| 57 |
|
storageLayout_ = sman_->getStorageLayout(); |
| 58 |
|
ff_ = info_->getForceField(); |
| 59 |
|
nLocal_ = snap_->getNumberOfAtoms(); |
| 60 |
– |
nGroups_ = snap_->getNumberOfCutoffGroups(); |
| 60 |
|
|
| 61 |
+ |
nGroups_ = info_->getNLocalCutoffGroups(); |
| 62 |
|
// gather the information for atomtype IDs (atids): |
| 63 |
|
identsLocal = info_->getIdentArray(); |
| 64 |
|
AtomLocalToGlobal = info_->getGlobalAtomIndices(); |
| 104 |
|
cgColData.resize(nGroupsInCol_); |
| 105 |
|
cgColData.setStorageLayout(DataStorage::dslPosition); |
| 106 |
|
|
| 107 |
< |
identsRow.reserve(nAtomsInRow_); |
| 108 |
< |
identsCol.reserve(nAtomsInCol_); |
| 107 |
> |
identsRow.resize(nAtomsInRow_); |
| 108 |
> |
identsCol.resize(nAtomsInCol_); |
| 109 |
|
|
| 110 |
|
AtomCommIntRow->gather(identsLocal, identsRow); |
| 111 |
|
AtomCommIntColumn->gather(identsLocal, identsCol); |
| 120 |
|
AtomCommRealColumn->gather(massFactorsLocal, massFactorsCol); |
| 121 |
|
|
| 122 |
|
groupListRow_.clear(); |
| 123 |
< |
groupListRow_.reserve(nGroupsInRow_); |
| 123 |
> |
groupListRow_.resize(nGroupsInRow_); |
| 124 |
|
for (int i = 0; i < nGroupsInRow_; i++) { |
| 125 |
|
int gid = cgRowToGlobal[i]; |
| 126 |
|
for (int j = 0; j < nAtomsInRow_; j++) { |
| 131 |
|
} |
| 132 |
|
|
| 133 |
|
groupListCol_.clear(); |
| 134 |
< |
groupListCol_.reserve(nGroupsInCol_); |
| 134 |
> |
groupListCol_.resize(nGroupsInCol_); |
| 135 |
|
for (int i = 0; i < nGroupsInCol_; i++) { |
| 136 |
|
int gid = cgColToGlobal[i]; |
| 137 |
|
for (int j = 0; j < nAtomsInCol_; j++) { |
| 142 |
|
} |
| 143 |
|
|
| 144 |
|
skipsForRowAtom.clear(); |
| 145 |
< |
skipsForRowAtom.reserve(nAtomsInRow_); |
| 145 |
> |
skipsForRowAtom.resize(nAtomsInRow_); |
| 146 |
|
for (int i = 0; i < nAtomsInRow_; i++) { |
| 147 |
|
int iglob = AtomRowToGlobal[i]; |
| 148 |
|
for (int j = 0; j < nAtomsInCol_; j++) { |
| 153 |
|
} |
| 154 |
|
|
| 155 |
|
toposForRowAtom.clear(); |
| 156 |
< |
toposForRowAtom.reserve(nAtomsInRow_); |
| 156 |
> |
toposForRowAtom.resize(nAtomsInRow_); |
| 157 |
|
for (int i = 0; i < nAtomsInRow_; i++) { |
| 158 |
|
int iglob = AtomRowToGlobal[i]; |
| 159 |
|
int nTopos = 0; |
| 178 |
|
} |
| 179 |
|
|
| 180 |
|
#endif |
| 181 |
– |
|
| 181 |
|
groupList_.clear(); |
| 182 |
< |
groupList_.reserve(nGroups_); |
| 182 |
> |
groupList_.resize(nGroups_); |
| 183 |
|
for (int i = 0; i < nGroups_; i++) { |
| 184 |
|
int gid = cgLocalToGlobal[i]; |
| 185 |
|
for (int j = 0; j < nLocal_; j++) { |
| 186 |
|
int aid = AtomLocalToGlobal[j]; |
| 187 |
< |
if (globalGroupMembership[aid] == gid) |
| 187 |
> |
if (globalGroupMembership[aid] == gid) { |
| 188 |
|
groupList_[i].push_back(j); |
| 189 |
+ |
|
| 190 |
+ |
} |
| 191 |
|
} |
| 192 |
|
} |
| 193 |
|
|
| 194 |
|
skipsForLocalAtom.clear(); |
| 195 |
< |
skipsForLocalAtom.reserve(nLocal_); |
| 195 |
> |
skipsForLocalAtom.resize(nLocal_); |
| 196 |
|
|
| 197 |
|
for (int i = 0; i < nLocal_; i++) { |
| 198 |
|
int iglob = AtomLocalToGlobal[i]; |
| 202 |
|
skipsForLocalAtom[i].push_back(j); |
| 203 |
|
} |
| 204 |
|
} |
| 204 |
– |
|
| 205 |
|
toposForLocalAtom.clear(); |
| 206 |
< |
toposForLocalAtom.reserve(nLocal_); |
| 206 |
> |
toposForLocalAtom.resize(nLocal_); |
| 207 |
|
for (int i = 0; i < nLocal_; i++) { |
| 208 |
|
int iglob = AtomLocalToGlobal[i]; |
| 209 |
|
int nTopos = 0; |
| 236 |
|
int atid; |
| 237 |
|
set<AtomType*> atypes = info_->getSimulatedAtomTypes(); |
| 238 |
|
vector<RealType> atypeCutoff; |
| 239 |
< |
atypeCutoff.reserve( atypes.size() ); |
| 239 |
> |
atypeCutoff.resize( atypes.size() ); |
| 240 |
|
|
| 241 |
|
for (set<AtomType*>::iterator at = atypes.begin(); at != atypes.end(); ++at){ |
| 242 |
|
rc = interactionMan_->getSuggestedCutoffRadius(*at); |
