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Revision 1576 by gezelter, Wed Jun 8 16:05:07 2011 UTC vs.
Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

# Line 36 | Line 36
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).                        
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_FORCEMATRIXDECOMPOSITION_HPP
# Line 55 | Line 56 | namespace OpenMD {
56    
57    class ForceMatrixDecomposition : public ForceDecomposition {
58    public:
59 <    ForceMatrixDecomposition(SimInfo* info) : ForceDecomposition(info) {};
59 >    ForceMatrixDecomposition(SimInfo* info, InteractionManager* iMan);
60  
61      void distributeInitialData();
62      void zeroWorkArrays();
# Line 84 | Line 85 | namespace OpenMD {
85        
86      // atom bookkeeping
87      int getNAtomsInRow();
88 <    vector<int> getSkipsForRowAtom(int atom1);
89 <    int getTopoDistance(int atom1, int atom2);
88 >    int getTopologicalDistance(int atom1, int atom2);
89 >    vector<int> getExcludesForAtom(int atom1);
90      bool skipAtomPair(int atom1, int atom2);
91 +    bool excludeAtomPair(int atom1, int atom2);
92      void addForceToAtomRow(int atom1, Vector3d fg);
93      void addForceToAtomColumn(int atom2, Vector3d fg);
94  
95      // filling interaction blocks with pointers
96 <    InteractionData fillInteractionData(int atom1, int atom2);
97 <    void unpackInteractionData(InteractionData idat, int atom1, int atom2);
96 <    InteractionData fillSkipData(int atom1, int atom2);
96 >    void fillInteractionData(InteractionData &idat, int atom1, int atom2);
97 >    void unpackInteractionData(InteractionData &idat, int atom1, int atom2);
98  
99    private:
100      void createGtypeCutoffMap();
101  
102      int nLocal_;
103      int nGroups_;
103 –    vector<int> identsLocal;
104      vector<int> AtomLocalToGlobal;
105      vector<int> cgLocalToGlobal;
106 –    vector<RealType> massFactorsLocal;
107 –    vector<vector<int> > skipsForLocalAtom;
108 –    vector<vector<int> > toposForLocalAtom;
109 –    vector<vector<int> > topoDistLocal;
106      vector<RealType> groupCutoff;
107      vector<int> groupToGtype;
108  
# Line 121 | Line 117 | namespace OpenMD {
117      int nGroupsInRow_;
118      int nGroupsInCol_;
119  
120 <    Communicator<Row, int>* AtomCommIntRow;
121 <    Communicator<Row, RealType>* AtomCommRealRow;
126 <    Communicator<Row, Vector3d>* AtomCommVectorRow;
127 <    Communicator<Row, Mat3x3d>*  AtomCommMatrixRow;
128 <    Communicator<Row, potVec>* AtomCommPotRow;
120 >    Communicator<Row> rowComm;
121 >    Communicator<Column> colComm;
122  
123 <    Communicator<Column, int>* AtomCommIntColumn;
124 <    Communicator<Column, RealType>* AtomCommRealColumn;
125 <    Communicator<Column, Vector3d>* AtomCommVectorColumn;
126 <    Communicator<Column, Mat3x3d>*  AtomCommMatrixColumn;
127 <    Communicator<Column, potVec>* AtomCommPotColumn;
123 >    Plan<int>* AtomPlanIntRow;
124 >    Plan<RealType>* AtomPlanRealRow;
125 >    Plan<Vector3d>* AtomPlanVectorRow;
126 >    Plan<Mat3x3d>*  AtomPlanMatrixRow;
127 >    Plan<potVec>* AtomPlanPotRow;
128  
129 <    Communicator<Row, int>* cgCommIntRow;
130 <    Communicator<Row, Vector3d>* cgCommVectorRow;
131 <    Communicator<Column, int>* cgCommIntColumn;
132 <    Communicator<Column, Vector3d>* cgCommVectorColumn;
129 >    Plan<int>* AtomPlanIntColumn;
130 >    Plan<RealType>* AtomPlanRealColumn;
131 >    Plan<Vector3d>* AtomPlanVectorColumn;
132 >    Plan<Mat3x3d>*  AtomPlanMatrixColumn;
133 >    Plan<potVec>* AtomPlanPotColumn;
134  
135 +    Plan<int>* cgPlanIntRow;
136 +    Plan<Vector3d>* cgPlanVectorRow;
137 +    Plan<int>* cgPlanIntColumn;
138 +    Plan<Vector3d>* cgPlanVectorColumn;
139 +
140      // work arrays for assembling potential energy
141      vector<potVec> pot_row;
142      vector<potVec> pot_col;
144 –    potVec pot_local;
143  
144      vector<int> identsRow;
145      vector<int> identsCol;
# Line 152 | Line 150 | namespace OpenMD {
150      vector<int> AtomRowToGlobal;
151      vector<int> AtomColToGlobal;
152  
153 + public:
154      vector<int> cgRowToGlobal;
155      vector<int> cgColToGlobal;
156  
157 + private:
158      vector<RealType> groupCutoffRow;
159      vector<RealType> groupCutoffCol;
160      vector<int> groupColToGtype;
# Line 168 | Line 168 | namespace OpenMD {
168  
169      vector<RealType> massFactorsRow;
170      vector<RealType> massFactorsCol;
171 –
172 –    vector<vector<int> > skipsForRowAtom;
173 –    vector<vector<int> > toposForRowAtom;
174 –    vector<vector<int> > topoDistRow;
171   #endif
172  
173    };

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