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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 1551 by gezelter, Thu Apr 28 18:38:21 2011 UTC vs.
trunk/src/parallel/ForceMatrixDecomposition.hpp (file contents), Revision 2057 by gezelter, Tue Mar 3 15:22:26 2015 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
44   #define PARALLEL_FORCEMATRIXDECOMPOSITION_HPP
45  
46 < #include "Parallel/ForceDecomposition.hpp"
46 > #include "parallel/ForceDecomposition.hpp"
47   #include "math/SquareMatrix3.hpp"
48   #include "brains/Snapshot.hpp"
49  
50   #ifdef IS_MPI
51 < #include "Parallel/Communicator.hpp"
51 > #include "parallel/Communicator.hpp"
52   #endif
53  
54   using namespace std;
# 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<int>& neighborList, vector<int>& point);
71  
72      // group bookkeeping
73 <    pair<int, int> getGroupTypes(int cg1, int cg2);
73 >    Vector3d& getGroupVelocityColumn(int cg2);
74  
75      // Group->atom bookkeeping
76 <    vector<int> getAtomsInGroupRow(int cg1);
77 <    vector<int> getAtomsInGroupColumn(int cg2);
76 >    vector<int>& getAtomsInGroupRow(int cg1);
77 >    vector<int>& getAtomsInGroupColumn(int cg2);
78      Vector3d getAtomToGroupVectorRow(int atom1, int cg1);
79      Vector3d getAtomToGroupVectorColumn(int atom2, int cg2);
80 <    RealType getMfactRow(int atom1);
81 <    RealType getMfactColumn(int atom2);
80 >    RealType& getMassFactorRow(int atom1);
81 >    RealType& getMassFactorColumn(int atom2);
82  
83      // spatial data
84      Vector3d getIntergroupVector(int cg1, int cg2);
85      Vector3d getInteratomicVector(int atom1, int atom2);
86        
87      // atom bookkeeping
88 <    vector<int> getAtomList();
89 <    vector<int> getSkipsForAtom(int atom1);
90 <    bool skipAtomPair(int atom1, int atom2);
88 >    int& getNAtomsInRow();
89 >    int getTopologicalDistance(int atom1, int atom2);
90 >    vector<int>& getExcludesForAtom(int atom1);
91 >    bool skipAtomPair(int atom1, int atom2, int cg1, int cg2);
92 >    bool excludeAtomPair(int atom1, int atom2);
93      void addForceToAtomRow(int atom1, Vector3d fg);
94      void addForceToAtomColumn(int atom2, Vector3d fg);
95 +    Vector3d& getAtomVelocityColumn(int atom2);
96  
97      // filling interaction blocks with pointers
98 <    InteractionData fillInteractionData(int atom1, int atom2);
99 <    InteractionData fillSkipData(int atom1, int atom2);
94 <    SelfData fillSelfData(int atom1);
98 >    void fillInteractionData(InteractionData &idat, int atom1, int atom2, bool newAtom1 = true);
99 >    void unpackInteractionData(InteractionData &idat, int atom1, int atom2);
100  
101 <  private:
102 <    SnapshotManager* sman_;    
103 <    Snapshot* snap_;
104 <    int storageLayout_;
105 < #ifdef IS_MPI    
101 >  private:    
102 >    int nLocal_;
103 >    int nGroups_;
104 >    vector<int> AtomLocalToGlobal;
105 >    vector<int> cgLocalToGlobal;
106 >    vector<RealType> groupCutoff;
107 >    vector<int> groupToGtype;
108  
109 + #ifdef IS_MPI    
110      DataStorage atomRowData;
111      DataStorage atomColData;
112      DataStorage cgRowData;
113      DataStorage cgColData;
114  
115 <    Communicator<Row, int>* AtomCommIntRow;
116 <    Communicator<Row, RealType>* AtomCommRealRow;
117 <    Communicator<Row, Vector3d>* AtomCommVectorRow;
118 <    Communicator<Row, Mat3x3d>*  AtomCommMatrixRow;
115 >    int nAtomsInRow_;
116 >    int nAtomsInCol_;
117 >    int nGroupsInRow_;
118 >    int nGroupsInCol_;
119  
120 <    Communicator<Column, int>* AtomCommIntColumn;
121 <    Communicator<Column, RealType>* AtomCommRealColumn;
114 <    Communicator<Column, Vector3d>* AtomCommVectorColumn;
115 <    Communicator<Column, Mat3x3d>*  AtomCommMatrixColumn;
120 >    Communicator<Row> rowComm;
121 >    Communicator<Column> colComm;
122  
123 <    Communicator<Row, int>* cgCommIntRow;
124 <    Communicator<Row, Vector3d>* cgCommVectorRow;
125 <    Communicator<Column, int>* cgCommIntColumn;
126 <    Communicator<Column, Vector3d>* cgCommVectorColumn;
123 >    Plan<int>* AtomPlanIntRow;
124 >    Plan<RealType>* AtomPlanRealRow;
125 >    Plan<Vector3d>* AtomPlanVectorRow;
126 >    Plan<Mat3x3d>*  AtomPlanMatrixRow;
127 >    Plan<potVec>* AtomPlanPotRow;
128  
129 <    vector<vector<RealType> > pot_row;
130 <    vector<vector<RealType> > pot_col;
129 >    Plan<int>* AtomPlanIntColumn;
130 >    Plan<RealType>* AtomPlanRealColumn;
131 >    Plan<Vector3d>* AtomPlanVectorColumn;
132 >    Plan<Mat3x3d>*  AtomPlanMatrixColumn;
133 >    Plan<potVec>* AtomPlanPotColumn;
134 >
135 >    Plan<int>* cgPlanIntRow;
136 >    Plan<Vector3d>* cgPlanVectorRow;
137 >    Plan<int>* cgPlanIntColumn;
138 >    Plan<Vector3d>* cgPlanVectorColumn;
139 >
140 >    // work arrays for assembling potential energy
141 >    vector<potVec> pot_row;
142 >    vector<potVec> pot_col;
143 >
144 >    vector<potVec> expot_row;
145 >    vector<potVec> expot_col;
146 >
147      vector<int> identsRow;
148      vector<int> identsCol;
149  
150 <    vector<int> AtomLocalToGlobal;
150 >    vector<int> regionsRow;
151 >    vector<int> regionsCol;
152 >
153 >    vector<AtomType*> atypesRow;
154 >    vector<AtomType*> atypesCol;
155 >
156      vector<int> AtomRowToGlobal;
157      vector<int> AtomColToGlobal;
158 <    vector<int> cgLocalToGlobal;
158 >
159 > public:
160      vector<int> cgRowToGlobal;
161      vector<int> cgColToGlobal;
162 +
163 + private:
164 +    vector<vector<int> > cellListRow_;
165 +    vector<vector<int> > cellListCol_;
166 +
167 +    vector<vector<int> > groupListRow_;
168 +    vector<vector<int> > groupListCol_;
169 +
170 +    vector<RealType> massFactorsRow;
171 +    vector<RealType> massFactorsCol;
172 +
173 +    vector<int> regionRow;
174 +    vector<int> regionCol;
175   #endif
176 <    vector<RealType> pot_local;
176 >
177    };
178  
179   }

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