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root/OpenMD/branches/devel_omp/src/parallel/ForceMatrixDecomposition.hpp
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Comparing:
branches/development/src/parallel/ForceMatrixDecomposition.hpp (file contents), Revision 1571 by gezelter, Fri May 27 16:45:44 2011 UTC vs.
branches/devel_omp/src/parallel/ForceMatrixDecomposition.hpp (file contents), Revision 1598 by mciznick, Wed Jul 27 14:26:53 2011 UTC

# Line 55 | Line 55 | namespace OpenMD {
55    
56    class ForceMatrixDecomposition : public ForceDecomposition {
57    public:
58 <    ForceMatrixDecomposition(SimInfo* info) : ForceDecomposition(info) {};
58 >    ForceMatrixDecomposition(SimInfo* info, InteractionManager* iMan);
59  
60      void distributeInitialData();
61 +    void zeroWorkArrays();
62      void distributeData();
63      void collectIntermediateData();
64      void distributeIntermediateData();
# Line 65 | Line 66 | namespace OpenMD {
66  
67      // neighbor list routines
68      vector<pair<int, int> >  buildNeighborList();
69 +    // neighbor list routines based on Rapaport
70 +    vector<vector<CutoffGroup *> > buildLayerBasedNeighborList();
71  
72      // group bookkeeping
73 <    pair<int, int> getGroupTypes(int cg1, int cg2);
73 >    groupCutoffs getGroupCutoffs(int cg1, int cg2);
74  
75      // Group->atom bookkeeping
76      vector<int> getAtomsInGroupRow(int cg1);
# Line 79 | Line 82 | namespace OpenMD {
82  
83      // spatial data
84      Vector3d getIntergroupVector(int cg1, int cg2);
85 +    Vector3d getIntergroupVector(CutoffGroup *cg1, CutoffGroup *cg2);
86      Vector3d getInteratomicVector(int atom1, int atom2);
87        
88      // atom bookkeeping
89      int getNAtomsInRow();
90 <    vector<int> getSkipsForRowAtom(int atom1);
91 <    int getTopoDistance(int atom1, int atom2);
90 >    int getTopologicalDistance(int atom1, int atom2);
91 >    vector<int> getExcludesForAtom(int atom1);
92      bool skipAtomPair(int atom1, int atom2);
93 +    bool excludeAtomPair(int atom1, int atom2);
94      void addForceToAtomRow(int atom1, Vector3d fg);
95      void addForceToAtomColumn(int atom2, Vector3d fg);
96  
97      // filling interaction blocks with pointers
98 <    InteractionData fillInteractionData(int atom1, int atom2);
99 <    InteractionData fillSkipData(int atom1, int atom2);
98 >    void fillInteractionData(InteractionData &idat, int atom1, int atom2);
99 >    void unpackInteractionData(InteractionData &idat, int atom1, int atom2);
100  
101 +    // memory reordering
102 +    void reorderGroupCutoffs(vector<int> &order);
103 +    void reorderPosition(vector<int> &order);
104 +    void reorderGroupList(vector<int> &order);
105 +    void reorderMemory(vector<vector<CutoffGroup *> > &H_c_l);
106 +
107    private:
108 +    void createGtypeCutoffMap();
109 +
110      int nLocal_;
111      int nGroups_;
99 –    vector<int> identsLocal;
112      vector<int> AtomLocalToGlobal;
113      vector<int> cgLocalToGlobal;
114 <    vector<RealType> pot_local;
115 <    vector<RealType> massFactorsLocal;
104 <    vector<vector<int> > skipsForLocalAtom;
105 <    vector<vector<int> > toposForLocalAtom;
106 <    vector<vector<int> > topoDistLocal;
114 >    vector<RealType> groupCutoff;
115 >    vector<int> groupToGtype;
116  
117   #ifdef IS_MPI    
118      DataStorage atomRowData;
# Line 116 | Line 125 | namespace OpenMD {
125      int nGroupsInRow_;
126      int nGroupsInCol_;
127  
128 <    Communicator<Row, int>* AtomCommIntRow;
129 <    Communicator<Row, RealType>* AtomCommRealRow;
121 <    Communicator<Row, Vector3d>* AtomCommVectorRow;
122 <    Communicator<Row, Mat3x3d>*  AtomCommMatrixRow;
128 >    Communicator<Row> rowComm;
129 >    Communicator<Column> colComm;
130  
131 <    Communicator<Column, int>* AtomCommIntColumn;
132 <    Communicator<Column, RealType>* AtomCommRealColumn;
133 <    Communicator<Column, Vector3d>* AtomCommVectorColumn;
134 <    Communicator<Column, Mat3x3d>*  AtomCommMatrixColumn;
131 >    Plan<int>* AtomPlanIntRow;
132 >    Plan<RealType>* AtomPlanRealRow;
133 >    Plan<Vector3d>* AtomPlanVectorRow;
134 >    Plan<Mat3x3d>*  AtomPlanMatrixRow;
135 >    Plan<potVec>* AtomPlanPotRow;
136  
137 <    Communicator<Row, int>* cgCommIntRow;
138 <    Communicator<Row, Vector3d>* cgCommVectorRow;
139 <    Communicator<Column, int>* cgCommIntColumn;
140 <    Communicator<Column, Vector3d>* cgCommVectorColumn;
137 >    Plan<int>* AtomPlanIntColumn;
138 >    Plan<RealType>* AtomPlanRealColumn;
139 >    Plan<Vector3d>* AtomPlanVectorColumn;
140 >    Plan<Mat3x3d>*  AtomPlanMatrixColumn;
141 >    Plan<potVec>* AtomPlanPotColumn;
142  
143 <    vector<vector<RealType> > pot_row;
144 <    vector<vector<RealType> > pot_col;
143 >    Plan<int>* cgPlanIntRow;
144 >    Plan<Vector3d>* cgPlanVectorRow;
145 >    Plan<int>* cgPlanIntColumn;
146 >    Plan<Vector3d>* cgPlanVectorColumn;
147  
148 +    // work arrays for assembling potential energy
149 +    vector<potVec> pot_row;
150 +    vector<potVec> pot_col;
151 +
152      vector<int> identsRow;
153      vector<int> identsCol;
154  
# Line 146 | Line 161 | namespace OpenMD {
161      vector<int> cgRowToGlobal;
162      vector<int> cgColToGlobal;
163  
164 +    vector<RealType> groupCutoffRow;
165 +    vector<RealType> groupCutoffCol;
166 +    vector<int> groupColToGtype;
167 +    vector<int> groupRowToGtype;
168 +
169      vector<vector<int> > cellListRow_;
170      vector<vector<int> > cellListCol_;
171  
# Line 154 | Line 174 | namespace OpenMD {
174  
175      vector<RealType> massFactorsRow;
176      vector<RealType> massFactorsCol;
157 –
158 –    vector<vector<int> > skipsForRowAtom;
159 –    vector<vector<int> > toposForRowAtom;
160 –    vector<vector<int> > topoDistRow;
177   #endif
178  
179    };

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