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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 1539 by gezelter, Fri Jan 14 22:31:31 2011 UTC vs.
branches/development/src/parallel/ForceMatrixDecomposition.hpp (file contents), 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_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 collectData();
67  
68 <    unsigned int getNcutoffGroupsI();
69 <    unsigned int getNcutoffGroupsJ();
68 >    // neighbor list routines
69 >    vector<pair<int, int> >  buildNeighborList();
70  
71 <    vector<int> getAtomsInGroupI(int whichCGI);
72 <    vector<int> getAtomsInGroupJ(int whichCGJ);
71 >    // group bookkeeping
72 >    groupCutoffs getGroupCutoffs(int cg1, int cg2);
73  
74 <    AtomType* getAtomTypeI(int whichAtomI);
75 <    AtomType* getAtomTypeJ(int whichAtomJ);  
74 >    // Group->atom bookkeeping
75 >    vector<int> getAtomsInGroupRow(int cg1);
76 >    vector<int> getAtomsInGroupColumn(int cg2);
77 >    Vector3d getAtomToGroupVectorRow(int atom1, int cg1);
78 >    Vector3d getAtomToGroupVectorColumn(int atom2, int cg2);
79 >    RealType getMassFactorRow(int atom1);
80 >    RealType getMassFactorColumn(int atom2);
81  
82 < #ifdef IS_MPI
83 <    
84 <    Comm<I, RealType>* AtomCommRealI;
85 <    Comm<I, Vector3d>* AtomCommVectorI;
86 <    Comm<I, Mat3x3d>*  AtomCommMatrixI;
82 >    // spatial data
83 >    Vector3d getIntergroupVector(int cg1, int cg2);
84 >    Vector3d getInteratomicVector(int atom1, int atom2);
85 >      
86 >    // atom bookkeeping
87 >    int getNAtomsInRow();
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 <    Comm<J, RealType>* AtomCommRealJ;
96 <    Comm<J, Vector3d>* AtomCommVectorJ;
97 <    Comm<J, Mat3x3d>*  AtomCommMatrixJ;
95 >    // filling interaction blocks with pointers
96 >    void fillInteractionData(InteractionData &idat, int atom1, int atom2);
97 >    void unpackInteractionData(InteractionData &idat, int atom1, int atom2);
98  
99 <    Comm<I, Vector3d>* cgCommVectorI;
100 <    Comm<J, Vector3d>* cgCommVectorJ;
101 <    
99 >  private:
100 >    void createGtypeCutoffMap();
101 >
102 >    int nLocal_;
103 >    int nGroups_;
104 >    vector<int> AtomLocalToGlobal;
105 >    vector<int> cgLocalToGlobal;
106 >    vector<RealType> groupCutoff;
107 >    vector<int> groupToGtype;
108 >
109 > #ifdef IS_MPI    
110 >    DataStorage atomRowData;
111 >    DataStorage atomColData;
112 >    DataStorage cgRowData;
113 >    DataStorage cgColData;
114 >
115 >    int nAtomsInRow_;
116 >    int nAtomsInCol_;
117 >    int nGroupsInRow_;
118 >    int nGroupsInCol_;
119 >
120 >    Communicator<Row> rowComm;
121 >    Communicator<Column> colComm;
122 >
123 >    Plan<int>* AtomPlanIntRow;
124 >    Plan<RealType>* AtomPlanRealRow;
125 >    Plan<Vector3d>* AtomPlanVectorRow;
126 >    Plan<Mat3x3d>*  AtomPlanMatrixRow;
127 >    Plan<potVec>* AtomPlanPotRow;
128 >
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;
143 >
144 >    vector<int> identsRow;
145 >    vector<int> identsCol;
146 >
147 >    vector<AtomType*> atypesRow;
148 >    vector<AtomType*> atypesCol;
149 >
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;
161 >    vector<int> groupRowToGtype;
162 >
163 >    vector<vector<int> > cellListRow_;
164 >    vector<vector<int> > cellListCol_;
165 >
166 >    vector<vector<int> > groupListRow_;
167 >    vector<vector<int> > groupListCol_;
168 >
169 >    vector<RealType> massFactorsRow;
170 >    vector<RealType> massFactorsCol;
171   #endif
172 +
173    };
174  
175   }

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