# | Line 247 | Line 247 | namespace OpenMD { | |
---|---|---|
247 | for (int j = 0; j < nLocal_; j++) { | |
248 | int jglob = AtomLocalToGlobal[j]; | |
249 | ||
250 | < | if (excludes->hasPair(iglob, jglob)) |
250 | > | if (excludes->hasPair(iglob, jglob)) |
251 | excludesForAtom[i].push_back(j); | |
252 | – | |
252 | ||
253 | if (oneTwo->hasPair(iglob, jglob)) { | |
254 | toposForAtom[i].push_back(j); | |
# | Line 836 | Line 835 | namespace OpenMD { | |
835 | */ | |
836 | bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) { | |
837 | int unique_id_1, unique_id_2; | |
838 | < | |
838 | > | |
839 | #ifdef IS_MPI | |
840 | // in MPI, we have to look up the unique IDs for each atom | |
841 | unique_id_1 = AtomRowToGlobal[atom1]; | |
842 | unique_id_2 = AtomColToGlobal[atom2]; | |
843 | < | |
844 | < | // this situation should only arise in MPI simulations |
843 | > | #else |
844 | > | unique_id_1 = AtomLocalToGlobal[atom1]; |
845 | > | unique_id_2 = AtomLocalToGlobal[atom2]; |
846 | > | #endif |
847 | > | |
848 | if (unique_id_1 == unique_id_2) return true; | |
849 | < | |
849 | > | |
850 | > | #ifdef IS_MPI |
851 | // this prevents us from doing the pair on multiple processors | |
852 | if (unique_id_1 < unique_id_2) { | |
853 | if ((unique_id_1 + unique_id_2) % 2 == 0) return true; | |
854 | } else { | |
855 | < | if ((unique_id_1 + unique_id_2) % 2 == 1) return true; |
855 | > | if ((unique_id_1 + unique_id_2) % 2 == 1) return true; |
856 | } | |
857 | #endif | |
858 | + | |
859 | return false; | |
860 | } | |
861 | ||
# | Line 871 | Line 875 | namespace OpenMD { | |
875 | ||
876 | for (vector<int>::iterator i = excludesForAtom[atom1].begin(); | |
877 | i != excludesForAtom[atom1].end(); ++i) { | |
878 | < | if ( (*i) == atom2 ) return true; |
878 | > | if ( (*i) == atom2 ) return true; |
879 | } | |
880 | ||
881 | return false; | |
# | Line 1190 | Line 1194 | namespace OpenMD { | |
1194 | } | |
1195 | } | |
1196 | #else | |
1193 | – | |
1197 | for (vector<int>::iterator j1 = cellList_[m1].begin(); | |
1198 | j1 != cellList_[m1].end(); ++j1) { | |
1199 | for (vector<int>::iterator j2 = cellList_[m2].begin(); | |
1200 | j2 != cellList_[m2].end(); ++j2) { | |
1201 | < | |
1201 | > | |
1202 | // Always do this if we're in different cells or if | |
1203 | < | // we're in the same cell and the global index of the |
1204 | < | // j2 cutoff group is less than the j1 cutoff group |
1205 | < | |
1206 | < | if (m2 != m1 || (*j2) < (*j1)) { |
1203 | > | // we're in the same cell and the global index of |
1204 | > | // the j2 cutoff group is greater than or equal to |
1205 | > | // the j1 cutoff group. Note that Rappaport's code |
1206 | > | // has a "less than" conditional here, but that |
1207 | > | // deals with atom-by-atom computation. OpenMD |
1208 | > | // allows atoms within a single cutoff group to |
1209 | > | // interact with each other. |
1210 | > | |
1211 | > | |
1212 | > | |
1213 | > | if (m2 != m1 || (*j2) >= (*j1) ) { |
1214 | > | |
1215 | dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)]; | |
1216 | snap_->wrapVector(dr); | |
1217 | cuts = getGroupCutoffs( (*j1), (*j2) ); | |
# | Line 1219 | Line 1230 | namespace OpenMD { | |
1230 | // branch to do all cutoff group pairs | |
1231 | #ifdef IS_MPI | |
1232 | for (int j1 = 0; j1 < nGroupsInRow_; j1++) { | |
1233 | < | for (int j2 = 0; j2 < nGroupsInCol_; j2++) { |
1233 | > | for (int j2 = 0; j2 < nGroupsInCol_; j2++) { |
1234 | dr = cgColData.position[j2] - cgRowData.position[j1]; | |
1235 | snap_->wrapVector(dr); | |
1236 | cuts = getGroupCutoffs( j1, j2 ); | |
# | Line 1227 | Line 1238 | namespace OpenMD { | |
1238 | neighborList.push_back(make_pair(j1, j2)); | |
1239 | } | |
1240 | } | |
1241 | < | } |
1241 | > | } |
1242 | #else | |
1243 | < | for (int j1 = 0; j1 < nGroups_ - 1; j1++) { |
1244 | < | for (int j2 = j1 + 1; j2 < nGroups_; j2++) { |
1243 | > | // include all groups here. |
1244 | > | for (int j1 = 0; j1 < nGroups_; j1++) { |
1245 | > | // include self group interactions j2 == j1 |
1246 | > | for (int j2 = j1; j2 < nGroups_; j2++) { |
1247 | dr = snap_->cgData.position[j2] - snap_->cgData.position[j1]; | |
1248 | snap_->wrapVector(dr); | |
1249 | cuts = getGroupCutoffs( j1, j2 ); | |
1250 | if (dr.lengthSquare() < cuts.third) { | |
1251 | neighborList.push_back(make_pair(j1, j2)); | |
1252 | } | |
1253 | < | } |
1254 | < | } |
1253 | > | } |
1254 | > | } |
1255 | #endif | |
1256 | } | |
1257 |
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