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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.
trunk/src/parallel/ForceMatrixDecomposition.hpp (file contents), Revision 1782 by gezelter, Wed Aug 22 02:28:28 2012 UTC

# Line 36 | Line 36
36   * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).            
37   * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
38   * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
39 < * [4]  Vardeman & Gezelter, in progress (2009).                        
39 > * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40 > * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
42  
43   #ifndef PARALLEL_FORCEMATRIXDECOMPOSITION_HPP
# Line 55 | Line 56 | namespace OpenMD {
56    
57    class ForceMatrixDecomposition : public ForceDecomposition {
58    public:
59 <    ForceMatrixDecomposition(SimInfo* info) : ForceDecomposition(info) {};
59 >    ForceMatrixDecomposition(SimInfo* info, InteractionManager* iMan);
60  
61      void distributeInitialData();
62 +    void zeroWorkArrays();
63      void distributeData();
64      void collectIntermediateData();
65      void distributeIntermediateData();
66 +    void collectSelfData();
67      void collectData();
68  
69      // neighbor list routines
70      vector<pair<int, int> >  buildNeighborList();
71  
72      // group bookkeeping
73 <    pair<int, int> getGroupTypes(int cg1, int cg2);
73 >    groupCutoffs getGroupCutoffs(int cg1, int cg2);
74 >    Vector3d getGroupVelocityColumn(int cg2);
75  
76      // Group->atom bookkeeping
77      vector<int> getAtomsInGroupRow(int cg1);
# Line 82 | Line 86 | namespace OpenMD {
86      Vector3d getInteratomicVector(int atom1, int atom2);
87        
88      // atom bookkeeping
89 <    vector<int> getAtomList();
90 <    vector<int> getSkipsForAtom(int atom1);
91 <    bool skipAtomPair(int atom1, int atom2);
89 >    int getNAtomsInRow();
90 >    int getTopologicalDistance(int atom1, int atom2);
91 >    vector<int> getExcludesForAtom(int atom1);
92 >    bool skipAtomPair(int atom1, int atom2, int cg1, int cg2);
93 >    bool excludeAtomPair(int atom1, int atom2);
94      void addForceToAtomRow(int atom1, Vector3d fg);
95      void addForceToAtomColumn(int atom2, Vector3d fg);
96 +    Vector3d getAtomVelocityColumn(int atom2);
97  
98      // filling interaction blocks with pointers
99 <    InteractionData fillInteractionData(int atom1, int atom2);
100 <    InteractionData fillSkipData(int atom1, int atom2);
99 >    void fillInteractionData(InteractionData &idat, int atom1, int atom2);
100 >    void unpackInteractionData(InteractionData &idat, int atom1, int atom2);
101  
102    private:
103 +    void createGtypeCutoffMap();
104 +
105      int nLocal_;
106      int nGroups_;
107      vector<int> AtomLocalToGlobal;
108      vector<int> cgLocalToGlobal;
109 <    vector<RealType> pot_local;
110 <    vector<RealType> massFactorsLocal;
109 >    vector<RealType> groupCutoff;
110 >    vector<int> groupToGtype;
111  
112   #ifdef IS_MPI    
113 <    DataStorage atomRowData;
105 <    DataStorage atomColData;
113 >    DataStorage atomRowData;    DataStorage atomColData;
114      DataStorage cgRowData;
115      DataStorage cgColData;
116  
# Line 111 | Line 119 | namespace OpenMD {
119      int nGroupsInRow_;
120      int nGroupsInCol_;
121  
122 <    Communicator<Row, int>* AtomCommIntRow;
123 <    Communicator<Row, RealType>* AtomCommRealRow;
116 <    Communicator<Row, Vector3d>* AtomCommVectorRow;
117 <    Communicator<Row, Mat3x3d>*  AtomCommMatrixRow;
122 >    Communicator<Row> rowComm;
123 >    Communicator<Column> colComm;
124  
125 <    Communicator<Column, int>* AtomCommIntColumn;
126 <    Communicator<Column, RealType>* AtomCommRealColumn;
127 <    Communicator<Column, Vector3d>* AtomCommVectorColumn;
128 <    Communicator<Column, Mat3x3d>*  AtomCommMatrixColumn;
125 >    Plan<int>* AtomPlanIntRow;
126 >    Plan<RealType>* AtomPlanRealRow;
127 >    Plan<Vector3d>* AtomPlanVectorRow;
128 >    Plan<Mat3x3d>*  AtomPlanMatrixRow;
129 >    Plan<potVec>* AtomPlanPotRow;
130  
131 <    Communicator<Row, int>* cgCommIntRow;
132 <    Communicator<Row, Vector3d>* cgCommVectorRow;
133 <    Communicator<Column, int>* cgCommIntColumn;
134 <    Communicator<Column, Vector3d>* cgCommVectorColumn;
131 >    Plan<int>* AtomPlanIntColumn;
132 >    Plan<RealType>* AtomPlanRealColumn;
133 >    Plan<Vector3d>* AtomPlanVectorColumn;
134 >    Plan<Mat3x3d>*  AtomPlanMatrixColumn;
135 >    Plan<potVec>* AtomPlanPotColumn;
136  
137 <    vector<vector<RealType> > pot_row;
138 <    vector<vector<RealType> > pot_col;
137 >    Plan<int>* cgPlanIntRow;
138 >    Plan<Vector3d>* cgPlanVectorRow;
139 >    Plan<int>* cgPlanIntColumn;
140 >    Plan<Vector3d>* cgPlanVectorColumn;
141  
142 +    // work arrays for assembling potential energy
143 +    vector<potVec> pot_row;
144 +    vector<potVec> pot_col;
145 +
146 +    vector<potVec> expot_row;
147 +    vector<potVec> expot_col;
148 +
149      vector<int> identsRow;
150      vector<int> identsCol;
151  
152 +    vector<AtomType*> atypesRow;
153 +    vector<AtomType*> atypesCol;
154 +
155      vector<int> AtomRowToGlobal;
156      vector<int> AtomColToGlobal;
157  
158 + public:
159      vector<int> cgRowToGlobal;
160      vector<int> cgColToGlobal;
161  
162 + private:
163 +    vector<RealType> groupCutoffRow;
164 +    vector<RealType> groupCutoffCol;
165 +    vector<int> groupColToGtype;
166 +    vector<int> groupRowToGtype;
167 +
168      vector<vector<int> > cellListRow_;
169      vector<vector<int> > cellListCol_;
170  
# Line 146 | Line 173 | namespace OpenMD {
173  
174      vector<RealType> massFactorsRow;
175      vector<RealType> massFactorsCol;
149 –
176   #endif
177  
178    };

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