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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 1551 by gezelter, Thu Apr 28 18:38:21 2011 UTC vs.
Revision 1569 by gezelter, Thu May 26 13:55:04 2011 UTC

# Line 42 | Line 42
42   #ifndef PARALLEL_FORCEMATRIXDECOMPOSITION_HPP
43   #define PARALLEL_FORCEMATRIXDECOMPOSITION_HPP
44  
45 < #include "Parallel/ForceDecomposition.hpp"
45 > #include "parallel/ForceDecomposition.hpp"
46   #include "math/SquareMatrix3.hpp"
47   #include "brains/Snapshot.hpp"
48  
49   #ifdef IS_MPI
50 < #include "Parallel/Communicator.hpp"
50 > #include "parallel/Communicator.hpp"
51   #endif
52  
53   using namespace std;
# Line 55 | Line 55 | namespace OpenMD {
55    
56    class ForceMatrixDecomposition : public ForceDecomposition {
57    public:
58 <    ForceMatrixDecomposition(SimInfo* info) : ForceDecomposition(info) {sman_ = info_->getSnapshotManager();}
58 >    ForceMatrixDecomposition(SimInfo* info) : ForceDecomposition(info) {};
59 >
60      void distributeInitialData();
61      void distributeData();
62      void collectIntermediateData();
# Line 63 | Line 64 | namespace OpenMD {
64      void collectData();
65  
66      // neighbor list routines
66 –    bool checkNeighborList();
67      vector<pair<int, int> >  buildNeighborList();
68  
69      // group bookkeeping
# 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);
# Line 91 | Line 91 | namespace OpenMD {
91      // filling interaction blocks with pointers
92      InteractionData fillInteractionData(int atom1, int atom2);
93      InteractionData fillSkipData(int atom1, int atom2);
94 –    SelfData fillSelfData(int atom1);
94  
95    private:
96 <    SnapshotManager* sman_;    
97 <    Snapshot* snap_;
98 <    int storageLayout_;
99 < #ifdef IS_MPI    
96 >    int nLocal_;
97 >    int nGroups_;
98 >    vector<int> AtomLocalToGlobal;
99 >    vector<int> cgLocalToGlobal;
100 >    vector<RealType> pot_local;
101 >    vector<RealType> massFactorsLocal;
102  
103 + #ifdef IS_MPI    
104      DataStorage atomRowData;
105      DataStorage atomColData;
106      DataStorage cgRowData;
107      DataStorage cgColData;
108  
109 +    int nAtomsInRow_;
110 +    int nAtomsInCol_;
111 +    int nGroupsInRow_;
112 +    int nGroupsInCol_;
113 +
114      Communicator<Row, int>* AtomCommIntRow;
115      Communicator<Row, RealType>* AtomCommRealRow;
116      Communicator<Row, Vector3d>* AtomCommVectorRow;
# Line 121 | Line 128 | namespace OpenMD {
128  
129      vector<vector<RealType> > pot_row;
130      vector<vector<RealType> > pot_col;
131 +
132      vector<int> identsRow;
133      vector<int> identsCol;
134  
127 –    vector<int> AtomLocalToGlobal;
135      vector<int> AtomRowToGlobal;
136      vector<int> AtomColToGlobal;
137 <    vector<int> cgLocalToGlobal;
137 >
138      vector<int> cgRowToGlobal;
139      vector<int> cgColToGlobal;
140 +
141 +    vector<vector<int> > cellListRow_;
142 +    vector<vector<int> > cellListCol_;
143 +
144 +    vector<vector<int> > groupListRow_;
145 +    vector<vector<int> > groupListCol_;
146 +
147 +    vector<RealType> massFactorsRow;
148 +    vector<RealType> massFactorsCol;
149 +
150   #endif
151 <    vector<RealType> pot_local;
151 >
152    };
153  
154   }

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