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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 1575 by gezelter, Fri Jun 3 21:39:49 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;
94 +    virtual void zeroWorkArrays() = 0;
95      virtual void collectIntermediateData() = 0;
96      virtual void distributeIntermediateData() = 0;
97      virtual void collectData() = 0;
98 +    virtual potVec getLongRangePotential() { return longRangePot_; }
99  
100 <    virtual unsigned int getNcutoffGroupsI() = 0;
101 <    virtual unsigned int getNcutoffGroupsJ() = 0;
100 >    // neighbor list routines
101 >    virtual bool checkNeighborList();
102 >    virtual vector<pair<int, int> >  buildNeighborList() = 0;
103  
104 <    virtual vector<int> getAtomsInGroupI(int whichCGI) = 0;
105 <    virtual vector<int> getAtomsInGroupJ(int whichCGJ) = 0;
104 >    // group bookkeeping
105 >    virtual pair<int, int> getGroupTypes(int cg1, int cg2) = 0;
106  
107 <    virtual AtomType* getAtomTypeI(int whichAtomI) = 0;
108 <    virtual AtomType* getAtomTypeJ(int whichAtomJ) = 0;
107 >    // Group->atom bookkeeping
108 >    virtual vector<int> getAtomsInGroupRow(int cg1) = 0;
109 >    virtual vector<int> getAtomsInGroupColumn(int cg2) = 0;
110 >
111 >    virtual Vector3d getAtomToGroupVectorRow(int atom1, int cg1) = 0;
112 >    virtual Vector3d getAtomToGroupVectorColumn(int atom2, int cg2) = 0;
113 >    virtual RealType getMassFactorRow(int atom1) = 0;
114 >    virtual RealType getMassFactorColumn(int atom2) = 0;
115 >
116 >    // spatial data
117 >    virtual Vector3d getIntergroupVector(int cg1, int cg2) = 0;
118 >    virtual Vector3d getInteratomicVector(int atom1, int atom2) = 0;
119 >      
120 >    // atom bookkeeping
121 >    virtual int getNAtomsInRow() = 0;
122 >    virtual vector<int> getSkipsForRowAtom(int atom1) = 0;
123 >    virtual bool skipAtomPair(int atom1, int atom2) = 0;
124 >    virtual void addForceToAtomRow(int atom1, Vector3d fg) = 0;
125 >    virtual void addForceToAtomColumn(int atom2, Vector3d fg) = 0;
126 >
127 >    // filling interaction blocks with pointers
128 >    virtual InteractionData fillInteractionData(int atom1, int atom2) = 0;
129 >    virtual void unpackInteractionData(InteractionData idat, int atom1, int atom2) = 0;
130 >    virtual InteractionData fillSkipData(int atom1, int atom2) = 0;
131 >    virtual SelfData fillSelfData(int atom1);
132      
133    protected:
134 <    SnapshotManager* sman_;
134 >    SimInfo* info_;  
135 >    SnapshotManager* sman_;    
136 >    Snapshot* snap_;
137 >    ForceField* ff_;
138 >    int storageLayout_;
139 >    RealType skinThickness_;   /**< Verlet neighbor list skin thickness */    
140 >
141 >    map<pair<int, int>, int> topoDist; //< topoDist gives the
142 >                                       //topological distance between
143 >                                       //two atomic sites.  This
144 >                                       //declaration is agnostic
145 >                                       //regarding the parallel
146 >                                       //decomposition.  The two
147 >                                       //indices could be local or row
148 >                                       //& column.  It will be up to
149 >                                       //the specific decomposition
150 >                                       //method to fill this.
151 >    map<pair<int, int>, bool> exclude; //< exclude is the set of pairs
152 >                                       //to leave out of non-bonded
153 >                                       //force evaluations.  This
154 >                                       //declaration is agnostic
155 >                                       //regarding the parallel
156 >                                       //decomposition.  The two
157 >                                       //indices could be local or row
158 >                                       //& column.  It will be up to
159 >                                       //the specific decomposition
160 >                                       //method to fill this.
161 >
162 >    vector<vector<int> > groupList_;
163 >    vector<Vector3i> cellOffsets_;
164 >    Vector3i nCells_;
165 >    vector<vector<int> > cellList_;
166 >    vector<Vector3d> saved_CG_positions_;
167 >    potVec longRangePot_;
168 >
169    };    
170   }
171   #endif

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