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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 1583 by gezelter, Thu Jun 16 22:00:08 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, InteractionManager* iMan) : ForceDecomposition(info, iMan) {};
59  
60 < namespace OpenMD{
60 >    void distributeInitialData();
61 >    void zeroWorkArrays();
62 >    void distributeData();
63 >    void collectIntermediateData();
64 >    void distributeIntermediateData();
65 >    void collectData();
66  
67 < class ForceDecomposition
68 < {
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 < };
67 >    // neighbor list routines
68 >    vector<pair<int, int> >  buildNeighborList();
69  
70 +    // group bookkeeping
71 +    groupCutoffs getGroupCutoffs(int cg1, int cg2);
72  
73 +    // Group->atom bookkeeping
74 +    vector<int> getAtomsInGroupRow(int cg1);
75 +    vector<int> getAtomsInGroupColumn(int cg2);
76 +    Vector3d getAtomToGroupVectorRow(int atom1, int cg1);
77 +    Vector3d getAtomToGroupVectorColumn(int atom2, int cg2);
78 +    RealType getMassFactorRow(int atom1);
79 +    RealType getMassFactorColumn(int atom2);
80  
81 < }
81 >    // spatial data
82 >    Vector3d getIntergroupVector(int cg1, int cg2);
83 >    Vector3d getInteratomicVector(int atom1, int atom2);
84 >      
85 >    // atom bookkeeping
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 +    void fillInteractionData(InteractionData &idat, int atom1, int atom2);
95 +    void unpackInteractionData(InteractionData &idat, int atom1, int atom2);
96 +    void fillSkipData(InteractionData &idat, int atom1, int atom2);
97 +    void unpackSkipData(InteractionData &idat, int atom1, int atom2);
98  
99 +  private:
100 +    void createGtypeCutoffMap();
101  
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 +    int nAtomsInRow_;
116 +    int nAtomsInCol_;
117 +    int nGroupsInRow_;
118 +    int nGroupsInCol_;
119  
120 +    Communicator<Row, int>* AtomCommIntRow;
121 +    Communicator<Row, RealType>* AtomCommRealRow;
122 +    Communicator<Row, Vector3d>* AtomCommVectorRow;
123 +    Communicator<Row, Mat3x3d>*  AtomCommMatrixRow;
124 +    Communicator<Row, potVec>* AtomCommPotRow;
125  
126 +    Communicator<Column, int>* AtomCommIntColumn;
127 +    Communicator<Column, RealType>* AtomCommRealColumn;
128 +    Communicator<Column, Vector3d>* AtomCommVectorColumn;
129 +    Communicator<Column, Mat3x3d>*  AtomCommMatrixColumn;
130 +    Communicator<Column, potVec>* AtomCommPotColumn;
131  
132 +    Communicator<Row, int>* cgCommIntRow;
133 +    Communicator<Row, Vector3d>* cgCommVectorRow;
134 +    Communicator<Column, int>* cgCommIntColumn;
135 +    Communicator<Column, Vector3d>* cgCommVectorColumn;
136 +
137 +    // work arrays for assembling potential energy
138 +    vector<potVec> pot_row;
139 +    vector<potVec> pot_col;
140 +
141 +    vector<int> identsRow;
142 +    vector<int> identsCol;
143 +
144 +    vector<AtomType*> atypesRow;
145 +    vector<AtomType*> atypesCol;
146 +
147 +    vector<int> AtomRowToGlobal;
148 +    vector<int> AtomColToGlobal;
149 +
150 +    vector<int> cgRowToGlobal;
151 +    vector<int> cgColToGlobal;
152 +
153 +    vector<RealType> groupCutoffRow;
154 +    vector<RealType> groupCutoffCol;
155 +    vector<int> groupColToGtype;
156 +    vector<int> groupRowToGtype;
157 +
158 +    vector<vector<int> > cellListRow_;
159 +    vector<vector<int> > cellListCol_;
160 +
161 +    vector<vector<int> > groupListRow_;
162 +    vector<vector<int> > groupListCol_;
163 +
164 +    vector<RealType> massFactorsRow;
165 +    vector<RealType> massFactorsCol;
166   #endif
167  
168 +  };
169  
170 + }
171 + #endif
172 +

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