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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 1929 by gezelter, Mon Aug 19 13:12:00 2013 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/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)
87 <   *  distributeIntermediateData (parallel communication)
88 <   *  loop over i
89 <   *  | loop over j
90 <   *  | | localComputation
75 <   *  |  end
76 <   *  end
77 <   * collectData                  (parallel communication)
86 >   * collectData                        (parallel communication)
87 >   * loop over i
88 >   * | localComputation
89 >   * end
90 >   * collectSelfData                    (parallel communication)
91     *
92 <   * Decomposition provides the interface for ForceLoop to do the
92 >   * ForceDecomposition provides the interface for ForceLoop to do the
93     * communication steps and to iterate using the correct set of atoms
94     * and cutoff groups.
95     */
96 <  class Decomposition {
96 >  class ForceDecomposition {
97    public:
98  
99 <    Decomposition(SnapshotManager* sman) : sman_(sman) {}
100 <    virtual ~Decomposition() {}
99 >    ForceDecomposition(SimInfo* info, InteractionManager* iMan);
100 >    virtual ~ForceDecomposition() {}
101      
102      virtual void distributeInitialData() = 0;
103      virtual void distributeData() = 0;
104 +    virtual void zeroWorkArrays() = 0;
105      virtual void collectIntermediateData() = 0;
106      virtual void distributeIntermediateData() = 0;
107      virtual void collectData() = 0;
108 +    virtual void collectSelfData() = 0;
109 +    virtual potVec* getEmbeddingPotential() { return &embeddingPot; }
110 +    virtual potVec* getPairwisePotential() { return &pairwisePot; }
111 +    virtual potVec* getExcludedPotential() { return &excludedPot; }
112 +    virtual potVec* getExcludedSelfPotential() { return &excludedSelfPot; }
113  
114 <    virtual unsigned int getNcutoffGroupsI() = 0;
115 <    virtual unsigned int getNcutoffGroupsJ() = 0;
114 >    // neighbor list routines
115 >    virtual bool checkNeighborList();
116 >    virtual void buildNeighborList(vector<pair<int, int> >& neighborList) = 0;
117  
118 <    virtual vector<int> getAtomsInGroupI(int whichCGI) = 0;
119 <    virtual vector<int> getAtomsInGroupJ(int whichCGJ) = 0;
118 >    // how to handle cutoffs:
119 >    void setCutoffPolicy(CutoffPolicy cp) {cutoffPolicy_ = cp;}
120 >    void setUserCutoff(RealType rcut) {userCutoff_ = rcut; userChoseCutoff_ = true; }
121  
122 <    virtual AtomType* getAtomTypeI(int whichAtomI) = 0;
123 <    virtual AtomType* getAtomTypeJ(int whichAtomJ) = 0;
122 >    // group bookkeeping
123 >    virtual void getGroupCutoffs(int &cg1, int &cg2, RealType &rcut, RealType &rcutsq, RealType &rlistsq) = 0;
124 >    virtual Vector3d& getGroupVelocityColumn(int atom2) = 0;
125 >
126 >    // Group->atom bookkeeping
127 >    virtual vector<int>& getAtomsInGroupRow(int cg1) = 0;
128 >    virtual vector<int>& getAtomsInGroupColumn(int cg2) = 0;
129 >
130 >    virtual Vector3d getAtomToGroupVectorRow(int atom1, int cg1) = 0;
131 >    virtual Vector3d getAtomToGroupVectorColumn(int atom2, int cg2) = 0;
132 >    virtual RealType& getMassFactorRow(int atom1) = 0;
133 >    virtual RealType& getMassFactorColumn(int atom2) = 0;
134 >
135 >    // spatial data
136 >    virtual Vector3d getIntergroupVector(int cg1, int cg2) = 0;
137 >    virtual Vector3d getInteratomicVector(int atom1, int atom2) = 0;
138 >      
139 >    // atom bookkeeping
140 >    virtual int& getNAtomsInRow() = 0;
141 >    virtual vector<int>& getExcludesForAtom(int atom1) = 0;
142 >    virtual bool skipAtomPair(int atom1, int atom2, int cg1, int cg2) = 0;
143 >    virtual bool excludeAtomPair(int atom1, int atom2) = 0;
144 >    virtual int getTopologicalDistance(int atom1, int atom2) = 0;
145 >    virtual void addForceToAtomRow(int atom1, Vector3d fg) = 0;
146 >    virtual void addForceToAtomColumn(int atom2, Vector3d fg) = 0;
147 >    virtual Vector3d& getAtomVelocityColumn(int atom2) = 0;
148 >
149 >    // filling interaction blocks with pointers
150 >    virtual void fillInteractionData(InteractionData &idat, int atom1, int atom2) = 0;
151 >    virtual void unpackInteractionData(InteractionData &idat, int atom1, int atom2) = 0;
152 >
153 >    virtual void fillSelfData(SelfData &sdat, int atom1);
154 >
155 >    virtual void addToHeatFlux(Vector3d hf);
156 >    virtual void setHeatFlux(Vector3d hf);
157      
158    protected:
159 <    SnapshotManager* sman_;
159 >    SimInfo* info_;  
160 >    SnapshotManager* sman_;    
161 >    Snapshot* snap_;
162 >    ForceField* ff_;
163 >    InteractionManager* interactionMan_;
164 >
165 >    int storageLayout_;
166 >    bool needVelocities_;
167 >    bool usePeriodicBoundaryConditions_;
168 >    RealType skinThickness_;   /**< Verlet neighbor list skin thickness */    
169 >    RealType largestRcut_;
170 >
171 >    vector<int> idents;
172 >    vector<int> regions;
173 >    potVec pairwisePot;
174 >    potVec embeddingPot;
175 >    potVec excludedPot;
176 >    potVec excludedSelfPot;
177 >
178 >    /**
179 >     * The topological distance between two atomic sites is handled
180 >     * via two vector structures for speed.  These structures agnostic
181 >     * regarding the parallel decomposition.  The index for
182 >     * toposForAtom could be local or row, while the values could be
183 >     * local or column.  It will be up to the specific decomposition
184 >     * method to fill these.
185 >     */
186 >    vector<vector<int> > toposForAtom;
187 >    vector<vector<int> > topoDist;                                      
188 >    vector<vector<int> > excludesForAtom;
189 >    vector<vector<int> > groupList_;
190 >    vector<RealType> massFactors;
191 >    vector<AtomType*> atypesLocal;
192 >
193 >    vector<Vector3i> cellOffsets_;
194 >    Vector3i nCells_;
195 >    vector<vector<int> > cellList_;
196 >    vector<Vector3d> saved_CG_positions_;
197 >
198 >    bool userChoseCutoff_;
199 >    RealType userCutoff_;
200 >    CutoffPolicy cutoffPolicy_;
201 >
202 >    //map<pair<int, int>, tuple3<RealType, RealType, RealType> > gTypeCutoffMap;
203 >    vector<vector<RealType> > GrCut;
204 >    vector<vector<RealType> > GrCutSq;
205 >    vector<vector<RealType> > GrlistSq;
206 >
207    };    
208   }
209   #endif

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