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root/OpenMD/trunk/src/parallel/ForceMatrixDecomposition.hpp
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Comparing:
branches/development/src/parallel/ForceDecomposition.hpp (file contents), Revision 1538 by chuckv, Tue Jan 11 18:58:12 2011 UTC vs.
branches/development/src/parallel/ForceMatrixDecomposition.hpp (file contents), Revision 1567 by gezelter, Tue May 24 21:24:45 2011 UTC

# Line 1 | Line 1
1 < /**
2 < * @file ForceDecomposition.cpp
3 < * @author Charles Vardeman <cvardema.at.nd.edu>
4 < * @date 08/18/2010
5 < * @time 11:56am
6 < * @version 1.0
1 > /*
2 > * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3   *
8 – * @section LICENSE
9 – * Copyright (c) 2010 The University of Notre Dame. All Rights Reserved.
10 – *
4   * The University of Notre Dame grants you ("Licensee") a
5   * non-exclusive, royalty free, license to use, modify and
6   * redistribute this software in source and binary code form, provided
# Line 45 | Line 38
38   * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
39   * [4]  Vardeman & Gezelter, in progress (2009).                        
40   */
41 +
42 + #ifndef PARALLEL_FORCEMATRIXDECOMPOSITION_HPP
43 + #define PARALLEL_FORCEMATRIXDECOMPOSITION_HPP
44  
45 + #include "parallel/ForceDecomposition.hpp"
46 + #include "math/SquareMatrix3.hpp"
47 + #include "brains/Snapshot.hpp"
48  
49 < /*  -*- c++ -*-  */
50 < #ifndef FORCEDECOMPOSITION_PARALLEL_HPP
51 < #define FORCEDECOMPOSITION_PARALLEL_HPP
49 > #ifdef IS_MPI
50 > #include "parallel/Communicator.hpp"
51 > #endif
52  
53 + using namespace std;
54 + namespace OpenMD {
55 +  
56 +  class ForceMatrixDecomposition : public ForceDecomposition {
57 +  public:
58 +    ForceMatrixDecomposition(SimInfo* info) : ForceDecomposition(info) {sman_ = info_->getSnapshotManager();}
59 +    void distributeInitialData();
60 +    void distributeData();
61 +    void collectIntermediateData();
62 +    void distributeIntermediateData();
63 +    void collectData();
64  
65 < namespace OpenMD{
65 >    // neighbor list routines
66 >    bool checkNeighborList();
67 >    vector<pair<int, int> >  buildNeighborList();
68  
69 < class ForceDecomposition
70 < {
59 < public:
60 <  ForceDecomposition();
61 <  virtual ~ForceDecomposition();
62 <  void gather();
63 <  void scatter();
64 <  
65 < protected:
66 < private:
67 <  int myRank_;
68 <  static bool isColumn_;
69 <  static int myIndex_:
70 < };
69 >    // group bookkeeping
70 >    pair<int, int> getGroupTypes(int cg1, int cg2);
71  
72 +    // Group->atom bookkeeping
73 +    vector<int> getAtomsInGroupRow(int cg1);
74 +    vector<int> getAtomsInGroupColumn(int cg2);
75 +    Vector3d getAtomToGroupVectorRow(int atom1, int cg1);
76 +    Vector3d getAtomToGroupVectorColumn(int atom2, int cg2);
77 +    RealType getMfactRow(int atom1);
78 +    RealType getMfactColumn(int atom2);
79  
80 +    // spatial data
81 +    Vector3d getIntergroupVector(int cg1, int cg2);
82 +    Vector3d getInteratomicVector(int atom1, int atom2);
83 +      
84 +    // atom bookkeeping
85 +    vector<int> getAtomList();
86 +    vector<int> getSkipsForAtom(int atom1);
87 +    bool skipAtomPair(int atom1, int atom2);
88 +    void addForceToAtomRow(int atom1, Vector3d fg);
89 +    void addForceToAtomColumn(int atom2, Vector3d fg);
90  
91 < }
91 >    // filling interaction blocks with pointers
92 >    InteractionData fillInteractionData(int atom1, int atom2);
93 >    InteractionData fillSkipData(int atom1, int atom2);
94 >    SelfData fillSelfData(int atom1);
95  
96 +  private:
97 +    SnapshotManager* sman_;    
98 +    Snapshot* snap_;
99 +    int storageLayout_;
100 +    vector<Vector3i> Cells;
101  
102 +    int nLocal_;
103 +    int nGroups_;
104  
105 + #ifdef IS_MPI    
106 +    DataStorage atomRowData;
107 +    DataStorage atomColData;
108 +    DataStorage cgRowData;
109 +    DataStorage cgColData;
110  
111 +    int nAtomsInRow_;
112 +    int nAtomsInCol_;
113 +    int nGroupsInRow_;
114 +    int nGroupsInCol_;
115  
116 +    Communicator<Row, int>* AtomCommIntRow;
117 +    Communicator<Row, RealType>* AtomCommRealRow;
118 +    Communicator<Row, Vector3d>* AtomCommVectorRow;
119 +    Communicator<Row, Mat3x3d>*  AtomCommMatrixRow;
120  
121 +    Communicator<Column, int>* AtomCommIntColumn;
122 +    Communicator<Column, RealType>* AtomCommRealColumn;
123 +    Communicator<Column, Vector3d>* AtomCommVectorColumn;
124 +    Communicator<Column, Mat3x3d>*  AtomCommMatrixColumn;
125  
126 +    Communicator<Row, int>* cgCommIntRow;
127 +    Communicator<Row, Vector3d>* cgCommVectorRow;
128 +    Communicator<Column, int>* cgCommIntColumn;
129 +    Communicator<Column, Vector3d>* cgCommVectorColumn;
130  
131 +    vector<vector<RealType> > pot_row;
132 +    vector<vector<RealType> > pot_col;
133 +    vector<int> identsRow;
134 +    vector<int> identsCol;
135 +
136 +    vector<int> AtomLocalToGlobal;
137 +    vector<int> AtomRowToGlobal;
138 +    vector<int> AtomColToGlobal;
139 +    vector<int> cgLocalToGlobal;
140 +    vector<int> cgRowToGlobal;
141 +    vector<int> cgColToGlobal;
142 +
143 +    vector<vector<int> > CellListRow;
144 +    vector<vector<int> > CellListCol;
145 + #else
146 +    vector<vector<int> > CellList;
147   #endif
148 +    vector<RealType> pot_local;
149  
150 +  };
151  
152 + }
153 + #endif
154 +

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