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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 1570 by gezelter, Thu May 26 21:56:04 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);
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 91 | Line 92 | namespace OpenMD {
92      // filling interaction blocks with pointers
93      InteractionData fillInteractionData(int atom1, int atom2);
94      InteractionData fillSkipData(int atom1, int atom2);
94 –    SelfData fillSelfData(int atom1);
95  
96    private:
97 <    SnapshotManager* sman_;    
98 <    Snapshot* snap_;
99 <    int storageLayout_;
100 < #ifdef IS_MPI    
97 >    int nLocal_;
98 >    int nGroups_;
99 >    vector<int> AtomLocalToGlobal;
100 >    vector<int> cgLocalToGlobal;
101 >    vector<RealType> pot_local;
102 >    vector<RealType> massFactorsLocal;
103 >    vector<vector<int> > skipsForLocalAtom;
104 >    vector<vector<int> > toposForLocalAtom;
105 >    vector<vector<int> > topoDistLocal;
106  
107 + #ifdef IS_MPI    
108      DataStorage atomRowData;
109      DataStorage atomColData;
110      DataStorage cgRowData;
111      DataStorage cgColData;
112  
113 +    int nAtomsInRow_;
114 +    int nAtomsInCol_;
115 +    int nGroupsInRow_;
116 +    int nGroupsInCol_;
117 +
118      Communicator<Row, int>* AtomCommIntRow;
119      Communicator<Row, RealType>* AtomCommRealRow;
120      Communicator<Row, Vector3d>* AtomCommVectorRow;
# Line 121 | Line 132 | namespace OpenMD {
132  
133      vector<vector<RealType> > pot_row;
134      vector<vector<RealType> > pot_col;
135 +
136      vector<int> identsRow;
137      vector<int> identsCol;
138  
127 –    vector<int> AtomLocalToGlobal;
139      vector<int> AtomRowToGlobal;
140      vector<int> AtomColToGlobal;
141 <    vector<int> cgLocalToGlobal;
141 >
142      vector<int> cgRowToGlobal;
143      vector<int> cgColToGlobal;
144 +
145 +    vector<vector<int> > cellListRow_;
146 +    vector<vector<int> > cellListCol_;
147 +
148 +    vector<vector<int> > groupListRow_;
149 +    vector<vector<int> > groupListCol_;
150 +
151 +    vector<RealType> massFactorsRow;
152 +    vector<RealType> massFactorsCol;
153 +
154 +    vector<vector<int> > skipsForRowAtom;
155 +    vector<vector<int> > toposForRowAtom;
156 +    vector<vector<int> > topoDistRow;
157 +
158 +
159   #endif
160 <    vector<RealType> pot_local;
160 >
161    };
162  
163   }

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