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root/OpenMD/branches/devel_omp/src/parallel/ForceDecomposition.hpp
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Comparing:
branches/development/src/parallel/Decomposition.hpp (file contents), Revision 1539 by gezelter, Fri Jan 14 22:31:31 2011 UTC vs.
branches/devel_omp/src/parallel/ForceDecomposition.hpp (file contents), Revision 1608 by mciznick, Tue Aug 9 01:58:56 2011 UTC

# Line 1 | Line 1
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 39 | Line 39
39   * [4]  Vardeman & Gezelter, in progress (2009).                        
40   */
41  
42 < #ifndef PARALLEL_DECOMPOSITION_HPP
43 < #define PARALLEL_DECOMPOSITION_HPP
42 > #ifndef PARALLEL_FORCEDECOMPOSITION_HPP
43 > #define PARALLEL_FORCEDECOMPOSITION_HPP
44  
45 + #include "brains/SimInfo.hpp"
46   #include "brains/SnapshotManager.hpp"
47 < #include "types/AtomType.hpp"
47 > #include "nonbonded/NonBondedInteraction.hpp"
48 > #include "nonbonded/Cutoffs.hpp"
49 > #include "nonbonded/InteractionManager.hpp"
50 > #include "utils/Tuple.hpp"
51 > #include "primitives/Molecule.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 >    virtual vector<vector<CutoffGroup *> >  buildLayerBasedNeighborList() = 0;
111  
112 <    virtual vector<int> getAtomsInGroupI(int whichCGI) = 0;
113 <    virtual vector<int> getAtomsInGroupJ(int whichCGJ) = 0;
112 >    // how to handle cutoffs:
113 >    void setCutoffPolicy(CutoffPolicy cp) {cutoffPolicy_ = cp;}
114 >    void setUserCutoff(RealType rcut) {userCutoff_ = rcut; userChoseCutoff_ = true; }
115  
116 <    virtual AtomType* getAtomTypeI(int whichAtomI) = 0;
117 <    virtual AtomType* getAtomTypeJ(int whichAtomJ) = 0;
116 >    // group bookkeeping
117 >    virtual groupCutoffs getGroupCutoffs(int cg1, int cg2) = 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 getIntergroupVector(CutoffGroup *cg1, CutoffGroup *cg2) = 0;
131 >    virtual Vector3d getInteratomicVector(int atom1, int atom2) = 0;
132 >      
133 >    // atom bookkeeping
134 >    virtual int getNAtomsInRow() = 0;
135 >    virtual vector<int> getExcludesForAtom(int atom1) = 0;
136 >    virtual bool skipAtomPair(int atom1, int atom2) = 0;
137 >    virtual bool excludeAtomPair(int atom1, int atom2) = 0;
138 >    virtual int getTopologicalDistance(int atom1, int atom2) = 0;
139 >    virtual void addForceToAtomRow(int atom1, Vector3d fg) = 0;
140 >    virtual void addForceToAtomColumn(int atom2, Vector3d fg) = 0;
141 >
142 >    virtual void addForceToAtomRowOMP(int atom1, Vector3d fg) = 0;
143 >    virtual void addForceToAtomColumnOMP(int atom2, Vector3d fg) = 0;
144 >
145 >
146 >    // filling interaction blocks with pointers
147 >    virtual void fillInteractionData(InteractionData &idat, int atom1, int atom2) = 0;
148 >    virtual void fillInteractionDataOMP(InteractionDataPrv &idat, int atom1, int atom2) = 0;
149 >    virtual void unpackInteractionData(InteractionData &idat, int atom1, int atom2) = 0;
150 >
151 >    virtual void unpackInteractionDataOMP(InteractionDataPrv &idat, int atom1, int atom2) = 0;
152 >
153 >    virtual void fillSelfData(SelfData &sdat, int atom1);
154      
155    protected:
156 <    SnapshotManager* sman_;
156 >    SimInfo* info_;  
157 >    SnapshotManager* sman_;    
158 >    Snapshot* snap_;
159 >    ForceField* ff_;
160 >    InteractionManager* interactionMan_;
161 >
162 >    int storageLayout_;
163 >    RealType skinThickness_;   /**< Verlet neighbor list skin thickness */    
164 >    RealType largestRcut_;
165 >
166 >    vector<int> idents;
167 >    potVec pairwisePot;
168 >    potVec embeddingPot;
169 >
170 >    /**
171 >     * The topological distance between two atomic sites is handled
172 >     * via two vector structures for speed.  These structures agnostic
173 >     * regarding the parallel decomposition.  The index for
174 >     * toposForAtom could be local or row, while the values could be
175 >     * local or column.  It will be up to the specific decomposition
176 >     * method to fill these.
177 >     */
178 >    vector<vector<int> > toposForAtom;
179 >    vector<vector<int> > topoDist;                                      
180 >    vector<vector<int> > excludesForAtom;
181 >    vector<vector<int> > groupList_;
182 >    vector<RealType> massFactors;
183 >    vector<AtomType*> atypesLocal;
184 >
185 >    vector<Vector3i> cellOffsets_;
186 >    vector<Vector3i> cellAllOffsets_;
187 >    Vector3i nCells_;
188 >    vector<vector<int> > cellList_;
189 >    vector<Vector3d> saved_CG_positions_;
190 >
191 >    bool userChoseCutoff_;
192 >    RealType userCutoff_;
193 >    CutoffPolicy cutoffPolicy_;
194 >
195 >    map<pair<int, int>, tuple3<RealType, RealType, RealType> > gTypeCutoffMap;
196 >
197    };    
198   }
199   #endif

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