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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 1581 by gezelter, Mon Jun 13 22:13:12 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 82 | Line 83 | namespace OpenMD {
83      Vector3d getInteratomicVector(int atom1, int atom2);
84        
85      // atom bookkeeping
86 <    vector<int> getAtomList();
87 <    vector<int> getSkipsForAtom(int atom1);
86 >    int getNAtomsInRow();
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  
98    private:
99 +    void createGtypeCutoffMap();
100 +
101      int nLocal_;
102      int nGroups_;
103 +    vector<int> identsLocal;
104      vector<int> AtomLocalToGlobal;
105      vector<int> cgLocalToGlobal;
106 <    vector<RealType> pot_local;
107 <    vector<RealType> massFactorsLocal;
106 >    vector<RealType> groupCutoff;
107 >    vector<int> groupToGtype;
108  
109   #ifdef IS_MPI    
110      DataStorage atomRowData;
# Line 115 | 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 >    potVec pot_local;
141  
142      vector<int> identsRow;
143      vector<int> identsCol;
144  
145 +    vector<AtomType*> atypesRow;
146 +    vector<AtomType*> atypesCol;
147 +
148      vector<int> AtomRowToGlobal;
149      vector<int> AtomColToGlobal;
150  
151      vector<int> cgRowToGlobal;
152      vector<int> cgColToGlobal;
153  
154 +    vector<RealType> groupCutoffRow;
155 +    vector<RealType> groupCutoffCol;
156 +    vector<int> groupColToGtype;
157 +    vector<int> groupRowToGtype;
158 +
159      vector<vector<int> > cellListRow_;
160      vector<vector<int> > cellListCol_;
161  
# Line 146 | Line 164 | namespace OpenMD {
164  
165      vector<RealType> massFactorsRow;
166      vector<RealType> massFactorsCol;
149 –
167   #endif
168  
169    };

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