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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 1723 by gezelter, Thu May 24 20:59:54 2012 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 36 | Line 36
36   * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).            
37   * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
38   * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
39 < * [4]  Vardeman & Gezelter, in progress (2009).                        
39 > * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40 > * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
42  
43 < #ifndef PARALLEL_DECOMPOSITION_HPP
44 < #define PARALLEL_DECOMPOSITION_HPP
43 > #ifndef PARALLEL_FORCEDECOMPOSITION_HPP
44 > #define PARALLEL_FORCEDECOMPOSITION_HPP
45  
46 + #include "brains/SimInfo.hpp"
47   #include "brains/SnapshotManager.hpp"
48 < #include "types/AtomType.hpp"
48 > #include "nonbonded/NonBondedInteraction.hpp"
49 > #include "nonbonded/Cutoffs.hpp"
50 > #include "nonbonded/InteractionManager.hpp"
51 > #include "utils/Tuple.hpp"
52  
53   using namespace std;
54   namespace OpenMD {
55    
56 +  typedef tuple3<RealType, RealType, RealType> groupCutoffs;
57 +
58    /**
59 <   * @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.
59 >   * @class ForceDecomposition
60     *
61 +   * ForceDecomposition is an interface for passing out and collecting
62 +   * information from many processors at various stages of the main
63 +   * non-bonded ForceLoop.
64 +   *
65     * The pairwise force calculation has an outer-running loop (the "I"
66     * loop) and an inner-running loop (the "J" loop).  In parallel
67     * decompositions, these loop over different groups of atoms on
# Line 62 | Line 71 | namespace OpenMD {
71     *
72     *  distributeInitialData      (parallel communication - one time only)
73     *  distributeData             (parallel communication - every ForceLoop)
74 <   *  loop over i
75 <   *  | loop over j
76 <   *  | | localComputation
74 >   *
75 >   *  loop iLoop over nLoops     (nLoops may be 1, 2, or until self consistent)
76 >   *  |  loop over i
77 >   *  |  | loop over j
78 >   *  |  | | localComputation
79 >   *  |  |  end
80     *  |  end
81 +   *  |  if (nLoops > 1):
82 +   *  |  |   collectIntermediateData    (parallel communication)
83 +   *  |  |   distributeIntermediateData (parallel communication)
84 +   *  |  endif
85     *  end
86 <   *  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)
86 >   * collectData                        (parallel communication)
87     *
88 <   * Decomposition provides the interface for ForceLoop to do the
88 >   * ForceDecomposition provides the interface for ForceLoop to do the
89     * communication steps and to iterate using the correct set of atoms
90     * and cutoff groups.
91     */
92 <  class Decomposition {
92 >  class ForceDecomposition {
93    public:
94  
95 <    Decomposition(SnapshotManager* sman) : sman_(sman) {}
96 <    virtual ~Decomposition() {}
95 >    ForceDecomposition(SimInfo* info, InteractionManager* iMan);
96 >    virtual ~ForceDecomposition() {}
97      
98      virtual void distributeInitialData() = 0;
99      virtual void distributeData() = 0;
100 +    virtual void zeroWorkArrays() = 0;
101      virtual void collectIntermediateData() = 0;
102      virtual void distributeIntermediateData() = 0;
103      virtual void collectData() = 0;
104 +    virtual potVec* getEmbeddingPotential() { return &embeddingPot; }
105 +    virtual potVec* getPairwisePotential() { return &pairwisePot; }
106  
107 <    virtual unsigned int getNcutoffGroupsI() = 0;
108 <    virtual unsigned int getNcutoffGroupsJ() = 0;
107 >    // neighbor list routines
108 >    virtual bool checkNeighborList();
109 >    virtual vector<pair<int, int> >  buildNeighborList() = 0;
110  
111 <    virtual vector<int> getAtomsInGroupI(int whichCGI) = 0;
112 <    virtual vector<int> getAtomsInGroupJ(int whichCGJ) = 0;
111 >    // how to handle cutoffs:
112 >    void setCutoffPolicy(CutoffPolicy cp) {cutoffPolicy_ = cp;}
113 >    void setUserCutoff(RealType rcut) {userCutoff_ = rcut; userChoseCutoff_ = true; }
114  
115 <    virtual AtomType* getAtomTypeI(int whichAtomI) = 0;
116 <    virtual AtomType* getAtomTypeJ(int whichAtomJ) = 0;
115 >    // group bookkeeping
116 >    virtual groupCutoffs getGroupCutoffs(int cg1, int cg2) = 0;
117 >    virtual Vector3d getGroupVelocityColumn(int atom2) = 0;
118 >
119 >    // Group->atom bookkeeping
120 >    virtual vector<int> getAtomsInGroupRow(int cg1) = 0;
121 >    virtual vector<int> getAtomsInGroupColumn(int cg2) = 0;
122 >
123 >    virtual Vector3d getAtomToGroupVectorRow(int atom1, int cg1) = 0;
124 >    virtual Vector3d getAtomToGroupVectorColumn(int atom2, int cg2) = 0;
125 >    virtual RealType getMassFactorRow(int atom1) = 0;
126 >    virtual RealType getMassFactorColumn(int atom2) = 0;
127 >
128 >    // spatial data
129 >    virtual Vector3d getIntergroupVector(int cg1, int cg2) = 0;
130 >    virtual Vector3d getInteratomicVector(int atom1, int atom2) = 0;
131 >      
132 >    // atom bookkeeping
133 >    virtual int getNAtomsInRow() = 0;
134 >    virtual vector<int> getExcludesForAtom(int atom1) = 0;
135 >    virtual bool skipAtomPair(int atom1, int atom2) = 0;
136 >    virtual bool excludeAtomPair(int atom1, int atom2) = 0;
137 >    virtual int getTopologicalDistance(int atom1, int atom2) = 0;
138 >    virtual void addForceToAtomRow(int atom1, Vector3d fg) = 0;
139 >    virtual void addForceToAtomColumn(int atom2, Vector3d fg) = 0;
140 >    virtual Vector3d getAtomVelocityColumn(int atom2) = 0;
141 >
142 >    // filling interaction blocks with pointers
143 >    virtual void fillInteractionData(InteractionData &idat, int atom1, int atom2) = 0;
144 >    virtual void unpackInteractionData(InteractionData &idat, int atom1, int atom2) = 0;
145 >
146 >    virtual void fillSelfData(SelfData &sdat, int atom1);
147 >
148 >    virtual void addToHeatFlux(Vector3d hf);
149 >    virtual void setHeatFlux(Vector3d hf);
150      
151    protected:
152 <    SnapshotManager* sman_;
152 >    SimInfo* info_;  
153 >    SnapshotManager* sman_;    
154 >    Snapshot* snap_;
155 >    ForceField* ff_;
156 >    InteractionManager* interactionMan_;
157 >
158 >    int storageLayout_;
159 >    bool needVelocities_;
160 >    RealType skinThickness_;   /**< Verlet neighbor list skin thickness */    
161 >    RealType largestRcut_;
162 >
163 >    vector<int> idents;
164 >    potVec pairwisePot;
165 >    potVec embeddingPot;
166 >
167 >    /**
168 >     * The topological distance between two atomic sites is handled
169 >     * via two vector structures for speed.  These structures agnostic
170 >     * regarding the parallel decomposition.  The index for
171 >     * toposForAtom could be local or row, while the values could be
172 >     * local or column.  It will be up to the specific decomposition
173 >     * method to fill these.
174 >     */
175 >    vector<vector<int> > toposForAtom;
176 >    vector<vector<int> > topoDist;                                      
177 >    vector<vector<int> > excludesForAtom;
178 >    vector<vector<int> > groupList_;
179 >    vector<RealType> massFactors;
180 >    vector<AtomType*> atypesLocal;
181 >
182 >    vector<Vector3i> cellOffsets_;
183 >    Vector3i nCells_;
184 >    vector<vector<int> > cellList_;
185 >    vector<Vector3d> saved_CG_positions_;
186 >
187 >    bool userChoseCutoff_;
188 >    RealType userCutoff_;
189 >    CutoffPolicy cutoffPolicy_;
190 >
191 >    map<pair<int, int>, tuple3<RealType, RealType, RealType> > gTypeCutoffMap;
192 >
193    };    
194   }
195   #endif

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