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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 1608 by mciznick, Tue Aug 9 01:58:56 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 +    void addForceToAtomRowOMP(int atom1, Vector3d fg);
98 +    void addForceToAtomColumnOMP(int atom2, Vector3d fg);
99 +
100      // filling interaction blocks with pointers
101 <    InteractionData fillInteractionData(int atom1, int atom2);
102 <    InteractionData fillSkipData(int atom1, int atom2);
101 >    void fillInteractionData(InteractionData &idat, int atom1, int atom2);
102 >    void fillInteractionDataOMP(InteractionDataPrv &idat, int atom1, int atom2);
103 >    void unpackInteractionData(InteractionData &idat, int atom1, int atom2);
104  
105 +    void unpackInteractionDataOMP(InteractionDataPrv &idat, int atom1, int atom2);
106 +
107 +    // memory reordering
108 +    void reorderGroupCutoffs(vector<int> &order);
109 +    void reorderPosition(vector<int> &order);
110 +    void reorderGroupList(vector<int> &order);
111 +    void reorderMemory(vector<vector<CutoffGroup *> > &H_c_l);
112 +
113    private:
114 +    void createGtypeCutoffMap();
115 +
116      int nLocal_;
117      int nGroups_;
99 –    vector<int> identsLocal;
118      vector<int> AtomLocalToGlobal;
119      vector<int> cgLocalToGlobal;
120 <    vector<RealType> pot_local;
121 <    vector<RealType> massFactorsLocal;
104 <    vector<vector<int> > skipsForLocalAtom;
105 <    vector<vector<int> > toposForLocalAtom;
106 <    vector<vector<int> > topoDistLocal;
120 >    vector<RealType> groupCutoff;
121 >    vector<int> groupToGtype;
122  
123 +    /* XXX */
124 +    int neighborListReorderFreq;
125 +    int reorderFreqCounter;
126 +
127   #ifdef IS_MPI    
128      DataStorage atomRowData;
129      DataStorage atomColData;
# Line 116 | Line 135 | namespace OpenMD {
135      int nGroupsInRow_;
136      int nGroupsInCol_;
137  
138 <    Communicator<Row, int>* AtomCommIntRow;
139 <    Communicator<Row, RealType>* AtomCommRealRow;
121 <    Communicator<Row, Vector3d>* AtomCommVectorRow;
122 <    Communicator<Row, Mat3x3d>*  AtomCommMatrixRow;
138 >    Communicator<Row> rowComm;
139 >    Communicator<Column> colComm;
140  
141 <    Communicator<Column, int>* AtomCommIntColumn;
142 <    Communicator<Column, RealType>* AtomCommRealColumn;
143 <    Communicator<Column, Vector3d>* AtomCommVectorColumn;
144 <    Communicator<Column, Mat3x3d>*  AtomCommMatrixColumn;
141 >    Plan<int>* AtomPlanIntRow;
142 >    Plan<RealType>* AtomPlanRealRow;
143 >    Plan<Vector3d>* AtomPlanVectorRow;
144 >    Plan<Mat3x3d>*  AtomPlanMatrixRow;
145 >    Plan<potVec>* AtomPlanPotRow;
146  
147 <    Communicator<Row, int>* cgCommIntRow;
148 <    Communicator<Row, Vector3d>* cgCommVectorRow;
149 <    Communicator<Column, int>* cgCommIntColumn;
150 <    Communicator<Column, Vector3d>* cgCommVectorColumn;
147 >    Plan<int>* AtomPlanIntColumn;
148 >    Plan<RealType>* AtomPlanRealColumn;
149 >    Plan<Vector3d>* AtomPlanVectorColumn;
150 >    Plan<Mat3x3d>*  AtomPlanMatrixColumn;
151 >    Plan<potVec>* AtomPlanPotColumn;
152  
153 <    vector<vector<RealType> > pot_row;
154 <    vector<vector<RealType> > pot_col;
153 >    Plan<int>* cgPlanIntRow;
154 >    Plan<Vector3d>* cgPlanVectorRow;
155 >    Plan<int>* cgPlanIntColumn;
156 >    Plan<Vector3d>* cgPlanVectorColumn;
157  
158 +    // work arrays for assembling potential energy
159 +    vector<potVec> pot_row;
160 +    vector<potVec> pot_col;
161 +
162      vector<int> identsRow;
163      vector<int> identsCol;
164  
# Line 146 | Line 171 | namespace OpenMD {
171      vector<int> cgRowToGlobal;
172      vector<int> cgColToGlobal;
173  
174 +    vector<RealType> groupCutoffRow;
175 +    vector<RealType> groupCutoffCol;
176 +    vector<int> groupColToGtype;
177 +    vector<int> groupRowToGtype;
178 +
179      vector<vector<int> > cellListRow_;
180      vector<vector<int> > cellListCol_;
181  
# Line 154 | Line 184 | namespace OpenMD {
184  
185      vector<RealType> massFactorsRow;
186      vector<RealType> massFactorsCol;
157 –
158 –    vector<vector<int> > skipsForRowAtom;
159 –    vector<vector<int> > toposForRowAtom;
160 –    vector<vector<int> > topoDistRow;
187   #endif
188  
189    };

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