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root/OpenMD/branches/devel_omp/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/devel_omp/src/parallel/ForceMatrixDecomposition.hpp (file contents), Revision 1598 by mciznick, Wed Jul 27 14:26:53 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);
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 < {
69 < public:
70 <  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 >    // neighbor list routines based on Rapaport
70 >    vector<vector<CutoffGroup *> > buildLayerBasedNeighborList();
71  
72 +    // group bookkeeping
73 +    groupCutoffs getGroupCutoffs(int cg1, int cg2);
74  
75 +    // Group->atom bookkeeping
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 getMassFactorRow(int atom1);
81 +    RealType getMassFactorColumn(int atom2);
82  
83 < }
83 >    // spatial data
84 >    Vector3d getIntergroupVector(int cg1, int cg2);
85 >    Vector3d getIntergroupVector(CutoffGroup *cg1, CutoffGroup *cg2);
86 >    Vector3d getInteratomicVector(int atom1, int atom2);
87 >      
88 >    // atom bookkeeping
89 >    int getNAtomsInRow();
90 >    int getTopologicalDistance(int atom1, int atom2);
91 >    vector<int> getExcludesForAtom(int atom1);
92 >    bool skipAtomPair(int atom1, int atom2);
93 >    bool excludeAtomPair(int atom1, int atom2);
94 >    void addForceToAtomRow(int atom1, Vector3d fg);
95 >    void addForceToAtomColumn(int atom2, Vector3d fg);
96  
97 +    // filling interaction blocks with pointers
98 +    void fillInteractionData(InteractionData &idat, int atom1, int atom2);
99 +    void unpackInteractionData(InteractionData &idat, int atom1, int atom2);
100  
101 +    // memory reordering
102 +    void reorderGroupCutoffs(vector<int> &order);
103 +    void reorderPosition(vector<int> &order);
104 +    void reorderGroupList(vector<int> &order);
105 +    void reorderMemory(vector<vector<CutoffGroup *> > &H_c_l);
106  
107 +  private:
108 +    void createGtypeCutoffMap();
109  
110 +    int nLocal_;
111 +    int nGroups_;
112 +    vector<int> AtomLocalToGlobal;
113 +    vector<int> cgLocalToGlobal;
114 +    vector<RealType> groupCutoff;
115 +    vector<int> groupToGtype;
116  
117 + #ifdef IS_MPI    
118 +    DataStorage atomRowData;
119 +    DataStorage atomColData;
120 +    DataStorage cgRowData;
121 +    DataStorage cgColData;
122  
123 +    int nAtomsInRow_;
124 +    int nAtomsInCol_;
125 +    int nGroupsInRow_;
126 +    int nGroupsInCol_;
127  
128 +    Communicator<Row> rowComm;
129 +    Communicator<Column> colComm;
130  
131 +    Plan<int>* AtomPlanIntRow;
132 +    Plan<RealType>* AtomPlanRealRow;
133 +    Plan<Vector3d>* AtomPlanVectorRow;
134 +    Plan<Mat3x3d>*  AtomPlanMatrixRow;
135 +    Plan<potVec>* AtomPlanPotRow;
136 +
137 +    Plan<int>* AtomPlanIntColumn;
138 +    Plan<RealType>* AtomPlanRealColumn;
139 +    Plan<Vector3d>* AtomPlanVectorColumn;
140 +    Plan<Mat3x3d>*  AtomPlanMatrixColumn;
141 +    Plan<potVec>* AtomPlanPotColumn;
142 +
143 +    Plan<int>* cgPlanIntRow;
144 +    Plan<Vector3d>* cgPlanVectorRow;
145 +    Plan<int>* cgPlanIntColumn;
146 +    Plan<Vector3d>* cgPlanVectorColumn;
147 +
148 +    // work arrays for assembling potential energy
149 +    vector<potVec> pot_row;
150 +    vector<potVec> pot_col;
151 +
152 +    vector<int> identsRow;
153 +    vector<int> identsCol;
154 +
155 +    vector<AtomType*> atypesRow;
156 +    vector<AtomType*> atypesCol;
157 +
158 +    vector<int> AtomRowToGlobal;
159 +    vector<int> AtomColToGlobal;
160 +
161 +    vector<int> cgRowToGlobal;
162 +    vector<int> cgColToGlobal;
163 +
164 +    vector<RealType> groupCutoffRow;
165 +    vector<RealType> groupCutoffCol;
166 +    vector<int> groupColToGtype;
167 +    vector<int> groupRowToGtype;
168 +
169 +    vector<vector<int> > cellListRow_;
170 +    vector<vector<int> > cellListCol_;
171 +
172 +    vector<vector<int> > groupListRow_;
173 +    vector<vector<int> > groupListCol_;
174 +
175 +    vector<RealType> massFactorsRow;
176 +    vector<RealType> massFactorsCol;
177   #endif
178  
179 +  };
180  
181 + }
182 + #endif
183 +

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