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root/OpenMD/trunk/src/parallel/ForceDecomposition.hpp
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branches/development/src/parallel/ForceDecomposition.hpp (file contents), Revision 1583 by gezelter, Thu Jun 16 22:00:08 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"
48 – #include "nonbonded/Cutoffs.hpp"
49   #include "nonbonded/InteractionManager.hpp"
50   #include "utils/Tuple.hpp"
51  
52   using namespace std;
53 < namespace OpenMD {
54 <  
55 <  typedef tuple3<RealType, RealType, RealType> groupCutoffs;
53 > namespace OpenMD {
54  
55    /**
56     * @class ForceDecomposition
# Line 83 | 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 100 | Line 102 | namespace OpenMD {
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 <    // how to handle cutoffs:
116 <    void setCutoffPolicy(CutoffPolicy cp) {cutoffPolicy_ = cp;}
112 <    void setUserCutoff(RealType rcut) {userCutoff_ = rcut; userChoseCutoff_ = true; }
113 <
115 >    void setCutoffRadius(RealType rCut);
116 >    
117      // group bookkeeping
118 <    virtual groupCutoffs getGroupCutoffs(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 int getNAtomsInRow() = 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 int getTopologicalDistance(int atom1, int atom2) = 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) = 0;
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  
142 –    virtual void fillSkipData(InteractionData &idat, int atom1, int atom2) = 0;
143 –    virtual void unpackSkipData(InteractionData &idat, int atom1, int atom2) = 0;
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_;  
# Line 151 | Line 157 | namespace OpenMD {
157      InteractionManager* interactionMan_;
158  
159      int storageLayout_;
160 <    RealType skinThickness_;   /**< Verlet neighbor list skin thickness */    
161 <    RealType largestRcut_;
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
# Line 168 | Line 181 | namespace OpenMD {
181       */
182      vector<vector<int> > toposForAtom;
183      vector<vector<int> > topoDist;                                      
184 <    vector<vector<int> > skipsForAtom;
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_;
179 –
180 –    bool userChoseCutoff_;
181 –    RealType userCutoff_;
182 –    CutoffPolicy cutoffPolicy_;
183 –
184 –    map<pair<int, int>, tuple3<RealType, RealType, RealType> > gTypeCutoffMap;
185 –
193    };    
194   }
195   #endif

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