# | Line 58 | Line 58 | namespace OpenMD { | |
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58 | ForceMatrixDecomposition(SimInfo* info) : ForceDecomposition(info) {}; | |
59 | ||
60 | void distributeInitialData(); | |
61 | + | void zeroWorkArrays(); |
62 | void distributeData(); | |
63 | void collectIntermediateData(); | |
64 | void distributeIntermediateData(); | |
# | Line 67 | Line 68 | namespace OpenMD { | |
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); | |
# | Line 82 | Line 83 | namespace OpenMD { | |
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 | > | vector<int> getSkipsForRowAtom(int atom1); |
88 | > | int getTopoDistance(int atom1, int atom2); |
89 | bool skipAtomPair(int atom1, int atom2); | |
90 | void addForceToAtomRow(int atom1, Vector3d fg); | |
91 | void addForceToAtomColumn(int atom2, Vector3d fg); | |
92 | ||
93 | // filling interaction blocks with pointers | |
94 | InteractionData fillInteractionData(int atom1, int atom2); | |
95 | + | void unpackInteractionData(InteractionData idat, int atom1, int atom2); |
96 | InteractionData fillSkipData(int atom1, int atom2); | |
97 | ||
98 | private: | |
99 | + | void createGtypeCutoffMap(); |
100 | + | |
101 | int nLocal_; | |
102 | int nGroups_; | |
103 | + | vector<int> identsLocal; |
104 | vector<int> AtomLocalToGlobal; | |
105 | vector<int> cgLocalToGlobal; | |
100 | – | vector<RealType> pot_local; |
106 | vector<RealType> massFactorsLocal; | |
107 | + | vector<vector<int> > skipsForLocalAtom; |
108 | + | vector<vector<int> > toposForLocalAtom; |
109 | + | vector<vector<int> > topoDistLocal; |
110 | + | vector<RealType> groupCutoff; |
111 | + | vector<int> groupToGtype; |
112 | ||
113 | #ifdef IS_MPI | |
114 | DataStorage atomRowData; | |
# | Line 115 | Line 125 | namespace OpenMD { | |
125 | Communicator<Row, RealType>* AtomCommRealRow; | |
126 | Communicator<Row, Vector3d>* AtomCommVectorRow; | |
127 | Communicator<Row, Mat3x3d>* AtomCommMatrixRow; | |
128 | + | Communicator<Row, potVec>* AtomCommPotRow; |
129 | ||
130 | Communicator<Column, int>* AtomCommIntColumn; | |
131 | Communicator<Column, RealType>* AtomCommRealColumn; | |
132 | Communicator<Column, Vector3d>* AtomCommVectorColumn; | |
133 | < | Communicator<Column, Mat3x3d>* AtomCommMatrixColumn; |
133 | > | Communicator<Column, Mat3x3d>* AtomCommMatrixColumn; |
134 | > | Communicator<Column, potVec>* AtomCommPotColumn; |
135 | ||
136 | Communicator<Row, int>* cgCommIntRow; | |
137 | Communicator<Row, Vector3d>* cgCommVectorRow; | |
138 | Communicator<Column, int>* cgCommIntColumn; | |
139 | Communicator<Column, Vector3d>* cgCommVectorColumn; | |
140 | ||
141 | < | vector<vector<RealType> > pot_row; |
142 | < | vector<vector<RealType> > pot_col; |
141 | > | // work arrays for assembling potential energy |
142 | > | vector<potVec> pot_row; |
143 | > | vector<potVec> pot_col; |
144 | > | potVec pot_local; |
145 | ||
146 | vector<int> identsRow; | |
147 | vector<int> identsCol; | |
148 | ||
149 | + | vector<AtomType*> atypesRow; |
150 | + | vector<AtomType*> atypesCol; |
151 | + | |
152 | vector<int> AtomRowToGlobal; | |
153 | vector<int> AtomColToGlobal; | |
154 | ||
155 | vector<int> cgRowToGlobal; | |
156 | vector<int> cgColToGlobal; | |
157 | ||
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 | ||
# | Line 147 | Line 169 | namespace OpenMD { | |
169 | vector<RealType> massFactorsRow; | |
170 | vector<RealType> massFactorsCol; | |
171 | ||
172 | + | vector<vector<int> > skipsForRowAtom; |
173 | + | vector<vector<int> > toposForRowAtom; |
174 | + | vector<vector<int> > topoDistRow; |
175 | #endif | |
176 | ||
177 | }; |
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