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root/OpenMD/trunk/src/parallel/ForceMatrixDecomposition.hpp
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branches/development/src/parallel/ForceMatrixDecomposition.hpp (file contents), Revision 1567 by gezelter, Tue May 24 21:24:45 2011 UTC vs.
trunk/src/parallel/ForceMatrixDecomposition.hpp (file contents), Revision 1895 by gezelter, Mon Jul 1 21:09:37 2013 UTC

# Line 35 | Line 35
35   *                                                                      
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).                        
38 > * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
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) {sman_ = info_->getSnapshotManager();}
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 <    bool checkNeighborList();
67 <    vector<pair<int, int> >  buildNeighborList();
70 >    void buildNeighborList(vector<pair<int, int> >& neighborList);
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);
78 <    vector<int> getAtomsInGroupColumn(int cg2);
77 >    vector<int>& getAtomsInGroupRow(int cg1);
78 >    vector<int>& getAtomsInGroupColumn(int cg2);
79      Vector3d getAtomToGroupVectorRow(int atom1, int cg1);
80      Vector3d getAtomToGroupVectorColumn(int atom2, int cg2);
81 <    RealType getMfactRow(int atom1);
82 <    RealType getMfactColumn(int atom2);
81 >    RealType& getMassFactorRow(int atom1);
82 >    RealType& getMassFactorColumn(int atom2);
83  
84      // spatial data
85      Vector3d getIntergroupVector(int cg1, int cg2);
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);
94 <    SelfData fillSelfData(int atom1);
99 >    void fillInteractionData(InteractionData &idat, int atom1, int atom2);
100 >    void unpackInteractionData(InteractionData &idat, int atom1, int atom2);
101  
102    private:
103 <    SnapshotManager* sman_;    
98 <    Snapshot* snap_;
99 <    int storageLayout_;
100 <    vector<Vector3i> Cells;
103 >    void createGtypeCutoffMap();
104  
105      int nLocal_;
106      int nGroups_;
107 +    vector<int> AtomLocalToGlobal;
108 +    vector<int> cgLocalToGlobal;
109 +    vector<RealType> groupCutoff;
110 +    vector<int> groupToGtype;
111  
112   #ifdef IS_MPI    
113 <    DataStorage atomRowData;
107 <    DataStorage atomColData;
113 >    DataStorage atomRowData;    DataStorage atomColData;
114      DataStorage cgRowData;
115      DataStorage cgColData;
116  
# Line 113 | Line 119 | namespace OpenMD {
119      int nGroupsInRow_;
120      int nGroupsInCol_;
121  
122 <    Communicator<Row, int>* AtomCommIntRow;
123 <    Communicator<Row, RealType>* AtomCommRealRow;
118 <    Communicator<Row, Vector3d>* AtomCommVectorRow;
119 <    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<int> AtomLocalToGlobal;
152 >    vector<AtomType*> atypesRow;
153 >    vector<AtomType*> atypesCol;
154 >
155      vector<int> AtomRowToGlobal;
156      vector<int> AtomColToGlobal;
157 <    vector<int> cgLocalToGlobal;
157 >
158 > public:
159      vector<int> cgRowToGlobal;
160      vector<int> cgColToGlobal;
161  
162 <    vector<vector<int> > CellListRow;
163 <    vector<vector<int> > CellListCol;
164 < #else
165 <    vector<vector<int> > CellList;
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 >
171 >    vector<vector<int> > groupListRow_;
172 >    vector<vector<int> > groupListCol_;
173 >
174 >    vector<RealType> massFactorsRow;
175 >    vector<RealType> massFactorsCol;
176   #endif
148 –    vector<RealType> pot_local;
177  
178    };
179  

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