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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 1544 by gezelter, Fri Mar 18 19:31:52 2011 UTC

# Line 42 | Line 42
42   #ifndef PARALLEL_DECOMPOSITION_HPP
43   #define PARALLEL_DECOMPOSITION_HPP
44  
45 < #include "brains/SnapshotManager.hpp"
45 > #include "brains/SimInfo.hpp"
46   #include "types/AtomType.hpp"
47  
48   using namespace std;
# 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 102 | Line 102 | namespace OpenMD {
102      virtual AtomType* getAtomTypeJ(int whichAtomJ) = 0;
103      
104    protected:
105 <    SnapshotManager* sman_;
105 >    SimInfo* info_;  
106 >    map<pair<int, int>, int> topoDist; //< topoDist gives the
107 >                                       //topological distance between
108 >                                       //two atomic sites.  This
109 >                                       //declaration is agnostic
110 >                                       //regarding the parallel
111 >                                       //decomposition.  The two
112 >                                       //indices could be local or row
113 >                                       //& column.  It will be up to
114 >                                       //the specific decomposition
115 >                                       //method to fill this.
116 >    map<pair<int, int>, bool> exclude; //< exclude is the set of pairs
117 >                                       //to leave out of non-bonded
118 >                                       //force evaluations.  This
119 >                                       //declaration is agnostic
120 >                                       //regarding the parallel
121 >                                       //decomposition.  The two
122 >                                       //indices could be local or row
123 >                                       //& column.  It will be up to
124 >                                       //the specific decomposition
125 >                                       //method to fill this.
126    };    
127   }
128   #endif

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