# | Line 36 | Line 36 | |
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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_FORCEDECOMPOSITION_HPP | |
# | Line 45 | Line 46 | |
46 | #include "brains/SimInfo.hpp" | |
47 | #include "brains/SnapshotManager.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 ForceDecomposition | |
60 | * | |
# | Line 78 | Line 84 | namespace OpenMD { | |
84 | * | endif | |
85 | * end | |
86 | * collectData (parallel communication) | |
87 | + | * loop over i |
88 | + | * | localComputation |
89 | + | * end |
90 | + | * collectSelfData (parallel communication) |
91 | * | |
92 | * ForceDecomposition provides the interface for ForceLoop to do the | |
93 | * communication steps and to iterate using the correct set of atoms | |
# | Line 86 | Line 96 | namespace OpenMD { | |
96 | class ForceDecomposition { | |
97 | public: | |
98 | ||
99 | < | ForceDecomposition(SimInfo* info); |
99 | > | ForceDecomposition(SimInfo* info, InteractionManager* iMan); |
100 | virtual ~ForceDecomposition() {} | |
101 | ||
102 | virtual void distributeInitialData() = 0; | |
103 | virtual void distributeData() = 0; | |
104 | + | virtual void zeroWorkArrays() = 0; |
105 | virtual void collectIntermediateData() = 0; | |
106 | virtual void distributeIntermediateData() = 0; | |
107 | virtual void collectData() = 0; | |
108 | + | virtual void collectSelfData() = 0; |
109 | + | virtual potVec* getEmbeddingPotential() { return &embeddingPot; } |
110 | + | virtual potVec* getPairwisePotential() { return &pairwisePot; } |
111 | + | virtual potVec* getExcludedPotential() { return &excludedPot; } |
112 | + | virtual potVec* getExcludedSelfPotential() { return &excludedSelfPot; } |
113 | ||
114 | // neighbor list routines | |
115 | virtual bool checkNeighborList(); | |
116 | virtual vector<pair<int, int> > buildNeighborList() = 0; | |
117 | ||
118 | + | // how to handle cutoffs: |
119 | + | void setCutoffPolicy(CutoffPolicy cp) {cutoffPolicy_ = cp;} |
120 | + | void setUserCutoff(RealType rcut) {userCutoff_ = rcut; userChoseCutoff_ = true; } |
121 | + | |
122 | // group bookkeeping | |
123 | < | virtual pair<int, int> getGroupTypes(int cg1, int cg2) = 0; |
123 | > | virtual groupCutoffs getGroupCutoffs(int cg1, int cg2) = 0; |
124 | > | virtual Vector3d getGroupVelocityColumn(int atom2) = 0; |
125 | ||
126 | // Group->atom bookkeeping | |
127 | virtual vector<int> getAtomsInGroupRow(int cg1) = 0; | |
# | Line 116 | Line 137 | namespace OpenMD { | |
137 | virtual Vector3d getInteratomicVector(int atom1, int atom2) = 0; | |
138 | ||
139 | // atom bookkeeping | |
140 | < | virtual vector<int> getAtomList() = 0; |
141 | < | virtual vector<int> getSkipsForAtom(int atom1) = 0; |
142 | < | virtual bool skipAtomPair(int atom1, int atom2) = 0; |
140 | > | virtual int getNAtomsInRow() = 0; |
141 | > | virtual vector<int> getExcludesForAtom(int atom1) = 0; |
142 | > | virtual bool skipAtomPair(int atom1, int atom2, int cg1, int cg2) = 0; |
143 | > | virtual bool excludeAtomPair(int atom1, int atom2) = 0; |
144 | > | virtual int getTopologicalDistance(int atom1, int atom2) = 0; |
145 | virtual void addForceToAtomRow(int atom1, Vector3d fg) = 0; | |
146 | virtual void addForceToAtomColumn(int atom2, Vector3d fg) = 0; | |
147 | + | virtual Vector3d getAtomVelocityColumn(int atom2) = 0; |
148 | ||
149 | // filling interaction blocks with pointers | |
150 | < | virtual InteractionData fillInteractionData(int atom1, int atom2) = 0; |
151 | < | virtual InteractionData fillSkipData(int atom1, int atom2) = 0; |
152 | < | virtual SelfData fillSelfData(int atom1); |
150 | > | virtual void fillInteractionData(InteractionData &idat, int atom1, int atom2) = 0; |
151 | > | virtual void unpackInteractionData(InteractionData &idat, int atom1, int atom2) = 0; |
152 | > | |
153 | > | virtual void fillSelfData(SelfData &sdat, int atom1); |
154 | > | |
155 | > | virtual void addToHeatFlux(Vector3d hf); |
156 | > | virtual void setHeatFlux(Vector3d hf); |
157 | ||
158 | protected: | |
159 | SimInfo* info_; | |
160 | SnapshotManager* sman_; | |
161 | Snapshot* snap_; | |
162 | + | ForceField* ff_; |
163 | + | InteractionManager* interactionMan_; |
164 | + | |
165 | int storageLayout_; | |
166 | + | bool needVelocities_; |
167 | RealType skinThickness_; /**< Verlet neighbor list skin thickness */ | |
168 | + | RealType largestRcut_; |
169 | ||
170 | < | map<pair<int, int>, int> topoDist; //< topoDist gives the |
171 | < | //topological distance between |
172 | < | //two atomic sites. This |
173 | < | //declaration is agnostic |
174 | < | //regarding the parallel |
142 | < | //decomposition. The two |
143 | < | //indices could be local or row |
144 | < | //& column. It will be up to |
145 | < | //the specific decomposition |
146 | < | //method to fill this. |
147 | < | map<pair<int, int>, bool> exclude; //< exclude is the set of pairs |
148 | < | //to leave out of non-bonded |
149 | < | //force evaluations. This |
150 | < | //declaration is agnostic |
151 | < | //regarding the parallel |
152 | < | //decomposition. The two |
153 | < | //indices could be local or row |
154 | < | //& column. It will be up to |
155 | < | //the specific decomposition |
156 | < | //method to fill this. |
170 | > | vector<int> idents; |
171 | > | potVec pairwisePot; |
172 | > | potVec embeddingPot; |
173 | > | potVec excludedPot; |
174 | > | potVec excludedSelfPot; |
175 | ||
176 | + | /** |
177 | + | * The topological distance between two atomic sites is handled |
178 | + | * via two vector structures for speed. These structures agnostic |
179 | + | * regarding the parallel decomposition. The index for |
180 | + | * toposForAtom could be local or row, while the values could be |
181 | + | * local or column. It will be up to the specific decomposition |
182 | + | * method to fill these. |
183 | + | */ |
184 | + | vector<vector<int> > toposForAtom; |
185 | + | vector<vector<int> > topoDist; |
186 | + | vector<vector<int> > excludesForAtom; |
187 | vector<vector<int> > groupList_; | |
188 | + | vector<RealType> massFactors; |
189 | + | vector<AtomType*> atypesLocal; |
190 | + | |
191 | vector<Vector3i> cellOffsets_; | |
192 | Vector3i nCells_; | |
193 | vector<vector<int> > cellList_; | |
194 | vector<Vector3d> saved_CG_positions_; | |
195 | ||
196 | + | bool userChoseCutoff_; |
197 | + | RealType userCutoff_; |
198 | + | CutoffPolicy cutoffPolicy_; |
199 | + | |
200 | + | map<pair<int, int>, tuple3<RealType, RealType, RealType> > gTypeCutoffMap; |
201 | + | |
202 | }; | |
203 | } | |
204 | #endif |
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