);
88 <    int getTopoDistance(int atom1, int atom2);
87 >    int getTopologicalDistance(int atom1, int atom2);
88 >    vector<int> getSkipsForAtom(int atom1);
89      bool skipAtomPair(int atom1, int atom2);
90      void addForceToAtomRow(int atom1, Vector3d fg);
91      void addForceToAtomColumn(int atom2, Vector3d fg);
92  
93      // filling interaction blocks with pointers
94 <    InteractionData fillInteractionData(int atom1, int atom2);
95 <    InteractionData fillSkipData(int atom1, int atom2);
94 >    void fillInteractionData(InteractionData &idat, int atom1, int atom2);
95 >    void unpackInteractionData(InteractionData &idat, int atom1, int atom2);
96 >    void fillSkipData(InteractionData &idat, int atom1, int atom2);
97 >    void unpackSkipData(InteractionData &idat, int atom1, int atom2);
98  
99    private:
100 +    void createGtypeCutoffMap();
101 +
102      int nLocal_;
103      int nGroups_;
104      vector<int> AtomLocalToGlobal;
105      vector<int> cgLocalToGlobal;
106 <    vector<RealType> pot_local;
107 <    vector<RealType> massFactorsLocal;
103 <    vector<vector<int> > skipsForLocalAtom;
104 <    vector<vector<int> > toposForLocalAtom;
105 <    vector<vector<int> > topoDistLocal;
106 >    vector<RealType> groupCutoff;
107 >    vector<int> groupToGtype;
108  
109   #ifdef IS_MPI    
110      DataStorage atomRowData;
# Line 119 | Line 121 | namespace OpenMD {
121      Communicator<Row, RealType>* AtomCommRealRow;
122      Communicator<Row, Vector3d>* AtomCommVectorRow;
123      Communicator<Row, Mat3x3d>*  AtomCommMatrixRow;
124 +    Communicator<Row, potVec>* AtomCommPotRow;
125  
126      Communicator<Column, int>* AtomCommIntColumn;
127      Communicator<Column, RealType>* AtomCommRealColumn;
128      Communicator<Column, Vector3d>* AtomCommVectorColumn;
129 <    Communicator<Column, Mat3x3d>*  AtomCommMatrixColumn;
129 >    Communicator<Column, Mat3x3d>*  AtomCommMatrixColumn;
130 >    Communicator<Column, potVec>* AtomCommPotColumn;
131  
132      Communicator<Row, int>* cgCommIntRow;
133      Communicator<Row, Vector3d>* cgCommVectorRow;
134      Communicator<Column, int>* cgCommIntColumn;
135      Communicator<Column, Vector3d>* cgCommVectorColumn;
136  
137 <    vector<vector<RealType> > pot_row;
138 <    vector<vector<RealType> > pot_col;
137 >    // work arrays for assembling potential energy
138 >    vector<potVec> pot_row;
139 >    vector<potVec> pot_col;
140  
141      vector<int> identsRow;
142      vector<int> identsCol;
143  
144 +    vector<AtomType*> atypesRow;
145 +    vector<AtomType*> atypesCol;
146 +
147      vector<int> AtomRowToGlobal;
148      vector<int> AtomColToGlobal;
149  
150      vector<int> cgRowToGlobal;
151      vector<int> cgColToGlobal;
152  
153 +    vector<RealType> groupCutoffRow;
154 +    vector<RealType> groupCutoffCol;
155 +    vector<int> groupColToGtype;
156 +    vector<int> groupRowToGtype;
157 +
158      vector<vector<int> > cellListRow_;
159      vector<vector<int> > cellListCol_;
160  
# Line 150 | Line 163 | namespace OpenMD {
163  
164      vector<RealType> massFactorsRow;
165      vector<RealType> massFactorsCol;
153 –
154 –    vector<vector<int> > skipsForRowAtom;
155 –    vector<vector<int> > toposForRowAtom;
156 –    vector<vector<int> > topoDistRow;
157 –
158 –
166   #endif
167  
168    };

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