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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 1545 by gezelter, Fri Apr 8 21:25:19 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 "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 76 | Line 79 | namespace OpenMD {
79     *  end
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(SimInfo* info) : info_(info) {}
90 <    virtual ~Decomposition() {}
89 >    ForceDecomposition(SimInfo* info);
90 >    virtual ~ForceDecomposition() {}
91      
92      virtual void distributeInitialData() = 0;
93      virtual void distributeData() = 0;
# Line 93 | Line 96 | namespace OpenMD {
96      virtual void collectData() = 0;
97  
98      // neighbor list routines
99 <    virtual bool checkNeighborList() = 0;
99 >    virtual bool checkNeighborList();
100      virtual vector<pair<int, int> >  buildNeighborList() = 0;
101  
102      // group bookkeeping
103      virtual pair<int, int> getGroupTypes(int cg1, int cg2) = 0;
104  
105      // Group->atom bookkeeping
106 <    virtual vector<int> getAtomsInGroupI(int cg1) = 0;
107 <    virtual vector<int> getAtomsInGroupJ(int cg2) = 0;
108 <    virtual Vector3d getAtomToGroupVectorI(int atom1, int cg1) = 0;
109 <    virtual Vector3d getAtomToGroupVectorJ(int atom2, int cg2) = 0;
110 <    virtual RealType getMfactI(int atom1) = 0;
111 <    virtual RealType getMfactJ(int atom2) = 0;
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;
# Line 113 | Line 116 | namespace OpenMD {
116        
117      // atom bookkeeping
118      virtual vector<int> getAtomList() = 0;
119 <    virtual vector<int> getSkipsForAtom(int atom1) = 0
119 >    virtual vector<int> getSkipsForAtom(int atom1) = 0;
120      virtual bool skipAtomPair(int atom1, int atom2) = 0;
121 <    virtual void addForceToAtomI(int atom1, Vector3d fg) = 0;
122 <    virtual void addForceToAtomJ(int atom2, Vector3d fg) = 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) = 0;
127 >    virtual SelfData fillSelfData(int atom1);
128      
129    protected:
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
# Line 145 | Line 153 | namespace OpenMD {
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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