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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 1575 by gezelter, Fri Jun 3 21:39:49 2011 UTC vs.
branches/devel_omp/src/parallel/ForceMatrixDecomposition.hpp (file contents), Revision 1614 by mciznick, Tue Aug 23 20:55:51 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();
# Line 66 | 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 80 | 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 <    void unpackInteractionData(InteractionData idat, int atom1, int atom2);
100 <    InteractionData fillSkipData(int atom1, int atom2);
98 >    void fillInteractionData(InteractionData &idat, int atom1, int atom2);
99 >    void fillInteractionDataOMP(InteractionDataPrv &idat, int atom1, int atom2);
100 >    void unpackInteractionData(InteractionData &idat, int atom1, int atom2);
101  
102 +    void unpackInteractionDataOMP(InteractionDataPrv &idat, int atom1, int atom2);
103 +
104 +    // memory reordering
105 +    void reorderGroupCutoffs(vector<int> &order);
106 +    void reorderPosition(vector<int> &order);
107 +    void reorderGroupList(vector<int> &order);
108 +    void reorderMemory(vector<vector<CutoffGroup *> > &H_c_l);
109 +
110    private:
111 +    void createGtypeCutoffMap();
112 +
113      int nLocal_;
114      int nGroups_;
101 –    vector<int> identsLocal;
115      vector<int> AtomLocalToGlobal;
116      vector<int> cgLocalToGlobal;
117 <    vector<RealType> massFactorsLocal;
118 <    vector<vector<int> > skipsForLocalAtom;
106 <    vector<vector<int> > toposForLocalAtom;
107 <    vector<vector<int> > topoDistLocal;
117 >    vector<RealType> groupCutoff;
118 >    vector<int> groupToGtype;
119  
120 +    /* XXX */
121 +    int neighborListReorderFreq;
122 +    int reorderFreqCounter;
123 +
124   #ifdef IS_MPI    
125      DataStorage atomRowData;
126      DataStorage atomColData;
# Line 117 | Line 132 | namespace OpenMD {
132      int nGroupsInRow_;
133      int nGroupsInCol_;
134  
135 <    Communicator<Row, int>* AtomCommIntRow;
136 <    Communicator<Row, RealType>* AtomCommRealRow;
122 <    Communicator<Row, Vector3d>* AtomCommVectorRow;
123 <    Communicator<Row, Mat3x3d>*  AtomCommMatrixRow;
124 <    Communicator<Row, potVec>* AtomCommPotRow;
135 >    Communicator<Row> rowComm;
136 >    Communicator<Column> colComm;
137  
138 <    Communicator<Column, int>* AtomCommIntColumn;
139 <    Communicator<Column, RealType>* AtomCommRealColumn;
140 <    Communicator<Column, Vector3d>* AtomCommVectorColumn;
141 <    Communicator<Column, Mat3x3d>*  AtomCommMatrixColumn;
142 <    Communicator<Column, potVec>* AtomCommPotColumn;
138 >    Plan<int>* AtomPlanIntRow;
139 >    Plan<RealType>* AtomPlanRealRow;
140 >    Plan<Vector3d>* AtomPlanVectorRow;
141 >    Plan<Mat3x3d>*  AtomPlanMatrixRow;
142 >    Plan<potVec>* AtomPlanPotRow;
143  
144 <    Communicator<Row, int>* cgCommIntRow;
145 <    Communicator<Row, Vector3d>* cgCommVectorRow;
146 <    Communicator<Column, int>* cgCommIntColumn;
147 <    Communicator<Column, Vector3d>* cgCommVectorColumn;
144 >    Plan<int>* AtomPlanIntColumn;
145 >    Plan<RealType>* AtomPlanRealColumn;
146 >    Plan<Vector3d>* AtomPlanVectorColumn;
147 >    Plan<Mat3x3d>*  AtomPlanMatrixColumn;
148 >    Plan<potVec>* AtomPlanPotColumn;
149  
150 +    Plan<int>* cgPlanIntRow;
151 +    Plan<Vector3d>* cgPlanVectorRow;
152 +    Plan<int>* cgPlanIntColumn;
153 +    Plan<Vector3d>* cgPlanVectorColumn;
154 +
155      // work arrays for assembling potential energy
156      vector<potVec> pot_row;
157      vector<potVec> pot_col;
140 –    potVec pot_local;
158  
159      vector<int> identsRow;
160      vector<int> identsCol;
# Line 151 | Line 168 | namespace OpenMD {
168      vector<int> cgRowToGlobal;
169      vector<int> cgColToGlobal;
170  
171 +    vector<RealType> groupCutoffRow;
172 +    vector<RealType> groupCutoffCol;
173 +    vector<int> groupColToGtype;
174 +    vector<int> groupRowToGtype;
175 +
176      vector<vector<int> > cellListRow_;
177      vector<vector<int> > cellListCol_;
178  
# Line 159 | Line 181 | namespace OpenMD {
181  
182      vector<RealType> massFactorsRow;
183      vector<RealType> massFactorsCol;
162 –
163 –    vector<vector<int> > skipsForRowAtom;
164 –    vector<vector<int> > toposForRowAtom;
165 –    vector<vector<int> > topoDistRow;
184   #endif
185  
186    };

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