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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.
trunk/src/parallel/ForceDecomposition.hpp (file contents), Revision 2057 by gezelter, Tue Mar 3 15:22:26 2015 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 35 | Line 35
35   *                                                                      
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).                        
38 > * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
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/InteractionManager.hpp"
50 > #include "utils/Tuple.hpp"
51  
52   using namespace std;
53 < namespace OpenMD {
54 <  
53 > namespace OpenMD {
54 >
55    /**
56 <   * @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.
56 >   * @class ForceDecomposition
57     *
58 +   * ForceDecomposition is an interface for passing out and collecting
59 +   * information from many processors at various stages of the main
60 +   * non-bonded ForceLoop.
61 +   *
62     * The pairwise force calculation has an outer-running loop (the "I"
63     * loop) and an inner-running loop (the "J" loop).  In parallel
64     * decompositions, these loop over different groups of atoms on
# Line 62 | Line 68 | namespace OpenMD {
68     *
69     *  distributeInitialData      (parallel communication - one time only)
70     *  distributeData             (parallel communication - every ForceLoop)
71 <   *  loop over i
72 <   *  | loop over j
73 <   *  | | localComputation
71 >   *
72 >   *  loop iLoop over nLoops     (nLoops may be 1, 2, or until self consistent)
73 >   *  |  loop over i
74 >   *  |  | loop over j
75 >   *  |  | | localComputation
76 >   *  |  |  end
77     *  |  end
78 +   *  |  if (nLoops > 1):
79 +   *  |  |   collectIntermediateData    (parallel communication)
80 +   *  |  |   distributeIntermediateData (parallel communication)
81 +   *  |  endif
82     *  end
83 <   *  collectIntermediateData    (parallel communication)
84 <   *  distributeIntermediateData (parallel communication)
85 <   *  loop over i
86 <   *  | loop over j
87 <   *  | | localComputation
75 <   *  |  end
76 <   *  end
77 <   * collectData                  (parallel communication)
83 >   * collectData                        (parallel communication)
84 >   * loop over i
85 >   * | localComputation
86 >   * end
87 >   * collectSelfData                    (parallel communication)
88     *
89 <   * Decomposition provides the interface for ForceLoop to do the
89 >   * ForceDecomposition provides the interface for ForceLoop to do the
90     * communication steps and to iterate using the correct set of atoms
91     * and cutoff groups.
92     */
93 <  class Decomposition {
93 >  class ForceDecomposition {
94    public:
95  
96 <    Decomposition(SnapshotManager* sman) : sman_(sman) {}
97 <    virtual ~Decomposition() {}
96 >    ForceDecomposition(SimInfo* info, InteractionManager* iMan);
97 >    virtual ~ForceDecomposition() {}
98      
99      virtual void distributeInitialData() = 0;
100      virtual void distributeData() = 0;
101 +    virtual void zeroWorkArrays() = 0;
102      virtual void collectIntermediateData() = 0;
103      virtual void distributeIntermediateData() = 0;
104      virtual void collectData() = 0;
105 +    virtual void collectSelfData() = 0;
106 +    virtual potVec* getEmbeddingPotential() { return &embeddingPot; }
107 +    virtual potVec* getPairwisePotential() { return &pairwisePot; }
108 +    virtual potVec* getExcludedPotential() { return &excludedPot; }
109 +    virtual potVec* getExcludedSelfPotential() { return &excludedSelfPot; }
110  
111 <    virtual unsigned int getNcutoffGroupsI() = 0;
112 <    virtual unsigned int getNcutoffGroupsJ() = 0;
111 >    // neighbor list routines
112 >    virtual bool checkNeighborList();
113 >    virtual void buildNeighborList(vector<int>& neighborList, vector<int>& point) = 0;
114  
115 <    virtual vector<int> getAtomsInGroupI(int whichCGI) = 0;
116 <    virtual vector<int> getAtomsInGroupJ(int whichCGJ) = 0;
115 >    void setCutoffRadius(RealType rCut);
116 >    
117 >    // group bookkeeping
118 >    virtual Vector3d& getGroupVelocityColumn(int atom2) = 0;
119  
120 <    virtual AtomType* getAtomTypeI(int whichAtomI) = 0;
121 <    virtual AtomType* getAtomTypeJ(int whichAtomJ) = 0;
120 >    // Group->atom bookkeeping
121 >    virtual vector<int>& getAtomsInGroupRow(int cg1) = 0;
122 >    virtual vector<int>& getAtomsInGroupColumn(int cg2) = 0;
123 >
124 >    virtual Vector3d getAtomToGroupVectorRow(int atom1, int cg1) = 0;
125 >    virtual Vector3d getAtomToGroupVectorColumn(int atom2, int cg2) = 0;
126 >    virtual RealType& getMassFactorRow(int atom1) = 0;
127 >    virtual RealType& getMassFactorColumn(int atom2) = 0;
128 >
129 >    // spatial data
130 >    virtual Vector3d getIntergroupVector(int cg1, int cg2) = 0;
131 >    virtual Vector3d getInteratomicVector(int atom1, int atom2) = 0;
132 >      
133 >    // atom bookkeeping
134 >    virtual int& getNAtomsInRow() = 0;
135 >    virtual vector<int>& getExcludesForAtom(int atom1) = 0;
136 >    virtual bool skipAtomPair(int atom1, int atom2, int cg1, int cg2) = 0;
137 >    virtual bool excludeAtomPair(int atom1, int atom2) = 0;
138 >    virtual int getTopologicalDistance(int atom1, int atom2) = 0;
139 >    virtual void addForceToAtomRow(int atom1, Vector3d fg) = 0;
140 >    virtual void addForceToAtomColumn(int atom2, Vector3d fg) = 0;
141 >    virtual Vector3d& getAtomVelocityColumn(int atom2) = 0;
142 >
143 >    // filling interaction blocks with pointers
144 >    virtual void fillInteractionData(InteractionData &idat, int atom1, int atom2, bool newAtom1 = true) = 0;
145 >    virtual void unpackInteractionData(InteractionData &idat, int atom1, int atom2) = 0;
146 >
147 >    virtual void fillSelfData(SelfData &sdat, int atom1);
148 >
149 >    virtual void addToHeatFlux(Vector3d hf);
150 >    virtual void setHeatFlux(Vector3d hf);
151      
152    protected:
153 <    SnapshotManager* sman_;
153 >    SimInfo* info_;  
154 >    SnapshotManager* sman_;    
155 >    Snapshot* snap_;
156 >    ForceField* ff_;
157 >    InteractionManager* interactionMan_;
158 >
159 >    int storageLayout_;
160 >    bool needVelocities_;
161 >    bool usePeriodicBoundaryConditions_;
162 >    RealType skinThickness_;   /**< Verlet neighbor list skin thickness */
163 >    RealType rCut_;
164 >    RealType rList_;
165 >    RealType rListSq_;
166 >
167 >    vector<int> idents;
168 >    vector<int> regions;
169 >    potVec pairwisePot;
170 >    potVec embeddingPot;
171 >    potVec excludedPot;
172 >    potVec excludedSelfPot;
173 >
174 >    /**
175 >     * The topological distance between two atomic sites is handled
176 >     * via two vector structures for speed.  These structures agnostic
177 >     * regarding the parallel decomposition.  The index for
178 >     * toposForAtom could be local or row, while the values could be
179 >     * local or column.  It will be up to the specific decomposition
180 >     * method to fill these.
181 >     */
182 >    vector<vector<int> > toposForAtom;
183 >    vector<vector<int> > topoDist;                                      
184 >    vector<vector<int> > excludesForAtom;
185 >    vector<vector<int> > groupList_;
186 >    vector<RealType> massFactors;
187 >    vector<AtomType*> atypesLocal;
188 >
189 >    vector<Vector3i> cellOffsets_;
190 >    Vector3i nCells_;
191 >    vector<vector<int> > cellList_;
192 >    vector<Vector3d> saved_CG_positions_;
193    };    
194   }
195   #endif

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