# | Line 55 | Line 55 | namespace OpenMD { | |
---|---|---|
55 | ||
56 | class ForceMatrixDecomposition : public ForceDecomposition { | |
57 | public: | |
58 | < | ForceMatrixDecomposition(SimInfo* info) : ForceDecomposition(info) {sman_ = info_->getSnapshotManager();} |
58 | > | ForceMatrixDecomposition(SimInfo* info, InteractionManager* iMan) : ForceDecomposition(info, iMan) {}; |
59 | > | |
60 | void distributeInitialData(); | |
61 | + | void zeroWorkArrays(); |
62 | void distributeData(); | |
63 | void collectIntermediateData(); | |
64 | void distributeIntermediateData(); | |
65 | void collectData(); | |
66 | ||
67 | // neighbor list routines | |
66 | – | bool checkNeighborList(); |
68 | vector<pair<int, int> > buildNeighborList(); | |
69 | ||
70 | // group bookkeeping | |
71 | < | pair<int, int> getGroupTypes(int cg1, int cg2); |
71 | > | groupCutoffs getGroupCutoffs(int cg1, int cg2); |
72 | ||
73 | // Group->atom bookkeeping | |
74 | vector<int> getAtomsInGroupRow(int cg1); | |
75 | vector<int> getAtomsInGroupColumn(int cg2); | |
76 | Vector3d getAtomToGroupVectorRow(int atom1, int cg1); | |
77 | Vector3d getAtomToGroupVectorColumn(int atom2, int cg2); | |
78 | < | RealType getMfactRow(int atom1); |
79 | < | RealType getMfactColumn(int atom2); |
78 | > | RealType getMassFactorRow(int atom1); |
79 | > | RealType getMassFactorColumn(int atom2); |
80 | ||
81 | // spatial data | |
82 | Vector3d getIntergroupVector(int cg1, int cg2); | |
83 | Vector3d getInteratomicVector(int atom1, int atom2); | |
84 | ||
85 | // atom bookkeeping | |
86 | < | vector<int> getAtomList(); |
87 | < | vector<int> getSkipsForAtom(int atom1); |
86 | > | int getNAtomsInRow(); |
87 | > | int getTopologicalDistance(int atom1, int atom2); |
88 | > | vector<int> getExcludesForAtom(int atom1); |
89 | bool skipAtomPair(int atom1, int atom2); | |
90 | + | bool excludeAtomPair(int atom1, int atom2); |
91 | void addForceToAtomRow(int atom1, Vector3d fg); | |
92 | void addForceToAtomColumn(int atom2, Vector3d fg); | |
93 | ||
94 | // filling interaction blocks with pointers | |
95 | < | InteractionData fillInteractionData(int atom1, int atom2); |
96 | < | InteractionData fillSkipData(int atom1, int atom2); |
94 | < | SelfData fillSelfData(int atom1); |
95 | > | void fillInteractionData(InteractionData &idat, int atom1, int atom2); |
96 | > | void unpackInteractionData(InteractionData &idat, int atom1, int atom2); |
97 | ||
98 | private: | |
99 | < | SnapshotManager* sman_; |
98 | < | Snapshot* snap_; |
99 | < | int storageLayout_; |
100 | < | vector<Vector3i> Cells; |
99 | > | void createGtypeCutoffMap(); |
100 | ||
101 | int nLocal_; | |
102 | int nGroups_; | |
103 | + | vector<int> AtomLocalToGlobal; |
104 | + | vector<int> cgLocalToGlobal; |
105 | + | vector<RealType> groupCutoff; |
106 | + | vector<int> groupToGtype; |
107 | ||
108 | #ifdef IS_MPI | |
109 | DataStorage atomRowData; | |
# | Line 117 | Line 120 | namespace OpenMD { | |
120 | Communicator<Row, RealType>* AtomCommRealRow; | |
121 | Communicator<Row, Vector3d>* AtomCommVectorRow; | |
122 | Communicator<Row, Mat3x3d>* AtomCommMatrixRow; | |
123 | + | Communicator<Row, potVec>* AtomCommPotRow; |
124 | ||
125 | Communicator<Column, int>* AtomCommIntColumn; | |
126 | Communicator<Column, RealType>* AtomCommRealColumn; | |
127 | Communicator<Column, Vector3d>* AtomCommVectorColumn; | |
128 | < | Communicator<Column, Mat3x3d>* AtomCommMatrixColumn; |
128 | > | Communicator<Column, Mat3x3d>* AtomCommMatrixColumn; |
129 | > | Communicator<Column, potVec>* AtomCommPotColumn; |
130 | ||
131 | Communicator<Row, int>* cgCommIntRow; | |
132 | Communicator<Row, Vector3d>* cgCommVectorRow; | |
133 | Communicator<Column, int>* cgCommIntColumn; | |
134 | Communicator<Column, Vector3d>* cgCommVectorColumn; | |
135 | ||
136 | < | vector<vector<RealType> > pot_row; |
137 | < | vector<vector<RealType> > pot_col; |
136 | > | // work arrays for assembling potential energy |
137 | > | vector<potVec> pot_row; |
138 | > | vector<potVec> pot_col; |
139 | > | |
140 | vector<int> identsRow; | |
141 | vector<int> identsCol; | |
142 | ||
143 | < | vector<int> AtomLocalToGlobal; |
143 | > | vector<AtomType*> atypesRow; |
144 | > | vector<AtomType*> atypesCol; |
145 | > | |
146 | vector<int> AtomRowToGlobal; | |
147 | vector<int> AtomColToGlobal; | |
148 | < | vector<int> cgLocalToGlobal; |
148 | > | |
149 | vector<int> cgRowToGlobal; | |
150 | vector<int> cgColToGlobal; | |
151 | ||
152 | < | vector<vector<int> > CellListRow; |
153 | < | vector<vector<int> > CellListCol; |
154 | < | #else |
155 | < | vector<vector<int> > CellList; |
152 | > | vector<RealType> groupCutoffRow; |
153 | > | vector<RealType> groupCutoffCol; |
154 | > | vector<int> groupColToGtype; |
155 | > | vector<int> groupRowToGtype; |
156 | > | |
157 | > | vector<vector<int> > cellListRow_; |
158 | > | vector<vector<int> > cellListCol_; |
159 | > | |
160 | > | vector<vector<int> > groupListRow_; |
161 | > | vector<vector<int> > groupListCol_; |
162 | > | |
163 | > | vector<RealType> massFactorsRow; |
164 | > | vector<RealType> massFactorsCol; |
165 | #endif | |
148 | – | vector<RealType> pot_local; |
166 | ||
167 | }; | |
168 |
– | Removed lines |
+ | Added lines |
< | Changed lines |
> | Changed lines |