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1 | /* | |
2 | < | * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
2 | > | * Copyright (c) 2011 The University of Notre Dame. All Rights Reserved. |
3 | * | |
4 | * The University of Notre Dame grants you ("Licensee") a | |
5 | * non-exclusive, royalty free, license to use, modify and | |
# | Line 36 | 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_DECOMPOSITION_HPP |
44 | < | #define PARALLEL_DECOMPOSITION_HPP |
43 | > | #ifndef PARALLEL_FORCEDECOMPOSITION_HPP |
44 | > | #define PARALLEL_FORCEDECOMPOSITION_HPP |
45 | ||
46 | + | #include "brains/SimInfo.hpp" |
47 | #include "brains/SnapshotManager.hpp" | |
48 | < | #include "types/AtomType.hpp" |
48 | > | #include "nonbonded/NonBondedInteraction.hpp" |
49 | > | #include "nonbonded/Cutoffs.hpp" |
50 | > | #include "nonbonded/InteractionManager.hpp" |
51 | > | #include "utils/Tuple.hpp" |
52 | ||
53 | using namespace std; | |
54 | namespace OpenMD { | |
55 | ||
56 | + | typedef tuple3<RealType, RealType, RealType> groupCutoffs; |
57 | + | |
58 | /** | |
59 | < | * @class Decomposition |
53 | < | * Decomposition is an interface for passing out and collecting information |
54 | < | * from many processors at various stages of the main non-bonded ForceLoop. |
59 | > | * @class ForceDecomposition |
60 | * | |
61 | + | * ForceDecomposition is an interface for passing out and collecting |
62 | + | * information from many processors at various stages of the main |
63 | + | * non-bonded ForceLoop. |
64 | + | * |
65 | * The pairwise force calculation has an outer-running loop (the "I" | |
66 | * loop) and an inner-running loop (the "J" loop). In parallel | |
67 | * decompositions, these loop over different groups of atoms on | |
# | Line 62 | Line 71 | namespace OpenMD { | |
71 | * | |
72 | * distributeInitialData (parallel communication - one time only) | |
73 | * distributeData (parallel communication - every ForceLoop) | |
74 | < | * loop over i |
75 | < | * | loop over j |
76 | < | * | | localComputation |
74 | > | * |
75 | > | * loop iLoop over nLoops (nLoops may be 1, 2, or until self consistent) |
76 | > | * | loop over i |
77 | > | * | | loop over j |
78 | > | * | | | localComputation |
79 | > | * | | end |
80 | * | end | |
81 | + | * | if (nLoops > 1): |
82 | + | * | | collectIntermediateData (parallel communication) |
83 | + | * | | distributeIntermediateData (parallel communication) |
84 | + | * | endif |
85 | * end | |
86 | < | * collectIntermediateData (parallel communication) |
71 | < | * distributeIntermediateData (parallel communication) |
72 | < | * loop over i |
73 | < | * | loop over j |
74 | < | * | | localComputation |
75 | < | * | end |
76 | < | * end |
77 | < | * collectData (parallel communication) |
86 | > | * collectData (parallel communication) |
87 | * | |
88 | < | * Decomposition provides the interface for ForceLoop to do the |
88 | > | * ForceDecomposition provides the interface for ForceLoop to do the |
89 | * communication steps and to iterate using the correct set of atoms | |
90 | * and cutoff groups. | |
91 | */ | |
92 | < | class Decomposition { |
92 | > | class ForceDecomposition { |
93 | public: | |
94 | ||
95 | < | Decomposition(SnapshotManager* sman) : sman_(sman) {} |
96 | < | virtual ~Decomposition() {} |
95 | > | ForceDecomposition(SimInfo* info, InteractionManager* iMan); |
96 | > | virtual ~ForceDecomposition() {} |
97 | ||
98 | virtual void distributeInitialData() = 0; | |
99 | virtual void distributeData() = 0; | |
100 | + | virtual void zeroWorkArrays() = 0; |
101 | virtual void collectIntermediateData() = 0; | |
102 | virtual void distributeIntermediateData() = 0; | |
103 | virtual void collectData() = 0; | |
104 | + | virtual potVec* getEmbeddingPotential() { return &embeddingPot; } |
105 | + | virtual potVec* getPairwisePotential() { return &pairwisePot; } |
106 | ||
107 | < | virtual unsigned int getNcutoffGroupsI() = 0; |
108 | < | virtual unsigned int getNcutoffGroupsJ() = 0; |
107 | > | // neighbor list routines |
108 | > | virtual bool checkNeighborList(); |
109 | > | virtual vector<pair<int, int> > buildNeighborList() = 0; |
110 | ||
111 | < | virtual vector<int> getAtomsInGroupI(int whichCGI) = 0; |
112 | < | virtual vector<int> getAtomsInGroupJ(int whichCGJ) = 0; |
111 | > | // how to handle cutoffs: |
112 | > | void setCutoffPolicy(CutoffPolicy cp) {cutoffPolicy_ = cp;} |
113 | > | void setUserCutoff(RealType rcut) {userCutoff_ = rcut; userChoseCutoff_ = true; } |
114 | ||
115 | < | virtual AtomType* getAtomTypeI(int whichAtomI) = 0; |
116 | < | virtual AtomType* getAtomTypeJ(int whichAtomJ) = 0; |
115 | > | // group bookkeeping |
116 | > | virtual groupCutoffs getGroupCutoffs(int cg1, int cg2) = 0; |
117 | > | virtual Vector3d getGroupVelocityColumn(int atom2) = 0; |
118 | > | |
119 | > | // Group->atom bookkeeping |
120 | > | virtual vector<int> getAtomsInGroupRow(int cg1) = 0; |
121 | > | virtual vector<int> getAtomsInGroupColumn(int cg2) = 0; |
122 | > | |
123 | > | virtual Vector3d getAtomToGroupVectorRow(int atom1, int cg1) = 0; |
124 | > | virtual Vector3d getAtomToGroupVectorColumn(int atom2, int cg2) = 0; |
125 | > | virtual RealType getMassFactorRow(int atom1) = 0; |
126 | > | virtual RealType getMassFactorColumn(int atom2) = 0; |
127 | > | |
128 | > | // spatial data |
129 | > | virtual Vector3d getIntergroupVector(int cg1, int cg2) = 0; |
130 | > | virtual Vector3d getInteratomicVector(int atom1, int atom2) = 0; |
131 | > | |
132 | > | // atom bookkeeping |
133 | > | virtual int getNAtomsInRow() = 0; |
134 | > | virtual vector<int> getExcludesForAtom(int atom1) = 0; |
135 | > | virtual bool skipAtomPair(int atom1, int atom2) = 0; |
136 | > | virtual bool excludeAtomPair(int atom1, int atom2) = 0; |
137 | > | virtual int getTopologicalDistance(int atom1, int atom2) = 0; |
138 | > | virtual void addForceToAtomRow(int atom1, Vector3d fg) = 0; |
139 | > | virtual void addForceToAtomColumn(int atom2, Vector3d fg) = 0; |
140 | > | virtual Vector3d getAtomVelocityColumn(int atom2) = 0; |
141 | > | |
142 | > | // filling interaction blocks with pointers |
143 | > | virtual void fillInteractionData(InteractionData &idat, int atom1, int atom2) = 0; |
144 | > | virtual void unpackInteractionData(InteractionData &idat, int atom1, int atom2) = 0; |
145 | > | |
146 | > | virtual void fillSelfData(SelfData &sdat, int atom1); |
147 | > | |
148 | > | virtual void addToHeatFlux(Vector3d hf); |
149 | > | virtual void setHeatFlux(Vector3d hf); |
150 | ||
151 | protected: | |
152 | < | SnapshotManager* sman_; |
152 | > | SimInfo* info_; |
153 | > | SnapshotManager* sman_; |
154 | > | Snapshot* snap_; |
155 | > | ForceField* ff_; |
156 | > | InteractionManager* interactionMan_; |
157 | > | |
158 | > | int storageLayout_; |
159 | > | bool needVelocities_; |
160 | > | RealType skinThickness_; /**< Verlet neighbor list skin thickness */ |
161 | > | RealType largestRcut_; |
162 | > | |
163 | > | vector<int> idents; |
164 | > | potVec pairwisePot; |
165 | > | potVec embeddingPot; |
166 | > | |
167 | > | /** |
168 | > | * The topological distance between two atomic sites is handled |
169 | > | * via two vector structures for speed. These structures agnostic |
170 | > | * regarding the parallel decomposition. The index for |
171 | > | * toposForAtom could be local or row, while the values could be |
172 | > | * local or column. It will be up to the specific decomposition |
173 | > | * method to fill these. |
174 | > | */ |
175 | > | vector<vector<int> > toposForAtom; |
176 | > | vector<vector<int> > topoDist; |
177 | > | vector<vector<int> > excludesForAtom; |
178 | > | vector<vector<int> > groupList_; |
179 | > | vector<RealType> massFactors; |
180 | > | vector<AtomType*> atypesLocal; |
181 | > | |
182 | > | vector<Vector3i> cellOffsets_; |
183 | > | Vector3i nCells_; |
184 | > | vector<vector<int> > cellList_; |
185 | > | vector<Vector3d> saved_CG_positions_; |
186 | > | |
187 | > | bool userChoseCutoff_; |
188 | > | RealType userCutoff_; |
189 | > | CutoffPolicy cutoffPolicy_; |
190 | > | |
191 | > | map<pair<int, int>, tuple3<RealType, RealType, RealType> > gTypeCutoffMap; |
192 | > | |
193 | }; | |
194 | } | |
195 | #endif |
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