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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 1568 by gezelter, Wed May 25 16:20:37 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  
49   using namespace std;
50   namespace OpenMD {
51    
52    /**
53 <   * @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.
53 >   * @class ForceDecomposition
54     *
55 +   * ForceDecomposition is an interface for passing out and collecting
56 +   * information from many processors at various stages of the main
57 +   * non-bonded ForceLoop.
58 +   *
59     * The pairwise force calculation has an outer-running loop (the "I"
60     * loop) and an inner-running loop (the "J" loop).  In parallel
61     * decompositions, these loop over different groups of atoms on
# Line 62 | Line 65 | namespace OpenMD {
65     *
66     *  distributeInitialData      (parallel communication - one time only)
67     *  distributeData             (parallel communication - every ForceLoop)
68 <   *  loop over i
69 <   *  | loop over j
70 <   *  | | localComputation
68 >   *
69 >   *  loop iLoop over nLoops     (nLoops may be 1, 2, or until self consistent)
70 >   *  |  loop over i
71 >   *  |  | loop over j
72 >   *  |  | | localComputation
73 >   *  |  |  end
74     *  |  end
75 +   *  |  if (nLoops > 1):
76 +   *  |  |   collectIntermediateData    (parallel communication)
77 +   *  |  |   distributeIntermediateData (parallel communication)
78 +   *  |  endif
79     *  end
80 <   *  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)
80 >   * collectData                        (parallel communication)
81     *
82 <   * Decomposition provides the interface for ForceLoop to do the
82 >   * ForceDecomposition provides the interface for ForceLoop to do the
83     * communication steps and to iterate using the correct set of atoms
84     * and cutoff groups.
85     */
86 <  class Decomposition {
86 >  class ForceDecomposition {
87    public:
88  
89 <    Decomposition(SnapshotManager* sman) : sman_(sman) {}
90 <    virtual ~Decomposition() {}
89 >    ForceDecomposition(SimInfo* info);
90 >    virtual ~ForceDecomposition() {}
91      
92      virtual void distributeInitialData() = 0;
93      virtual void distributeData() = 0;
# Line 92 | Line 95 | namespace OpenMD {
95      virtual void distributeIntermediateData() = 0;
96      virtual void collectData() = 0;
97  
98 <    virtual unsigned int getNcutoffGroupsI() = 0;
99 <    virtual unsigned int getNcutoffGroupsJ() = 0;
98 >    // neighbor list routines
99 >    virtual bool checkNeighborList();
100 >    virtual vector<pair<int, int> >  buildNeighborList() = 0;
101  
102 <    virtual vector<int> getAtomsInGroupI(int whichCGI) = 0;
103 <    virtual vector<int> getAtomsInGroupJ(int whichCGJ) = 0;
102 >    // group bookkeeping
103 >    virtual pair<int, int> getGroupTypes(int cg1, int cg2) = 0;
104  
105 <    virtual AtomType* getAtomTypeI(int whichAtomI) = 0;
106 <    virtual AtomType* getAtomTypeJ(int whichAtomJ) = 0;
105 >    // Group->atom bookkeeping
106 >    virtual vector<int> getAtomsInGroupRow(int cg1) = 0;
107 >    virtual vector<int> getAtomsInGroupColumn(int cg2) = 0;
108 >    virtual Vector3d getAtomToGroupVectorRow(int atom1, int cg1) = 0;
109 >    virtual Vector3d getAtomToGroupVectorColumn(int atom2, int cg2) = 0;
110 >    virtual RealType getMfactRow(int atom1) = 0;
111 >    virtual RealType getMfactColumn(int atom2) = 0;
112 >
113 >    // spatial data
114 >    virtual Vector3d getIntergroupVector(int cg1, int cg2) = 0;
115 >    virtual Vector3d getInteratomicVector(int atom1, int atom2) = 0;
116 >      
117 >    // atom bookkeeping
118 >    virtual vector<int> getAtomList() = 0;
119 >    virtual vector<int> getSkipsForAtom(int atom1) = 0;
120 >    virtual bool skipAtomPair(int atom1, int atom2) = 0;
121 >    virtual void addForceToAtomRow(int atom1, Vector3d fg) = 0;
122 >    virtual void addForceToAtomColumn(int atom2, Vector3d fg) = 0;
123 >
124 >    // filling interaction blocks with pointers
125 >    virtual InteractionData fillInteractionData(int atom1, int atom2) = 0;
126 >    virtual InteractionData fillSkipData(int atom1, int atom2) = 0;
127 >    virtual SelfData fillSelfData(int atom1);
128      
129    protected:
130 <    SnapshotManager* sman_;
130 >    SimInfo* info_;  
131 >    SnapshotManager* sman_;    
132 >    Snapshot* snap_;
133 >    int storageLayout_;
134 >    RealType skinThickness_;   /**< Verlet neighbor list skin thickness */    
135 >
136 >    map<pair<int, int>, int> topoDist; //< topoDist gives the
137 >                                       //topological distance between
138 >                                       //two atomic sites.  This
139 >                                       //declaration is agnostic
140 >                                       //regarding the parallel
141 >                                       //decomposition.  The two
142 >                                       //indices could be local or row
143 >                                       //& column.  It will be up to
144 >                                       //the specific decomposition
145 >                                       //method to fill this.
146 >    map<pair<int, int>, bool> exclude; //< exclude is the set of pairs
147 >                                       //to leave out of non-bonded
148 >                                       //force evaluations.  This
149 >                                       //declaration is agnostic
150 >                                       //regarding the parallel
151 >                                       //decomposition.  The two
152 >                                       //indices could be local or row
153 >                                       //& column.  It will be up to
154 >                                       //the specific decomposition
155 >                                       //method to fill this.
156 >    vector<Vector3i> cellOffsets_;
157 >    Vector3i nCells_;
158 >    vector<vector<int> > cellList_;
159 >    vector<Vector3d> saved_CG_positions_;
160 >
161    };    
162   }
163   #endif

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