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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.
Revision 1545 by gezelter, Fri Apr 8 21:25:19 2011 UTC

# Line 42 | Line 42
42   #ifndef PARALLEL_DECOMPOSITION_HPP
43   #define PARALLEL_DECOMPOSITION_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 {
# Line 62 | Line 62 | namespace OpenMD {
62     *
63     *  distributeInitialData      (parallel communication - one time only)
64     *  distributeData             (parallel communication - every ForceLoop)
65 <   *  loop over i
66 <   *  | loop over j
67 <   *  | | localComputation
65 >   *
66 >   *  loop iLoop over nLoops     (nLoops may be 1, 2, or until self consistent)
67 >   *  |  loop over i
68 >   *  |  | loop over j
69 >   *  |  | | localComputation
70 >   *  |  |  end
71     *  |  end
72 +   *  |  if (nLoops > 1):
73 +   *  |  |   collectIntermediateData    (parallel communication)
74 +   *  |  |   distributeIntermediateData (parallel communication)
75 +   *  |  endif
76     *  end
77 <   *  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)
77 >   * collectData                        (parallel communication)
78     *
79     * Decomposition provides the interface for ForceLoop to do the
80     * communication steps and to iterate using the correct set of atoms
# Line 83 | Line 83 | namespace OpenMD {
83    class Decomposition {
84    public:
85  
86 <    Decomposition(SnapshotManager* sman) : sman_(sman) {}
86 >    Decomposition(SimInfo* info) : info_(info) {}
87      virtual ~Decomposition() {}
88      
89      virtual void distributeInitialData() = 0;
# Line 92 | Line 92 | namespace OpenMD {
92      virtual void distributeIntermediateData() = 0;
93      virtual void collectData() = 0;
94  
95 <    virtual unsigned int getNcutoffGroupsI() = 0;
96 <    virtual unsigned int getNcutoffGroupsJ() = 0;
95 >    // neighbor list routines
96 >    virtual bool checkNeighborList() = 0;
97 >    virtual vector<pair<int, int> >  buildNeighborList() = 0;
98  
99 <    virtual vector<int> getAtomsInGroupI(int whichCGI) = 0;
100 <    virtual vector<int> getAtomsInGroupJ(int whichCGJ) = 0;
99 >    // group bookkeeping
100 >    virtual pair<int, int> getGroupTypes(int cg1, int cg2) = 0;
101  
102 <    virtual AtomType* getAtomTypeI(int whichAtomI) = 0;
103 <    virtual AtomType* getAtomTypeJ(int whichAtomJ) = 0;
102 >    // Group->atom bookkeeping
103 >    virtual vector<int> getAtomsInGroupI(int cg1) = 0;
104 >    virtual vector<int> getAtomsInGroupJ(int cg2) = 0;
105 >    virtual Vector3d getAtomToGroupVectorI(int atom1, int cg1) = 0;
106 >    virtual Vector3d getAtomToGroupVectorJ(int atom2, int cg2) = 0;
107 >    virtual RealType getMfactI(int atom1) = 0;
108 >    virtual RealType getMfactJ(int atom2) = 0;
109 >
110 >    // spatial data
111 >    virtual Vector3d getIntergroupVector(int cg1, int cg2) = 0;
112 >    virtual Vector3d getInteratomicVector(int atom1, int atom2) = 0;
113 >      
114 >    // atom bookkeeping
115 >    virtual vector<int> getAtomList() = 0;
116 >    virtual vector<int> getSkipsForAtom(int atom1) = 0
117 >    virtual bool skipAtomPair(int atom1, int atom2) = 0;
118 >    virtual void addForceToAtomI(int atom1, Vector3d fg) = 0;
119 >    virtual void addForceToAtomJ(int atom2, Vector3d fg) = 0;
120 >
121 >    // filling interaction blocks with pointers
122 >    virtual InteractionData fillInteractionData(int atom1, int atom2) = 0;
123 >    virtual InteractionData fillSkipData(int atom1, int atom2) = 0;
124 >    virtual SelfData fillSelfData(int atom1) = 0;
125      
126    protected:
127 <    SnapshotManager* sman_;
127 >    SimInfo* info_;  
128 >    map<pair<int, int>, int> topoDist; //< topoDist gives the
129 >                                       //topological distance between
130 >                                       //two atomic sites.  This
131 >                                       //declaration is agnostic
132 >                                       //regarding the parallel
133 >                                       //decomposition.  The two
134 >                                       //indices could be local or row
135 >                                       //& column.  It will be up to
136 >                                       //the specific decomposition
137 >                                       //method to fill this.
138 >    map<pair<int, int>, bool> exclude; //< exclude is the set of pairs
139 >                                       //to leave out of non-bonded
140 >                                       //force evaluations.  This
141 >                                       //declaration is agnostic
142 >                                       //regarding the parallel
143 >                                       //decomposition.  The two
144 >                                       //indices could be local or row
145 >                                       //& column.  It will be up to
146 >                                       //the specific decomposition
147 >                                       //method to fill this.
148    };    
149   }
150   #endif

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