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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 1723 by gezelter, Thu May 24 20:59:54 2012 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 43 | Line 36
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).                        
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"
47 + #include "math/SquareMatrix3.hpp"
48 + #include "brains/Snapshot.hpp"
49  
50 < /*  -*- c++ -*-  */
51 < #ifndef FORCEDECOMPOSITION_PARALLEL_HPP
52 < #define FORCEDECOMPOSITION_PARALLEL_HPP
50 > #ifdef IS_MPI
51 > #include "parallel/Communicator.hpp"
52 > #endif
53  
54 + using namespace std;
55 + namespace OpenMD {
56 +  
57 +  class ForceMatrixDecomposition : public ForceDecomposition {
58 +  public:
59 +    ForceMatrixDecomposition(SimInfo* info, InteractionManager* iMan);
60  
61 < namespace OpenMD{
61 >    void distributeInitialData();
62 >    void zeroWorkArrays();
63 >    void distributeData();
64 >    void collectIntermediateData();
65 >    void distributeIntermediateData();
66 >    void collectData();
67  
68 < class ForceDecomposition
69 < {
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 < };
68 >    // neighbor list routines
69 >    vector<pair<int, int> >  buildNeighborList();
70  
71 +    // group bookkeeping
72 +    groupCutoffs getGroupCutoffs(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);
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 getInteratomicVector(int atom1, int atom2);
86 >      
87 >    // atom bookkeeping
88 >    int getNAtomsInRow();
89 >    int getTopologicalDistance(int atom1, int atom2);
90 >    vector<int> getExcludesForAtom(int atom1);
91 >    bool skipAtomPair(int atom1, int atom2);
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 +    void fillInteractionData(InteractionData &idat, int atom1, int atom2);
99 +    void unpackInteractionData(InteractionData &idat, int atom1, int atom2);
100  
101 +  private:
102 +    void createGtypeCutoffMap();
103  
104 +    int nLocal_;
105 +    int nGroups_;
106 +    vector<int> AtomLocalToGlobal;
107 +    vector<int> cgLocalToGlobal;
108 +    vector<RealType> groupCutoff;
109 +    vector<int> groupToGtype;
110  
111 + #ifdef IS_MPI    
112 +    DataStorage atomRowData;    DataStorage atomColData;
113 +    DataStorage cgRowData;
114 +    DataStorage cgColData;
115  
116 +    int nAtomsInRow_;
117 +    int nAtomsInCol_;
118 +    int nGroupsInRow_;
119 +    int nGroupsInCol_;
120  
121 +    Communicator<Row> rowComm;
122 +    Communicator<Column> colComm;
123  
124 +    Plan<int>* AtomPlanIntRow;
125 +    Plan<RealType>* AtomPlanRealRow;
126 +    Plan<Vector3d>* AtomPlanVectorRow;
127 +    Plan<Mat3x3d>*  AtomPlanMatrixRow;
128 +    Plan<potVec>* AtomPlanPotRow;
129  
130 +    Plan<int>* AtomPlanIntColumn;
131 +    Plan<RealType>* AtomPlanRealColumn;
132 +    Plan<Vector3d>* AtomPlanVectorColumn;
133 +    Plan<Mat3x3d>*  AtomPlanMatrixColumn;
134 +    Plan<potVec>* AtomPlanPotColumn;
135 +
136 +    Plan<int>* cgPlanIntRow;
137 +    Plan<Vector3d>* cgPlanVectorRow;
138 +    Plan<int>* cgPlanIntColumn;
139 +    Plan<Vector3d>* cgPlanVectorColumn;
140 +
141 +    // work arrays for assembling potential energy
142 +    vector<potVec> pot_row;
143 +    vector<potVec> pot_col;
144 +
145 +    vector<int> identsRow;
146 +    vector<int> identsCol;
147 +
148 +    vector<AtomType*> atypesRow;
149 +    vector<AtomType*> atypesCol;
150 +
151 +    vector<int> AtomRowToGlobal;
152 +    vector<int> AtomColToGlobal;
153 +
154 + public:
155 +    vector<int> cgRowToGlobal;
156 +    vector<int> cgColToGlobal;
157 +
158 + private:
159 +    vector<RealType> groupCutoffRow;
160 +    vector<RealType> groupCutoffCol;
161 +    vector<int> groupColToGtype;
162 +    vector<int> groupRowToGtype;
163 +
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   #endif
173  
174 +  };
175  
176 + }
177 + #endif
178 +

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