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Revision 1576 by gezelter, Wed Jun 8 16:05:07 2011 UTC vs.
Revision 1723 by gezelter, Thu May 24 20:59:54 2012 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 69 | Line 70 | namespace OpenMD {
70  
71      // group bookkeeping
72      groupCutoffs getGroupCutoffs(int cg1, int cg2);
73 +    Vector3d getGroupVelocityColumn(int cg2);
74  
75      // Group->atom bookkeeping
76      vector<int> getAtomsInGroupRow(int cg1);
# Line 84 | Line 86 | namespace OpenMD {
86        
87      // atom bookkeeping
88      int getNAtomsInRow();
89 <    vector<int> getSkipsForRowAtom(int atom1);
90 <    int getTopoDistance(int atom1, int atom2);
89 >    int getTopologicalDistance(int atom1, int atom2);
90 >    vector<int> getExcludesForAtom(int atom1);
91      bool skipAtomPair(int atom1, int atom2);
92 +    bool excludeAtomPair(int atom1, int atom2);
93      void addForceToAtomRow(int atom1, Vector3d fg);
94      void addForceToAtomColumn(int atom2, Vector3d fg);
95 +    Vector3d getAtomVelocityColumn(int atom2);
96  
97      // filling interaction blocks with pointers
98 <    InteractionData fillInteractionData(int atom1, int atom2);
99 <    void unpackInteractionData(InteractionData idat, int atom1, int atom2);
96 <    InteractionData fillSkipData(int atom1, int atom2);
98 >    void fillInteractionData(InteractionData &idat, int atom1, int atom2);
99 >    void unpackInteractionData(InteractionData &idat, int atom1, int atom2);
100  
101    private:
102      void createGtypeCutoffMap();
103  
104      int nLocal_;
105      int nGroups_;
103 –    vector<int> identsLocal;
106      vector<int> AtomLocalToGlobal;
107      vector<int> cgLocalToGlobal;
106 –    vector<RealType> massFactorsLocal;
107 –    vector<vector<int> > skipsForLocalAtom;
108 –    vector<vector<int> > toposForLocalAtom;
109 –    vector<vector<int> > topoDistLocal;
108      vector<RealType> groupCutoff;
109      vector<int> groupToGtype;
110  
111   #ifdef IS_MPI    
112 <    DataStorage atomRowData;
115 <    DataStorage atomColData;
112 >    DataStorage atomRowData;    DataStorage atomColData;
113      DataStorage cgRowData;
114      DataStorage cgColData;
115  
# Line 121 | Line 118 | namespace OpenMD {
118      int nGroupsInRow_;
119      int nGroupsInCol_;
120  
121 <    Communicator<Row, int>* AtomCommIntRow;
122 <    Communicator<Row, RealType>* AtomCommRealRow;
126 <    Communicator<Row, Vector3d>* AtomCommVectorRow;
127 <    Communicator<Row, Mat3x3d>*  AtomCommMatrixRow;
128 <    Communicator<Row, potVec>* AtomCommPotRow;
121 >    Communicator<Row> rowComm;
122 >    Communicator<Column> colComm;
123  
124 <    Communicator<Column, int>* AtomCommIntColumn;
125 <    Communicator<Column, RealType>* AtomCommRealColumn;
126 <    Communicator<Column, Vector3d>* AtomCommVectorColumn;
127 <    Communicator<Column, Mat3x3d>*  AtomCommMatrixColumn;
128 <    Communicator<Column, potVec>* AtomCommPotColumn;
124 >    Plan<int>* AtomPlanIntRow;
125 >    Plan<RealType>* AtomPlanRealRow;
126 >    Plan<Vector3d>* AtomPlanVectorRow;
127 >    Plan<Mat3x3d>*  AtomPlanMatrixRow;
128 >    Plan<potVec>* AtomPlanPotRow;
129  
130 <    Communicator<Row, int>* cgCommIntRow;
131 <    Communicator<Row, Vector3d>* cgCommVectorRow;
132 <    Communicator<Column, int>* cgCommIntColumn;
133 <    Communicator<Column, Vector3d>* cgCommVectorColumn;
130 >    Plan<int>* AtomPlanIntColumn;
131 >    Plan<RealType>* AtomPlanRealColumn;
132 >    Plan<Vector3d>* AtomPlanVectorColumn;
133 >    Plan<Mat3x3d>*  AtomPlanMatrixColumn;
134 >    Plan<potVec>* AtomPlanPotColumn;
135  
136 +    Plan<int>* cgPlanIntRow;
137 +    Plan<Vector3d>* cgPlanVectorRow;
138 +    Plan<int>* cgPlanIntColumn;
139 +    Plan<Vector3d>* cgPlanVectorColumn;
140 +
141      // work arrays for assembling potential energy
142      vector<potVec> pot_row;
143      vector<potVec> pot_col;
144 –    potVec pot_local;
144  
145      vector<int> identsRow;
146      vector<int> identsCol;
# Line 152 | Line 151 | namespace OpenMD {
151      vector<int> AtomRowToGlobal;
152      vector<int> AtomColToGlobal;
153  
154 + public:
155      vector<int> cgRowToGlobal;
156      vector<int> cgColToGlobal;
157  
158 + private:
159      vector<RealType> groupCutoffRow;
160      vector<RealType> groupCutoffCol;
161      vector<int> groupColToGtype;
# Line 168 | Line 169 | namespace OpenMD {
169  
170      vector<RealType> massFactorsRow;
171      vector<RealType> massFactorsCol;
171 –
172 –    vector<vector<int> > skipsForRowAtom;
173 –    vector<vector<int> > toposForRowAtom;
174 –    vector<vector<int> > topoDistRow;
172   #endif
173  
174    };

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