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root/OpenMD/trunk/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/development/src/parallel/ForceDecomposition.hpp (file contents), Revision 1581 by gezelter, Mon Jun 13 22:13:12 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  
52   using namespace std;
53   namespace OpenMD {
54    
55 +  typedef tuple3<RealType, RealType, RealType> groupCutoffs;
56 +
57    /**
58 <   * @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.
58 >   * @class ForceDecomposition
59     *
60 +   * ForceDecomposition is an interface for passing out and collecting
61 +   * information from many processors at various stages of the main
62 +   * non-bonded ForceLoop.
63 +   *
64     * The pairwise force calculation has an outer-running loop (the "I"
65     * loop) and an inner-running loop (the "J" loop).  In parallel
66     * decompositions, these loop over different groups of atoms on
# Line 62 | Line 70 | namespace OpenMD {
70     *
71     *  distributeInitialData      (parallel communication - one time only)
72     *  distributeData             (parallel communication - every ForceLoop)
73 <   *  loop over i
74 <   *  | loop over j
75 <   *  | | localComputation
73 >   *
74 >   *  loop iLoop over nLoops     (nLoops may be 1, 2, or until self consistent)
75 >   *  |  loop over i
76 >   *  |  | loop over j
77 >   *  |  | | localComputation
78 >   *  |  |  end
79     *  |  end
80 +   *  |  if (nLoops > 1):
81 +   *  |  |   collectIntermediateData    (parallel communication)
82 +   *  |  |   distributeIntermediateData (parallel communication)
83 +   *  |  endif
84     *  end
85 <   *  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)
85 >   * collectData                        (parallel communication)
86     *
87 <   * Decomposition provides the interface for ForceLoop to do the
87 >   * ForceDecomposition provides the interface for ForceLoop to do the
88     * communication steps and to iterate using the correct set of atoms
89     * and cutoff groups.
90     */
91 <  class Decomposition {
91 >  class ForceDecomposition {
92    public:
93  
94 <    Decomposition(SnapshotManager* sman) : sman_(sman) {}
95 <    virtual ~Decomposition() {}
94 >    ForceDecomposition(SimInfo* info, InteractionManager* iMan);
95 >    virtual ~ForceDecomposition() {}
96      
97      virtual void distributeInitialData() = 0;
98      virtual void distributeData() = 0;
99 +    virtual void zeroWorkArrays() = 0;
100      virtual void collectIntermediateData() = 0;
101      virtual void distributeIntermediateData() = 0;
102      virtual void collectData() = 0;
103 +    virtual potVec getLongRangePotential() { return longRangePot_; }
104  
105 <    virtual unsigned int getNcutoffGroupsI() = 0;
106 <    virtual unsigned int getNcutoffGroupsJ() = 0;
105 >    // neighbor list routines
106 >    virtual bool checkNeighborList();
107 >    virtual vector<pair<int, int> >  buildNeighborList() = 0;
108  
109 <    virtual vector<int> getAtomsInGroupI(int whichCGI) = 0;
110 <    virtual vector<int> getAtomsInGroupJ(int whichCGJ) = 0;
109 >    // how to handle cutoffs:
110 >    void setCutoffPolicy(CutoffPolicy cp) {cutoffPolicy_ = cp;}
111 >    void setUserCutoff(RealType rcut) {userCutoff_ = rcut; userChoseCutoff_ = true; }
112  
113 <    virtual AtomType* getAtomTypeI(int whichAtomI) = 0;
114 <    virtual AtomType* getAtomTypeJ(int whichAtomJ) = 0;
113 >    // group bookkeeping
114 >    virtual groupCutoffs getGroupCutoffs(int cg1, int cg2) = 0;
115 >
116 >    // Group->atom bookkeeping
117 >    virtual vector<int> getAtomsInGroupRow(int cg1) = 0;
118 >    virtual vector<int> getAtomsInGroupColumn(int cg2) = 0;
119 >
120 >    virtual Vector3d getAtomToGroupVectorRow(int atom1, int cg1) = 0;
121 >    virtual Vector3d getAtomToGroupVectorColumn(int atom2, int cg2) = 0;
122 >    virtual RealType getMassFactorRow(int atom1) = 0;
123 >    virtual RealType getMassFactorColumn(int atom2) = 0;
124 >
125 >    // spatial data
126 >    virtual Vector3d getIntergroupVector(int cg1, int cg2) = 0;
127 >    virtual Vector3d getInteratomicVector(int atom1, int atom2) = 0;
128 >      
129 >    // atom bookkeeping
130 >    virtual int getNAtomsInRow() = 0;
131 >    virtual vector<int> getSkipsForAtom(int atom1) = 0;
132 >    virtual bool skipAtomPair(int atom1, int atom2) = 0;
133 >    virtual void addForceToAtomRow(int atom1, Vector3d fg) = 0;
134 >    virtual void addForceToAtomColumn(int atom2, Vector3d fg) = 0;
135 >    virtual int getTopologicalDistance(int atom1, int atom2) = 0;
136 >
137 >    // filling interaction blocks with pointers
138 >    virtual void fillInteractionData(InteractionData idat, int atom1, int atom2) = 0;
139 >    virtual void unpackInteractionData(InteractionData idat, int atom1, int atom2) = 0;
140 >    virtual void fillSkipData(InteractionData idat, int atom1, int atom2) = 0;
141 >    virtual void fillSelfData(SelfData sdat, int atom1);
142      
143    protected:
144 <    SnapshotManager* sman_;
144 >    SimInfo* info_;  
145 >    SnapshotManager* sman_;    
146 >    Snapshot* snap_;
147 >    ForceField* ff_;
148 >    InteractionManager* interactionMan_;
149 >
150 >    int storageLayout_;
151 >    RealType skinThickness_;   /**< Verlet neighbor list skin thickness */    
152 >    RealType largestRcut_;
153 >
154 >    /**
155 >     * The topological distance between two atomic sites is handled
156 >     * via two vector structures for speed.  These structures agnostic
157 >     * regarding the parallel decomposition.  The index for
158 >     * toposForAtom could be local or row, while the values could be
159 >     * local or column.  It will be up to the specific decomposition
160 >     * method to fill these.
161 >     */
162 >    vector<vector<int> > toposForAtom;
163 >    vector<vector<int> > topoDist;                                      
164 >    vector<vector<int> > skipsForAtom;
165 >    vector<vector<int> > groupList_;
166 >    vector<RealType> massFactors;
167 >
168 >    vector<Vector3i> cellOffsets_;
169 >    Vector3i nCells_;
170 >    vector<vector<int> > cellList_;
171 >    vector<Vector3d> saved_CG_positions_;
172 >    potVec longRangePot_;
173 >
174 >    bool userChoseCutoff_;
175 >    RealType userCutoff_;
176 >    CutoffPolicy cutoffPolicy_;
177 >
178 >    map<pair<int, int>, tuple3<RealType, RealType, RealType> > gTypeCutoffMap;
179 >
180    };    
181   }
182   #endif

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