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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 1562 by gezelter, Thu May 12 17:00:14 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/SnapshotManager.hpp"
46 < #include "types/AtomType.hpp"
45 > #include "brains/SimInfo.hpp"
46 > #include "nonbonded/NonBondedInteraction.hpp"
47  
48   using namespace std;
49   namespace OpenMD {
50    
51    /**
52 <   * @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.
52 >   * @class ForceDecomposition
53     *
54 +   * ForceDecomposition is an interface for passing out and collecting
55 +   * information from many processors at various stages of the main
56 +   * non-bonded ForceLoop.
57 +   *
58     * The pairwise force calculation has an outer-running loop (the "I"
59     * loop) and an inner-running loop (the "J" loop).  In parallel
60     * decompositions, these loop over different groups of atoms on
# Line 62 | Line 64 | namespace OpenMD {
64     *
65     *  distributeInitialData      (parallel communication - one time only)
66     *  distributeData             (parallel communication - every ForceLoop)
67 <   *  loop over i
68 <   *  | loop over j
69 <   *  | | localComputation
67 >   *
68 >   *  loop iLoop over nLoops     (nLoops may be 1, 2, or until self consistent)
69 >   *  |  loop over i
70 >   *  |  | loop over j
71 >   *  |  | | localComputation
72 >   *  |  |  end
73     *  |  end
74 +   *  |  if (nLoops > 1):
75 +   *  |  |   collectIntermediateData    (parallel communication)
76 +   *  |  |   distributeIntermediateData (parallel communication)
77 +   *  |  endif
78     *  end
79 <   *  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)
79 >   * collectData                        (parallel communication)
80     *
81 <   * Decomposition provides the interface for ForceLoop to do the
81 >   * ForceDecomposition provides the interface for ForceLoop to do the
82     * communication steps and to iterate using the correct set of atoms
83     * and cutoff groups.
84     */
85 <  class Decomposition {
85 >  class ForceDecomposition {
86    public:
87  
88 <    Decomposition(SnapshotManager* sman) : sman_(sman) {}
89 <    virtual ~Decomposition() {}
88 >    ForceDecomposition(SimInfo* info);
89 >    virtual ~ForceDecomposition() {}
90      
91      virtual void distributeInitialData() = 0;
92      virtual void distributeData() = 0;
# Line 92 | Line 94 | namespace OpenMD {
94      virtual void distributeIntermediateData() = 0;
95      virtual void collectData() = 0;
96  
97 <    virtual unsigned int getNcutoffGroupsI() = 0;
98 <    virtual unsigned int getNcutoffGroupsJ() = 0;
97 >    // neighbor list routines
98 >    virtual bool checkNeighborList() = 0;
99 >    virtual vector<pair<int, int> >  buildNeighborList() = 0;
100  
101 <    virtual vector<int> getAtomsInGroupI(int whichCGI) = 0;
102 <    virtual vector<int> getAtomsInGroupJ(int whichCGJ) = 0;
101 >    // group bookkeeping
102 >    virtual pair<int, int> getGroupTypes(int cg1, int cg2) = 0;
103  
104 <    virtual AtomType* getAtomTypeI(int whichAtomI) = 0;
105 <    virtual AtomType* getAtomTypeJ(int whichAtomJ) = 0;
104 >    // Group->atom bookkeeping
105 >    virtual vector<int> getAtomsInGroupRow(int cg1) = 0;
106 >    virtual vector<int> getAtomsInGroupColumn(int cg2) = 0;
107 >    virtual Vector3d getAtomToGroupVectorRow(int atom1, int cg1) = 0;
108 >    virtual Vector3d getAtomToGroupVectorColumn(int atom2, int cg2) = 0;
109 >    virtual RealType getMfactRow(int atom1) = 0;
110 >    virtual RealType getMfactColumn(int atom2) = 0;
111 >
112 >    // spatial data
113 >    virtual Vector3d getIntergroupVector(int cg1, int cg2) = 0;
114 >    virtual Vector3d getInteratomicVector(int atom1, int atom2) = 0;
115 >      
116 >    // atom bookkeeping
117 >    virtual vector<int> getAtomList() = 0;
118 >    virtual vector<int> getSkipsForAtom(int atom1) = 0;
119 >    virtual bool skipAtomPair(int atom1, int atom2) = 0;
120 >    virtual void addForceToAtomRow(int atom1, Vector3d fg) = 0;
121 >    virtual void addForceToAtomColumn(int atom2, Vector3d fg) = 0;
122 >
123 >    // filling interaction blocks with pointers
124 >    virtual InteractionData fillInteractionData(int atom1, int atom2) = 0;
125 >    virtual InteractionData fillSkipData(int atom1, int atom2) = 0;
126 >    virtual SelfData fillSelfData(int atom1) = 0;
127      
128    protected:
129 <    SnapshotManager* sman_;
129 >    SimInfo* info_;  
130 >    map<pair<int, int>, int> topoDist; //< topoDist gives the
131 >                                       //topological distance between
132 >                                       //two atomic sites.  This
133 >                                       //declaration is agnostic
134 >                                       //regarding the parallel
135 >                                       //decomposition.  The two
136 >                                       //indices could be local or row
137 >                                       //& column.  It will be up to
138 >                                       //the specific decomposition
139 >                                       //method to fill this.
140 >    map<pair<int, int>, bool> exclude; //< exclude is the set of pairs
141 >                                       //to leave out of non-bonded
142 >                                       //force evaluations.  This
143 >                                       //declaration is agnostic
144 >                                       //regarding the parallel
145 >                                       //decomposition.  The two
146 >                                       //indices could be local or row
147 >                                       //& column.  It will be up to
148 >                                       //the specific decomposition
149 >                                       //method to fill this.
150 >    vector<Vector3i> cellOffsets_;
151 >    int nOffset_;
152    };    
153   }
154   #endif

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