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root/OpenMD/trunk/src/parallel/ForceDecomposition.hpp
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Comparing:
branches/development/src/parallel/ForceDecomposition.hpp (file contents), Revision 1569 by gezelter, Thu May 26 13:55:04 2011 UTC vs.
trunk/src/parallel/ForceDecomposition.hpp (file contents), Revision 2057 by gezelter, Tue Mar 3 15:22:26 2015 UTC

# 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_FORCEDECOMPOSITION_HPP
# Line 45 | Line 46
46   #include "brains/SimInfo.hpp"
47   #include "brains/SnapshotManager.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 ForceDecomposition
57     *
# Line 78 | Line 81 | namespace OpenMD {
81     *  |  endif
82     *  end
83     * collectData                        (parallel communication)
84 +   * loop over i
85 +   * | localComputation
86 +   * end
87 +   * collectSelfData                    (parallel communication)
88     *
89     * ForceDecomposition provides the interface for ForceLoop to do the
90     * communication steps and to iterate using the correct set of atoms
# Line 86 | Line 93 | namespace OpenMD {
93    class ForceDecomposition {
94    public:
95  
96 <    ForceDecomposition(SimInfo* info);
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      // neighbor list routines
112      virtual bool checkNeighborList();
113 <    virtual vector<pair<int, int> >  buildNeighborList() = 0;
113 >    virtual void buildNeighborList(vector<int>& neighborList, vector<int>& point) = 0;
114  
115 +    void setCutoffRadius(RealType rCut);
116 +    
117      // group bookkeeping
118 <    virtual pair<int, int> getGroupTypes(int cg1, int cg2) = 0;
118 >    virtual Vector3d& getGroupVelocityColumn(int atom2) = 0;
119  
120      // Group->atom bookkeeping
121 <    virtual vector<int> getAtomsInGroupRow(int cg1) = 0;
122 <    virtual vector<int> getAtomsInGroupColumn(int cg2) = 0;
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;
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 vector<int> getAtomList() = 0;
135 <    virtual vector<int> getSkipsForAtom(int atom1) = 0;
136 <    virtual bool skipAtomPair(int atom1, int atom2) = 0;
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 InteractionData fillInteractionData(int atom1, int atom2) = 0;
145 <    virtual InteractionData fillSkipData(int atom1, int atom2) = 0;
146 <    virtual SelfData fillSelfData(int atom1);
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      SimInfo* info_;  
154      SnapshotManager* sman_;    
155      Snapshot* snap_;
156 +    ForceField* ff_;
157 +    InteractionManager* interactionMan_;
158 +
159      int storageLayout_;
160 <    RealType skinThickness_;   /**< Verlet neighbor list skin thickness */    
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 <    map<pair<int, int>, int> topoDist; //< topoDist gives the
168 <                                       //topological distance between
169 <                                       //two atomic sites.  This
170 <                                       //declaration is agnostic
171 <                                       //regarding the parallel
172 <                                       //decomposition.  The two
143 <                                       //indices could be local or row
144 <                                       //& column.  It will be up to
145 <                                       //the specific decomposition
146 <                                       //method to fill this.
147 <    map<pair<int, int>, bool> exclude; //< exclude is the set of pairs
148 <                                       //to leave out of non-bonded
149 <                                       //force evaluations.  This
150 <                                       //declaration is agnostic
151 <                                       //regarding the parallel
152 <                                       //decomposition.  The two
153 <                                       //indices could be local or row
154 <                                       //& column.  It will be up to
155 <                                       //the specific decomposition
156 <                                       //method to fill this.
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_;
163 –
193    };    
194   }
195   #endif

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