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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 1761 by gezelter, Fri Jun 22 20:01:37 2012 UTC vs.
trunk/src/parallel/ForceDecomposition.hpp (file contents), Revision 1929 by gezelter, Mon Aug 19 13:12:00 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).          
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   */
# Line 113 | Line 113 | namespace OpenMD {
113  
114      // neighbor list routines
115      virtual bool checkNeighborList();
116 <    virtual vector<pair<int, int> >  buildNeighborList() = 0;
116 >    virtual void buildNeighborList(vector<pair<int, int> >& neighborList) = 0;
117  
118      // how to handle cutoffs:
119      void setCutoffPolicy(CutoffPolicy cp) {cutoffPolicy_ = cp;}
120      void setUserCutoff(RealType rcut) {userCutoff_ = rcut; userChoseCutoff_ = true; }
121  
122      // group bookkeeping
123 <    virtual groupCutoffs getGroupCutoffs(int cg1, int cg2) = 0;
124 <    virtual Vector3d getGroupVelocityColumn(int atom2) = 0;
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;
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> getExcludesForAtom(int atom1) = 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;
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;
# Line 164 | Line 164 | namespace OpenMD {
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;
# Line 197 | Line 199 | namespace OpenMD {
199      RealType userCutoff_;
200      CutoffPolicy cutoffPolicy_;
201  
202 <    map<pair<int, int>, tuple3<RealType, RealType, RealType> > gTypeCutoffMap;
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   }

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