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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 1571 by gezelter, Fri May 27 16:45:44 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> identsLocal;
100 >    vector<int> AtomLocalToGlobal;
101 >    vector<int> cgLocalToGlobal;
102 >    vector<RealType> pot_local;
103 >    vector<RealType> massFactorsLocal;
104 >    vector<vector<int> > skipsForLocalAtom;
105 >    vector<vector<int> > toposForLocalAtom;
106 >    vector<vector<int> > topoDistLocal;
107  
108 + #ifdef IS_MPI    
109      DataStorage atomRowData;
110      DataStorage atomColData;
111      DataStorage cgRowData;
112      DataStorage cgColData;
113  
114 +    int nAtomsInRow_;
115 +    int nAtomsInCol_;
116 +    int nGroupsInRow_;
117 +    int nGroupsInCol_;
118 +
119      Communicator<Row, int>* AtomCommIntRow;
120      Communicator<Row, RealType>* AtomCommRealRow;
121      Communicator<Row, Vector3d>* AtomCommVectorRow;
# Line 121 | Line 133 | namespace OpenMD {
133  
134      vector<vector<RealType> > pot_row;
135      vector<vector<RealType> > pot_col;
136 +
137      vector<int> identsRow;
138      vector<int> identsCol;
139  
140 <    vector<int> AtomLocalToGlobal;
140 >    vector<AtomType*> atypesRow;
141 >    vector<AtomType*> atypesCol;
142 >
143      vector<int> AtomRowToGlobal;
144      vector<int> AtomColToGlobal;
145 <    vector<int> cgLocalToGlobal;
145 >
146      vector<int> cgRowToGlobal;
147      vector<int> cgColToGlobal;
148 +
149 +    vector<vector<int> > cellListRow_;
150 +    vector<vector<int> > cellListCol_;
151 +
152 +    vector<vector<int> > groupListRow_;
153 +    vector<vector<int> > groupListCol_;
154 +
155 +    vector<RealType> massFactorsRow;
156 +    vector<RealType> massFactorsCol;
157 +
158 +    vector<vector<int> > skipsForRowAtom;
159 +    vector<vector<int> > toposForRowAtom;
160 +    vector<vector<int> > topoDistRow;
161   #endif
162 <    vector<RealType> pot_local;
162 >
163    };
164  
165   }

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