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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 1583 by gezelter, Thu Jun 16 22:00:08 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, InteractionManager* iMan) : ForceDecomposition(info, iMan) {};
59 >
60      void distributeInitialData();
61 +    void zeroWorkArrays();
62      void distributeData();
63      void collectIntermediateData();
64      void distributeIntermediateData();
65      void collectData();
66  
67      // neighbor list routines
66 –    bool checkNeighborList();
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);
75      vector<int> getAtomsInGroupColumn(int cg2);
76      Vector3d getAtomToGroupVectorRow(int atom1, int cg1);
77      Vector3d getAtomToGroupVectorColumn(int atom2, int cg2);
78 <    RealType getMfactRow(int atom1);
79 <    RealType getMfactColumn(int atom2);
78 >    RealType getMassFactorRow(int atom1);
79 >    RealType getMassFactorColumn(int atom2);
80  
81      // spatial data
82      Vector3d getIntergroupVector(int cg1, int cg2);
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);
96 <    SelfData fillSelfData(int atom1);
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 >    void unpackSkipData(InteractionData &idat, int atom1, int atom2);
98  
99    private:
100 <    SnapshotManager* sman_;    
98 <    Snapshot* snap_;
99 <    int storageLayout_;
100 < #ifdef IS_MPI    
100 >    void createGtypeCutoffMap();
101  
102 +    int nLocal_;
103 +    int nGroups_;
104 +    vector<int> AtomLocalToGlobal;
105 +    vector<int> cgLocalToGlobal;
106 +    vector<RealType> groupCutoff;
107 +    vector<int> groupToGtype;
108 +
109 + #ifdef IS_MPI    
110      DataStorage atomRowData;
111      DataStorage atomColData;
112      DataStorage cgRowData;
113      DataStorage cgColData;
114  
115 +    int nAtomsInRow_;
116 +    int nAtomsInCol_;
117 +    int nGroupsInRow_;
118 +    int nGroupsInCol_;
119 +
120      Communicator<Row, int>* AtomCommIntRow;
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 >
141      vector<int> identsRow;
142      vector<int> identsCol;
143  
144 <    vector<int> AtomLocalToGlobal;
144 >    vector<AtomType*> atypesRow;
145 >    vector<AtomType*> atypesCol;
146 >
147      vector<int> AtomRowToGlobal;
148      vector<int> AtomColToGlobal;
149 <    vector<int> cgLocalToGlobal;
149 >
150      vector<int> cgRowToGlobal;
151      vector<int> cgColToGlobal;
152 +
153 +    vector<RealType> groupCutoffRow;
154 +    vector<RealType> groupCutoffCol;
155 +    vector<int> groupColToGtype;
156 +    vector<int> groupRowToGtype;
157 +
158 +    vector<vector<int> > cellListRow_;
159 +    vector<vector<int> > cellListCol_;
160 +
161 +    vector<vector<int> > groupListRow_;
162 +    vector<vector<int> > groupListCol_;
163 +
164 +    vector<RealType> massFactorsRow;
165 +    vector<RealType> massFactorsCol;
166   #endif
167 <    vector<RealType> pot_local;
167 >
168    };
169  
170   }

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