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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 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_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 >    Vector3d getGroupVelocityColumn(int cg2);
74  
75 <    AtomType* getAtomTypeI(int whichAtomI);
76 <    AtomType* getAtomTypeJ(int whichAtomJ);  
75 >    // Group->atom bookkeeping
76 >    vector<int> getAtomsInGroupRow(int cg1);
77 >    vector<int> getAtomsInGroupColumn(int cg2);
78 >    Vector3d getAtomToGroupVectorRow(int atom1, int cg1);
79 >    Vector3d getAtomToGroupVectorColumn(int atom2, int cg2);
80 >    RealType getMassFactorRow(int atom1);
81 >    RealType getMassFactorColumn(int atom2);
82  
83 < #ifdef IS_MPI
84 <    
85 <    Comm<I, RealType>* AtomCommRealI;
86 <    Comm<I, Vector3d>* AtomCommVectorI;
87 <    Comm<I, Mat3x3d>*  AtomCommMatrixI;
83 >    // spatial data
84 >    Vector3d getIntergroupVector(int cg1, int cg2);
85 >    Vector3d getInteratomicVector(int atom1, int atom2);
86 >      
87 >    // atom bookkeeping
88 >    int getNAtomsInRow();
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 <    Comm<J, RealType>* AtomCommRealJ;
98 <    Comm<J, Vector3d>* AtomCommVectorJ;
99 <    Comm<J, Mat3x3d>*  AtomCommMatrixJ;
97 >    // filling interaction blocks with pointers
98 >    void fillInteractionData(InteractionData &idat, int atom1, int atom2);
99 >    void unpackInteractionData(InteractionData &idat, int atom1, int atom2);
100  
101 <    Comm<I, Vector3d>* cgCommVectorI;
102 <    Comm<J, Vector3d>* cgCommVectorJ;
103 <    
101 >  private:
102 >    void createGtypeCutoffMap();
103 >
104 >    int nLocal_;
105 >    int nGroups_;
106 >    vector<int> AtomLocalToGlobal;
107 >    vector<int> cgLocalToGlobal;
108 >    vector<RealType> groupCutoff;
109 >    vector<int> groupToGtype;
110 >
111 > #ifdef IS_MPI    
112 >    DataStorage atomRowData;    DataStorage atomColData;
113 >    DataStorage cgRowData;
114 >    DataStorage cgColData;
115 >
116 >    int nAtomsInRow_;
117 >    int nAtomsInCol_;
118 >    int nGroupsInRow_;
119 >    int nGroupsInCol_;
120 >
121 >    Communicator<Row> rowComm;
122 >    Communicator<Column> colComm;
123 >
124 >    Plan<int>* AtomPlanIntRow;
125 >    Plan<RealType>* AtomPlanRealRow;
126 >    Plan<Vector3d>* AtomPlanVectorRow;
127 >    Plan<Mat3x3d>*  AtomPlanMatrixRow;
128 >    Plan<potVec>* AtomPlanPotRow;
129 >
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 >
145 >    vector<int> identsRow;
146 >    vector<int> identsCol;
147 >
148 >    vector<AtomType*> atypesRow;
149 >    vector<AtomType*> atypesCol;
150 >
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;
162 >    vector<int> groupRowToGtype;
163 >
164 >    vector<vector<int> > cellListRow_;
165 >    vector<vector<int> > cellListCol_;
166 >
167 >    vector<vector<int> > groupListRow_;
168 >    vector<vector<int> > groupListCol_;
169 >
170 >    vector<RealType> massFactorsRow;
171 >    vector<RealType> massFactorsCol;
172   #endif
173 +
174    };
175  
176   }

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