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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 1571 by gezelter, Fri May 27 16:45:44 2011 UTC vs.
Revision 1612 by gezelter, Fri Aug 12 19:59:56 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);
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> getExcludesForAtom(int atom1);
89      bool skipAtomPair(int atom1, int atom2);
90 +    bool excludeAtomPair(int atom1, int atom2);
91      void addForceToAtomRow(int atom1, Vector3d fg);
92      void addForceToAtomColumn(int atom2, Vector3d fg);
93  
94      // filling interaction blocks with pointers
95 <    InteractionData fillInteractionData(int atom1, int atom2);
96 <    InteractionData fillSkipData(int atom1, int atom2);
95 >    void fillInteractionData(InteractionData &idat, int atom1, int atom2);
96 >    void unpackInteractionData(InteractionData &idat, int atom1, int atom2);
97  
98    private:
99 +    void createGtypeCutoffMap();
100 +
101      int nLocal_;
102      int nGroups_;
99 –    vector<int> identsLocal;
103      vector<int> AtomLocalToGlobal;
104      vector<int> cgLocalToGlobal;
105 <    vector<RealType> pot_local;
106 <    vector<RealType> massFactorsLocal;
104 <    vector<vector<int> > skipsForLocalAtom;
105 <    vector<vector<int> > toposForLocalAtom;
106 <    vector<vector<int> > topoDistLocal;
105 >    vector<RealType> groupCutoff;
106 >    vector<int> groupToGtype;
107  
108   #ifdef IS_MPI    
109      DataStorage atomRowData;
# Line 116 | Line 116 | namespace OpenMD {
116      int nGroupsInRow_;
117      int nGroupsInCol_;
118  
119 <    Communicator<Row, int>* AtomCommIntRow;
120 <    Communicator<Row, RealType>* AtomCommRealRow;
121 <    Communicator<Row, Vector3d>* AtomCommVectorRow;
122 <    Communicator<Row, Mat3x3d>*  AtomCommMatrixRow;
119 >    Communicator<Row> rowComm;
120 >    Communicator<Column> colComm;
121  
122 <    Communicator<Column, int>* AtomCommIntColumn;
123 <    Communicator<Column, RealType>* AtomCommRealColumn;
124 <    Communicator<Column, Vector3d>* AtomCommVectorColumn;
125 <    Communicator<Column, Mat3x3d>*  AtomCommMatrixColumn;
122 >    Plan<int>* AtomPlanIntRow;
123 >    Plan<RealType>* AtomPlanRealRow;
124 >    Plan<Vector3d>* AtomPlanVectorRow;
125 >    Plan<Mat3x3d>*  AtomPlanMatrixRow;
126 >    Plan<potVec>* AtomPlanPotRow;
127  
128 <    Communicator<Row, int>* cgCommIntRow;
129 <    Communicator<Row, Vector3d>* cgCommVectorRow;
130 <    Communicator<Column, int>* cgCommIntColumn;
131 <    Communicator<Column, Vector3d>* cgCommVectorColumn;
128 >    Plan<int>* AtomPlanIntColumn;
129 >    Plan<RealType>* AtomPlanRealColumn;
130 >    Plan<Vector3d>* AtomPlanVectorColumn;
131 >    Plan<Mat3x3d>*  AtomPlanMatrixColumn;
132 >    Plan<potVec>* AtomPlanPotColumn;
133  
134 <    vector<vector<RealType> > pot_row;
135 <    vector<vector<RealType> > pot_col;
134 >    Plan<int>* cgPlanIntRow;
135 >    Plan<Vector3d>* cgPlanVectorRow;
136 >    Plan<int>* cgPlanIntColumn;
137 >    Plan<Vector3d>* cgPlanVectorColumn;
138  
139 +    // work arrays for assembling potential energy
140 +    vector<potVec> pot_row;
141 +    vector<potVec> pot_col;
142 +
143      vector<int> identsRow;
144      vector<int> identsCol;
145  
# Line 143 | Line 149 | namespace OpenMD {
149      vector<int> AtomRowToGlobal;
150      vector<int> AtomColToGlobal;
151  
152 + public:
153      vector<int> cgRowToGlobal;
154      vector<int> cgColToGlobal;
155  
156 + private:
157 +    vector<RealType> groupCutoffRow;
158 +    vector<RealType> groupCutoffCol;
159 +    vector<int> groupColToGtype;
160 +    vector<int> groupRowToGtype;
161 +
162      vector<vector<int> > cellListRow_;
163      vector<vector<int> > cellListCol_;
164  
# Line 154 | Line 167 | namespace OpenMD {
167  
168      vector<RealType> massFactorsRow;
169      vector<RealType> massFactorsCol;
157 –
158 –    vector<vector<int> > skipsForRowAtom;
159 –    vector<vector<int> > toposForRowAtom;
160 –    vector<vector<int> > topoDistRow;
170   #endif
171  
172    };

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