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root/OpenMD/trunk/src/parallel/ForceMatrixDecomposition.hpp
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Comparing:
branches/development/src/parallel/ForceDecomposition.hpp (file contents), Revision 1540 by gezelter, Mon Jan 17 21:34:36 2011 UTC vs.
branches/development/src/parallel/ForceMatrixDecomposition.hpp (file contents), Revision 1760 by gezelter, Thu Jun 21 19:26:46 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_FORCEDECOMPOSITION_HPP
44 < #define PARALLEL_FORCEDECOMPOSITION_HPP
43 > #ifndef PARALLEL_FORCEMATRIXDECOMPOSITION_HPP
44 > #define PARALLEL_FORCEMATRIXDECOMPOSITION_HPP
45  
46 < #include "Parallel/Decomposition.hpp"
46 < #include "Parallel/Communicator.hpp"
46 > #include "parallel/ForceDecomposition.hpp"
47   #include "math/SquareMatrix3.hpp"
48 + #include "brains/Snapshot.hpp"
49  
50 + #ifdef IS_MPI
51 + #include "parallel/Communicator.hpp"
52 + #endif
53 +
54 + using namespace std;
55   namespace OpenMD {
56    
57 <  class ForceDecomposition : public Decomposition {
57 >  class ForceMatrixDecomposition : public ForceDecomposition {
58    public:
59 <    ForceDecomposition(Snapshot* sman);
59 >    ForceMatrixDecomposition(SimInfo* info, InteractionManager* iMan);
60 >
61      void distributeInitialData();
62 +    void zeroWorkArrays();
63      void distributeData();
64      void collectIntermediateData();
65      void distributeIntermediateData();
66 +    void collectSelfData();
67      void collectData();
68  
69 <    unsigned int getNcutoffGroupsI();
70 <    unsigned int getNcutoffGroupsJ();
69 >    // neighbor list routines
70 >    vector<pair<int, int> >  buildNeighborList();
71  
72 <    vector<int> getAtomsInGroupI(int whichCGI);
73 <    vector<int> getAtomsInGroupJ(int whichCGJ);
72 >    // group bookkeeping
73 >    groupCutoffs getGroupCutoffs(int cg1, int cg2);
74 >    Vector3d getGroupVelocityColumn(int cg2);
75  
76 <    AtomType* getAtomTypeI(int whichAtomI);
77 <    AtomType* getAtomTypeJ(int whichAtomJ);  
76 >    // Group->atom bookkeeping
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);
83  
84 < #ifdef IS_MPI
85 <    
86 <    Communicator<Row, RealType>* AtomCommRealI;
87 <    Communicator<Row, Vector3d>* AtomCommVectorI;
88 <    Communicator<Row, Mat3x3d>*  AtomCommMatrixI;
84 >    // spatial data
85 >    Vector3d getIntergroupVector(int cg1, int cg2);
86 >    Vector3d getInteratomicVector(int atom1, int atom2);
87 >      
88 >    // atom bookkeeping
89 >    int getNAtomsInRow();
90 >    int getTopologicalDistance(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);
97  
98 <    Communicator<Column, RealType>* AtomCommRealJ;
99 <    Communicator<Column, Vector3d>* AtomCommVectorJ;
100 <    Communicator<Column, Mat3x3d>*  AtomCommMatrixJ;
98 >    // filling interaction blocks with pointers
99 >    void fillInteractionData(InteractionData &idat, int atom1, int atom2);
100 >    void unpackInteractionData(InteractionData &idat, int atom1, int atom2);
101  
102 <    Communicator<Row, Vector3d>* cgCommVectorI;
103 <    Communicator<Column, Vector3d>* cgCommVectorJ;
104 <    
102 >  private:
103 >    void createGtypeCutoffMap();
104 >
105 >    int nLocal_;
106 >    int nGroups_;
107 >    vector<int> AtomLocalToGlobal;
108 >    vector<int> cgLocalToGlobal;
109 >    vector<RealType> groupCutoff;
110 >    vector<int> groupToGtype;
111 >
112 > #ifdef IS_MPI    
113 >    DataStorage atomRowData;    DataStorage atomColData;
114 >    DataStorage cgRowData;
115 >    DataStorage cgColData;
116 >
117 >    int nAtomsInRow_;
118 >    int nAtomsInCol_;
119 >    int nGroupsInRow_;
120 >    int nGroupsInCol_;
121 >
122 >    Communicator<Row> rowComm;
123 >    Communicator<Column> colComm;
124 >
125 >    Plan<int>* AtomPlanIntRow;
126 >    Plan<RealType>* AtomPlanRealRow;
127 >    Plan<Vector3d>* AtomPlanVectorRow;
128 >    Plan<Mat3x3d>*  AtomPlanMatrixRow;
129 >    Plan<potVec>* AtomPlanPotRow;
130 >
131 >    Plan<int>* AtomPlanIntColumn;
132 >    Plan<RealType>* AtomPlanRealColumn;
133 >    Plan<Vector3d>* AtomPlanVectorColumn;
134 >    Plan<Mat3x3d>*  AtomPlanMatrixColumn;
135 >    Plan<potVec>* AtomPlanPotColumn;
136 >
137 >    Plan<int>* cgPlanIntRow;
138 >    Plan<Vector3d>* cgPlanVectorRow;
139 >    Plan<int>* cgPlanIntColumn;
140 >    Plan<Vector3d>* cgPlanVectorColumn;
141 >
142 >    // work arrays for assembling potential energy
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<AtomType*> atypesRow;
153 >    vector<AtomType*> atypesCol;
154 >
155 >    vector<int> AtomRowToGlobal;
156 >    vector<int> AtomColToGlobal;
157 >
158 > public:
159 >    vector<int> cgRowToGlobal;
160 >    vector<int> cgColToGlobal;
161 >
162 > private:
163 >    vector<RealType> groupCutoffRow;
164 >    vector<RealType> groupCutoffCol;
165 >    vector<int> groupColToGtype;
166 >    vector<int> groupRowToGtype;
167 >
168 >    vector<vector<int> > cellListRow_;
169 >    vector<vector<int> > cellListCol_;
170 >
171 >    vector<vector<int> > groupListRow_;
172 >    vector<vector<int> > groupListCol_;
173 >
174 >    vector<RealType> massFactorsRow;
175 >    vector<RealType> massFactorsCol;
176   #endif
177 +
178    };
179  
180   }

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