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root/OpenMD/trunk/src/parallel/ForceDecomposition.hpp
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branches/development/src/parallel/ForceDecomposition.hpp (file contents), Revision 1576 by gezelter, Wed Jun 8 16:05:07 2011 UTC vs.
trunk/src/parallel/ForceDecomposition.hpp (file contents), Revision 1893 by gezelter, Wed Jun 19 17:19:07 2013 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 83 | Line 84 | namespace OpenMD {
84     *  |  endif
85     *  end
86     * collectData                        (parallel communication)
87 +   * loop over i
88 +   * | localComputation
89 +   * end
90 +   * collectSelfData                    (parallel communication)
91     *
92     * ForceDecomposition provides the interface for ForceLoop to do the
93     * communication steps and to iterate using the correct set of atoms
# Line 91 | Line 96 | namespace OpenMD {
96    class ForceDecomposition {
97    public:
98  
99 <    ForceDecomposition(SimInfo* info);
99 >    ForceDecomposition(SimInfo* info, InteractionManager* iMan);
100      virtual ~ForceDecomposition() {}
101      
102      virtual void distributeInitialData() = 0;
# Line 100 | Line 105 | namespace OpenMD {
105      virtual void collectIntermediateData() = 0;
106      virtual void distributeIntermediateData() = 0;
107      virtual void collectData() = 0;
108 <    virtual potVec getLongRangePotential() { return longRangePot_; }
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      // neighbor list routines
115      virtual bool checkNeighborList();
# Line 112 | Line 121 | namespace OpenMD {
121  
122      // group bookkeeping
123      virtual groupCutoffs getGroupCutoffs(int cg1, int cg2) = 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;
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;
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> getSkipsForRowAtom(int atom1) = 0;
142 <    virtual bool skipAtomPair(int atom1, int atom2) = 0;
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 InteractionData fillInteractionData(int atom1, int atom2) = 0;
151 <    virtual void unpackInteractionData(InteractionData idat, int atom1, int atom2) = 0;
152 <    virtual InteractionData fillSkipData(int atom1, int atom2) = 0;
153 <    virtual SelfData fillSelfData(int atom1);
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      SimInfo* info_;  
# Line 147 | Line 163 | namespace OpenMD {
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 <    map<pair<int, int>, int> topoDist; //< topoDist gives the
172 <                                       //topological distance between
173 <                                       //two atomic sites.  This
174 <                                       //declaration is agnostic
175 <                                       //regarding the parallel
158 <                                       //decomposition.  The two
159 <                                       //indices could be local or row
160 <                                       //& column.  It will be up to
161 <                                       //the specific decomposition
162 <                                       //method to fill this.
163 <    map<pair<int, int>, bool> exclude; //< exclude is the set of pairs
164 <                                       //to leave out of non-bonded
165 <                                       //force evaluations.  This
166 <                                       //declaration is agnostic
167 <                                       //regarding the parallel
168 <                                       //decomposition.  The two
169 <                                       //indices could be local or row
170 <                                       //& column.  It will be up to
171 <                                       //the specific decomposition
172 <                                       //method to fill this.
171 >    vector<int> idents;
172 >    potVec pairwisePot;
173 >    potVec embeddingPot;
174 >    potVec excludedPot;
175 >    potVec excludedSelfPot;
176  
177 +    /**
178 +     * The topological distance between two atomic sites is handled
179 +     * via two vector structures for speed.  These structures agnostic
180 +     * regarding the parallel decomposition.  The index for
181 +     * toposForAtom could be local or row, while the values could be
182 +     * local or column.  It will be up to the specific decomposition
183 +     * method to fill these.
184 +     */
185 +    vector<vector<int> > toposForAtom;
186 +    vector<vector<int> > topoDist;                                      
187 +    vector<vector<int> > excludesForAtom;
188      vector<vector<int> > groupList_;
189 +    vector<RealType> massFactors;
190 +    vector<AtomType*> atypesLocal;
191  
192      vector<Vector3i> cellOffsets_;
193      Vector3i nCells_;
194      vector<vector<int> > cellList_;
195      vector<Vector3d> saved_CG_positions_;
180 –    potVec longRangePot_;
196  
197      bool userChoseCutoff_;
198      RealType userCutoff_;

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