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root/OpenMD/trunk/src/parallel/ForceMatrixDecomposition.hpp
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branches/development/src/parallel/ForceMatrixDecomposition.hpp (file contents), Revision 1723 by gezelter, Thu May 24 20:59:54 2012 UTC vs.
trunk/src/parallel/ForceMatrixDecomposition.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 63 | Line 63 | namespace OpenMD {
63      void distributeData();
64      void collectIntermediateData();
65      void distributeIntermediateData();
66 +    void collectSelfData();
67      void collectData();
68  
69      // neighbor list routines
70 <    vector<pair<int, int> >  buildNeighborList();
70 >    void buildNeighborList(vector<pair<int, int> >& neighborList);
71  
72      // group bookkeeping
73 <    groupCutoffs getGroupCutoffs(int cg1, int cg2);
74 <    Vector3d getGroupVelocityColumn(int cg2);
73 >    void getGroupCutoffs(int &cg1, int &cg2, RealType &rcut, RealType &rcutsq, RealType &rlistsq);
74 >    Vector3d& getGroupVelocityColumn(int cg2);
75  
76      // Group->atom bookkeeping
77 <    vector<int> getAtomsInGroupRow(int cg1);
78 <    vector<int> getAtomsInGroupColumn(int cg2);
77 >    vector<int>& getAtomsInGroupRow(int cg1);
78 >    vector<int>& getAtomsInGroupColumn(int cg2);
79      Vector3d getAtomToGroupVectorRow(int atom1, int cg1);
80      Vector3d getAtomToGroupVectorColumn(int atom2, int cg2);
81 <    RealType getMassFactorRow(int atom1);
82 <    RealType getMassFactorColumn(int atom2);
81 >    RealType& getMassFactorRow(int atom1);
82 >    RealType& getMassFactorColumn(int atom2);
83  
84      // spatial data
85      Vector3d getIntergroupVector(int cg1, int cg2);
86      Vector3d getInteratomicVector(int atom1, int atom2);
87        
88      // atom bookkeeping
89 <    int getNAtomsInRow();
89 >    int& getNAtomsInRow();
90      int getTopologicalDistance(int atom1, int atom2);
91 <    vector<int> getExcludesForAtom(int atom1);
92 <    bool skipAtomPair(int atom1, int atom2);
91 >    vector<int>& getExcludesForAtom(int atom1);
92 >    bool skipAtomPair(int atom1, int atom2, int cg1, int cg2);
93      bool excludeAtomPair(int atom1, int atom2);
94      void addForceToAtomRow(int atom1, Vector3d fg);
95      void addForceToAtomColumn(int atom2, Vector3d fg);
96 <    Vector3d getAtomVelocityColumn(int atom2);
96 >    Vector3d& getAtomVelocityColumn(int atom2);
97  
98      // filling interaction blocks with pointers
99      void fillInteractionData(InteractionData &idat, int atom1, int atom2);
# Line 142 | Line 143 | namespace OpenMD {
143      vector<potVec> pot_row;
144      vector<potVec> pot_col;
145  
146 +    vector<potVec> expot_row;
147 +    vector<potVec> expot_col;
148 +
149      vector<int> identsRow;
150      vector<int> identsCol;
151  
152 +    vector<int> regionsRow;
153 +    vector<int> regionsCol;
154 +
155      vector<AtomType*> atypesRow;
156      vector<AtomType*> atypesCol;
157  

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