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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 1576 by gezelter, Wed Jun 8 16:05:07 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 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 >    vector<int> getSkipsForRowAtom(int atom1);
88 >    int getTopoDistance(int atom1, int atom2);
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 +    void unpackInteractionData(InteractionData idat, int atom1, int atom2);
96      InteractionData fillSkipData(int atom1, int atom2);
94 –    SelfData fillSelfData(int atom1);
97  
98    private:
99 <    SnapshotManager* sman_;    
98 <    Snapshot* snap_;
99 <    int storageLayout_;
100 < #ifdef IS_MPI    
99 >    void createGtypeCutoffMap();
100  
101 +    int nLocal_;
102 +    int nGroups_;
103 +    vector<int> identsLocal;
104 +    vector<int> AtomLocalToGlobal;
105 +    vector<int> cgLocalToGlobal;
106 +    vector<RealType> massFactorsLocal;
107 +    vector<vector<int> > skipsForLocalAtom;
108 +    vector<vector<int> > toposForLocalAtom;
109 +    vector<vector<int> > topoDistLocal;
110 +    vector<RealType> groupCutoff;
111 +    vector<int> groupToGtype;
112 +
113 + #ifdef IS_MPI    
114      DataStorage atomRowData;
115      DataStorage atomColData;
116      DataStorage cgRowData;
117      DataStorage cgColData;
118  
119 +    int nAtomsInRow_;
120 +    int nAtomsInCol_;
121 +    int nGroupsInRow_;
122 +    int nGroupsInCol_;
123 +
124      Communicator<Row, int>* AtomCommIntRow;
125      Communicator<Row, RealType>* AtomCommRealRow;
126      Communicator<Row, Vector3d>* AtomCommVectorRow;
127      Communicator<Row, Mat3x3d>*  AtomCommMatrixRow;
128 +    Communicator<Row, potVec>* AtomCommPotRow;
129  
130      Communicator<Column, int>* AtomCommIntColumn;
131      Communicator<Column, RealType>* AtomCommRealColumn;
132      Communicator<Column, Vector3d>* AtomCommVectorColumn;
133 <    Communicator<Column, Mat3x3d>*  AtomCommMatrixColumn;
133 >    Communicator<Column, Mat3x3d>*  AtomCommMatrixColumn;
134 >    Communicator<Column, potVec>* AtomCommPotColumn;
135  
136      Communicator<Row, int>* cgCommIntRow;
137      Communicator<Row, Vector3d>* cgCommVectorRow;
138      Communicator<Column, int>* cgCommIntColumn;
139      Communicator<Column, Vector3d>* cgCommVectorColumn;
140  
141 <    vector<vector<RealType> > pot_row;
142 <    vector<vector<RealType> > pot_col;
141 >    // work arrays for assembling potential energy
142 >    vector<potVec> pot_row;
143 >    vector<potVec> pot_col;
144 >    potVec pot_local;
145 >
146      vector<int> identsRow;
147      vector<int> identsCol;
148  
149 <    vector<int> AtomLocalToGlobal;
149 >    vector<AtomType*> atypesRow;
150 >    vector<AtomType*> atypesCol;
151 >
152      vector<int> AtomRowToGlobal;
153      vector<int> AtomColToGlobal;
154 <    vector<int> cgLocalToGlobal;
154 >
155      vector<int> cgRowToGlobal;
156      vector<int> cgColToGlobal;
157 +
158 +    vector<RealType> groupCutoffRow;
159 +    vector<RealType> groupCutoffCol;
160 +    vector<int> groupColToGtype;
161 +    vector<int> groupRowToGtype;
162 +
163 +    vector<vector<int> > cellListRow_;
164 +    vector<vector<int> > cellListCol_;
165 +
166 +    vector<vector<int> > groupListRow_;
167 +    vector<vector<int> > groupListCol_;
168 +
169 +    vector<RealType> massFactorsRow;
170 +    vector<RealType> massFactorsCol;
171 +
172 +    vector<vector<int> > skipsForRowAtom;
173 +    vector<vector<int> > toposForRowAtom;
174 +    vector<vector<int> > topoDistRow;
175   #endif
176 <    vector<RealType> pot_local;
176 >
177    };
178  
179   }

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