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/* |
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* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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* Copyright (c) 2011 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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* non-exclusive, royalty free, license to use, modify and |
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* [4] Vardeman & Gezelter, in progress (2009). |
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*/ |
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#ifndef PARALLEL_DECOMPOSITION_HPP |
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#define PARALLEL_DECOMPOSITION_HPP |
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#ifndef PARALLEL_FORCEDECOMPOSITION_HPP |
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#define PARALLEL_FORCEDECOMPOSITION_HPP |
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#include "brains/SimInfo.hpp" |
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#include "types/AtomType.hpp" |
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#include "brains/SnapshotManager.hpp" |
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#include "nonbonded/NonBondedInteraction.hpp" |
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#include "nonbonded/Cutoffs.hpp" |
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#include "nonbonded/InteractionManager.hpp" |
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#include "utils/Tuple.hpp" |
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using namespace std; |
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namespace OpenMD { |
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typedef tuple3<RealType, RealType, RealType> groupCutoffs; |
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/** |
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* @class Decomposition |
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* Decomposition is an interface for passing out and collecting information |
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* from many processors at various stages of the main non-bonded ForceLoop. |
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* @class ForceDecomposition |
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* |
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* ForceDecomposition is an interface for passing out and collecting |
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* information from many processors at various stages of the main |
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* non-bonded ForceLoop. |
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* |
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* The pairwise force calculation has an outer-running loop (the "I" |
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* loop) and an inner-running loop (the "J" loop). In parallel |
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* decompositions, these loop over different groups of atoms on |
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* end |
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* collectData (parallel communication) |
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* |
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* Decomposition provides the interface for ForceLoop to do the |
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* ForceDecomposition provides the interface for ForceLoop to do the |
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* communication steps and to iterate using the correct set of atoms |
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* and cutoff groups. |
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*/ |
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class Decomposition { |
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class ForceDecomposition { |
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public: |
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Decomposition(SimInfo* info) : info_(info) {} |
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virtual ~Decomposition() {} |
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ForceDecomposition(SimInfo* info, InteractionManager* iMan); |
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virtual ~ForceDecomposition() {} |
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virtual void distributeInitialData() = 0; |
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virtual void distributeData() = 0; |
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virtual void zeroWorkArrays() = 0; |
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virtual void collectIntermediateData() = 0; |
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virtual void distributeIntermediateData() = 0; |
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virtual void collectData() = 0; |
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virtual potVec* getEmbeddingPotential() { return &embeddingPot; } |
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virtual potVec* getPairwisePotential() { return &pairwisePot; } |
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virtual unsigned int getNcutoffGroupsI() = 0; |
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virtual unsigned int getNcutoffGroupsJ() = 0; |
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// neighbor list routines |
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virtual bool checkNeighborList(); |
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virtual vector<pair<int, int> > buildNeighborList() = 0; |
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virtual vector<int> getAtomsInGroupI(int whichCGI) = 0; |
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virtual vector<int> getAtomsInGroupJ(int whichCGJ) = 0; |
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// how to handle cutoffs: |
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void setCutoffPolicy(CutoffPolicy cp) {cutoffPolicy_ = cp;} |
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void setUserCutoff(RealType rcut) {userCutoff_ = rcut; userChoseCutoff_ = true; } |
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virtual AtomType* getAtomTypeI(int whichAtomI) = 0; |
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virtual AtomType* getAtomTypeJ(int whichAtomJ) = 0; |
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// group bookkeeping |
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virtual groupCutoffs getGroupCutoffs(int cg1, int cg2) = 0; |
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// Group->atom bookkeeping |
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virtual vector<int> getAtomsInGroupRow(int cg1) = 0; |
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virtual vector<int> getAtomsInGroupColumn(int cg2) = 0; |
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virtual Vector3d getAtomToGroupVectorRow(int atom1, int cg1) = 0; |
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virtual Vector3d getAtomToGroupVectorColumn(int atom2, int cg2) = 0; |
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virtual RealType getMassFactorRow(int atom1) = 0; |
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virtual RealType getMassFactorColumn(int atom2) = 0; |
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// spatial data |
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virtual Vector3d getIntergroupVector(int cg1, int cg2) = 0; |
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virtual Vector3d getInteratomicVector(int atom1, int atom2) = 0; |
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// atom bookkeeping |
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virtual int getNAtomsInRow() = 0; |
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virtual vector<int> getSkipsForAtom(int atom1) = 0; |
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virtual bool skipAtomPair(int atom1, int atom2) = 0; |
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virtual void addForceToAtomRow(int atom1, Vector3d fg) = 0; |
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virtual void addForceToAtomColumn(int atom2, Vector3d fg) = 0; |
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virtual int getTopologicalDistance(int atom1, int atom2) = 0; |
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// filling interaction blocks with pointers |
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virtual void fillInteractionData(InteractionData &idat, int atom1, int atom2) = 0; |
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virtual void unpackInteractionData(InteractionData &idat, int atom1, int atom2) = 0; |
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virtual void fillSkipData(InteractionData &idat, int atom1, int atom2) = 0; |
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virtual void unpackSkipData(InteractionData &idat, int atom1, int atom2) = 0; |
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virtual void fillSelfData(SelfData &sdat, int atom1); |
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protected: |
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SimInfo* info_; |
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map<pair<int, int>, int> topoDist; //< topoDist gives the |
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//topological distance between |
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//two atomic sites. This |
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//declaration is agnostic |
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//regarding the parallel |
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//decomposition. The two |
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//indices could be local or row |
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//& column. It will be up to |
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//the specific decomposition |
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//method to fill this. |
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map<pair<int, int>, bool> exclude; //< exclude is the set of pairs |
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//to leave out of non-bonded |
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//force evaluations. This |
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//declaration is agnostic |
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//regarding the parallel |
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//decomposition. The two |
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//indices could be local or row |
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//& column. It will be up to |
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//the specific decomposition |
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//method to fill this. |
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SnapshotManager* sman_; |
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Snapshot* snap_; |
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ForceField* ff_; |
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InteractionManager* interactionMan_; |
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int storageLayout_; |
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RealType skinThickness_; /**< Verlet neighbor list skin thickness */ |
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RealType largestRcut_; |
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vector<int> idents; |
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potVec pairwisePot; |
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potVec embeddingPot; |
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/** |
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* The topological distance between two atomic sites is handled |
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* via two vector structures for speed. These structures agnostic |
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* regarding the parallel decomposition. The index for |
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* toposForAtom could be local or row, while the values could be |
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* local or column. It will be up to the specific decomposition |
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* method to fill these. |
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*/ |
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vector<vector<int> > toposForAtom; |
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vector<vector<int> > topoDist; |
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vector<vector<int> > skipsForAtom; |
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vector<vector<int> > groupList_; |
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vector<RealType> massFactors; |
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vector<Vector3i> cellOffsets_; |
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Vector3i nCells_; |
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vector<vector<int> > cellList_; |
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vector<Vector3d> saved_CG_positions_; |
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bool userChoseCutoff_; |
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RealType userCutoff_; |
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CutoffPolicy cutoffPolicy_; |
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map<pair<int, int>, tuple3<RealType, RealType, RealType> > gTypeCutoffMap; |
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}; |
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} |
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#endif |
