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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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