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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 1569 by gezelter, Thu May 26 13:55:04 2011 UTC vs.
Revision 1579 by gezelter, Thu Jun 9 20:26:29 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) : ForceDecomposition(info, iMan) {};
59  
60      void distributeInitialData();
61 +    void zeroWorkArrays();
62      void distributeData();
63      void collectIntermediateData();
64      void distributeIntermediateData();
# Line 67 | Line 68 | namespace OpenMD {
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);
# Line 82 | Line 83 | namespace OpenMD {
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 +    void unpackInteractionData(InteractionData idat, int atom1, int atom2);
96      InteractionData fillSkipData(int atom1, int atom2);
97  
98    private:
99 +    void createGtypeCutoffMap();
100 +
101      int nLocal_;
102      int nGroups_;
103 +    vector<int> identsLocal;
104      vector<int> AtomLocalToGlobal;
105      vector<int> cgLocalToGlobal;
100 –    vector<RealType> pot_local;
106      vector<RealType> massFactorsLocal;
107 +    vector<RealType> groupCutoff;
108 +    vector<int> groupToGtype;
109  
110   #ifdef IS_MPI    
111      DataStorage atomRowData;
# Line 115 | Line 122 | namespace OpenMD {
122      Communicator<Row, RealType>* AtomCommRealRow;
123      Communicator<Row, Vector3d>* AtomCommVectorRow;
124      Communicator<Row, Mat3x3d>*  AtomCommMatrixRow;
125 +    Communicator<Row, potVec>* AtomCommPotRow;
126  
127      Communicator<Column, int>* AtomCommIntColumn;
128      Communicator<Column, RealType>* AtomCommRealColumn;
129      Communicator<Column, Vector3d>* AtomCommVectorColumn;
130 <    Communicator<Column, Mat3x3d>*  AtomCommMatrixColumn;
130 >    Communicator<Column, Mat3x3d>*  AtomCommMatrixColumn;
131 >    Communicator<Column, potVec>* AtomCommPotColumn;
132  
133      Communicator<Row, int>* cgCommIntRow;
134      Communicator<Row, Vector3d>* cgCommVectorRow;
135      Communicator<Column, int>* cgCommIntColumn;
136      Communicator<Column, Vector3d>* cgCommVectorColumn;
137  
138 <    vector<vector<RealType> > pot_row;
139 <    vector<vector<RealType> > pot_col;
138 >    // work arrays for assembling potential energy
139 >    vector<potVec> pot_row;
140 >    vector<potVec> pot_col;
141 >    potVec pot_local;
142  
143      vector<int> identsRow;
144      vector<int> identsCol;
145  
146 +    vector<AtomType*> atypesRow;
147 +    vector<AtomType*> atypesCol;
148 +
149      vector<int> AtomRowToGlobal;
150      vector<int> AtomColToGlobal;
151  
152      vector<int> cgRowToGlobal;
153      vector<int> cgColToGlobal;
154  
155 +    vector<RealType> groupCutoffRow;
156 +    vector<RealType> groupCutoffCol;
157 +    vector<int> groupColToGtype;
158 +    vector<int> groupRowToGtype;
159 +
160      vector<vector<int> > cellListRow_;
161      vector<vector<int> > cellListCol_;
162  
# Line 146 | Line 165 | namespace OpenMD {
165  
166      vector<RealType> massFactorsRow;
167      vector<RealType> massFactorsCol;
149 –
168   #endif
169  
170    };

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