# | Line 99 | Line 99 | namespace OpenMD { | |
---|---|---|
99 | nGroups_ = info_->getNLocalCutoffGroups(); | |
100 | // gather the information for atomtype IDs (atids): | |
101 | idents = info_->getIdentArray(); | |
102 | + | regions = info_->getRegions(); |
103 | AtomLocalToGlobal = info_->getGlobalAtomIndices(); | |
104 | cgLocalToGlobal = info_->getGlobalGroupIndices(); | |
105 | vector<int> globalGroupMembership = info_->getGlobalGroupMembership(); | |
# | Line 163 | Line 164 | namespace OpenMD { | |
164 | ||
165 | AtomPlanIntRow->gather(idents, identsRow); | |
166 | AtomPlanIntColumn->gather(idents, identsCol); | |
167 | + | |
168 | + | regionsRow.resize(nAtomsInRow_); |
169 | + | regionsCol.resize(nAtomsInCol_); |
170 | ||
171 | + | AtomPlanIntRow->gather(regions, regionsRow); |
172 | + | AtomPlanIntColumn->gather(regions, regionsCol); |
173 | + | |
174 | // allocate memory for the parallel objects | |
175 | atypesRow.resize(nAtomsInRow_); | |
176 | atypesCol.resize(nAtomsInCol_); | |
# | Line 1168 | Line 1175 | namespace OpenMD { | |
1175 | idat.excluded = excludeAtomPair(atom1, atom2); | |
1176 | ||
1177 | #ifdef IS_MPI | |
1178 | < | idat.atypes = make_pair( atypesRow[atom1], atypesCol[atom2]); |
1178 | > | //idat.atypes = make_pair( atypesRow[atom1], atypesCol[atom2]); |
1179 | idat.atid1 = identsRow[atom1]; | |
1180 | idat.atid2 = identsCol[atom2]; | |
1181 | < | //idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]), |
1182 | < | // ff_->getAtomType(identsCol[atom2]) ); |
1183 | < | |
1181 | > | |
1182 | > | if (regionsRow[atom1] >= 0 && regionsCol[atom2] >= 0) { |
1183 | > | idat.sameRegion = (regionsRow[atom1] == regionsCol[atom2]); |
1184 | > | } else { |
1185 | > | idat.sameRegion = false; |
1186 | > | } |
1187 | > | |
1188 | if (storageLayout_ & DataStorage::dslAmat) { | |
1189 | idat.A1 = &(atomRowData.aMat[atom1]); | |
1190 | idat.A2 = &(atomColData.aMat[atom2]); | |
# | Line 1226 | Line 1237 | namespace OpenMD { | |
1237 | ||
1238 | #else | |
1239 | ||
1240 | < | idat.atypes = make_pair( atypesLocal[atom1], atypesLocal[atom2]); |
1240 | > | //idat.atypes = make_pair( atypesLocal[atom1], atypesLocal[atom2]); |
1241 | idat.atid1 = idents[atom1]; | |
1242 | idat.atid2 = idents[atom2]; | |
1243 | ||
1244 | + | if (regions[atom1] >= 0 && regions[atom2] >= 0) { |
1245 | + | idat.sameRegion = (regions[atom1] == regions[atom2]); |
1246 | + | } else { |
1247 | + | idat.sameRegion = false; |
1248 | + | } |
1249 | + | |
1250 | if (storageLayout_ & DataStorage::dslAmat) { | |
1251 | idat.A1 = &(snap_->atomData.aMat[atom1]); | |
1252 | idat.A2 = &(snap_->atomData.aMat[atom2]); | |
# | Line 1375 | Line 1392 | namespace OpenMD { | |
1392 | Vector3d boxY = box.getColumn(1); | |
1393 | Vector3d boxZ = box.getColumn(2); | |
1394 | ||
1395 | < | nCells_.x() = (int) ( boxX.length() )/ rList_; |
1396 | < | nCells_.y() = (int) ( boxY.length() )/ rList_; |
1397 | < | nCells_.z() = (int) ( boxZ.length() )/ rList_; |
1395 | > | nCells_.x() = int( boxX.length() / rList_ ); |
1396 | > | nCells_.y() = int( boxY.length() / rList_ ); |
1397 | > | nCells_.z() = int( boxZ.length() / rList_ ); |
1398 | ||
1399 | // handle small boxes where the cell offsets can end up repeating cells | |
1400 | ||
# | Line 1473 | Line 1490 | namespace OpenMD { | |
1490 | } | |
1491 | ||
1492 | // find xyz-indices of cell that cutoffGroup is in. | |
1493 | < | whichCell.x() = nCells_.x() * scaled.x(); |
1494 | < | whichCell.y() = nCells_.y() * scaled.y(); |
1495 | < | whichCell.z() = nCells_.z() * scaled.z(); |
1493 | > | whichCell.x() = int(nCells_.x() * scaled.x()); |
1494 | > | whichCell.y() = int(nCells_.y() * scaled.y()); |
1495 | > | whichCell.z() = int(nCells_.z() * scaled.z()); |
1496 | ||
1497 | // find single index of this cell: | |
1498 | cellIndex = Vlinear(whichCell, nCells_); |
– | Removed lines |
+ | Added lines |
< | Changed lines |
> | Changed lines |