| 301 |
|
moleculeStamps_.push_back(molStamp); |
| 302 |
|
molStampIds_.insert(molStampIds_.end(), nmol, curStampId) |
| 303 |
|
} |
| 304 |
+ |
|
| 305 |
+ |
void SimInfo::update() { |
| 306 |
+ |
|
| 307 |
+ |
|
| 308 |
+ |
|
| 309 |
+ |
//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex |
| 310 |
+ |
std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0); |
| 311 |
+ |
std::vector<int> localToGlobalCutoffGroupIndex; |
| 312 |
+ |
typename SimInfo::MoleculeIterator mi; |
| 313 |
+ |
typename Molecule::AtomIterator ai; |
| 314 |
+ |
typename Molecule::CutoffGroupIterator ci; |
| 315 |
+ |
Molecule* mol; |
| 316 |
+ |
Atom* atom; |
| 317 |
+ |
CutoffGroup* cg; |
| 318 |
+ |
mpiSimData parallelData; |
| 319 |
+ |
int isError; |
| 320 |
|
|
| 321 |
+ |
for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
| 322 |
+ |
|
| 323 |
+ |
//local index(index in DataStorge) of atom is important |
| 324 |
+ |
for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
| 325 |
+ |
localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1; |
| 326 |
+ |
} |
| 327 |
+ |
|
| 328 |
+ |
//local index of cutoff group is trivial, it only depends on the order of travesing |
| 329 |
+ |
for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
| 330 |
+ |
localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1); |
| 331 |
+ |
} |
| 332 |
+ |
|
| 333 |
+ |
} |
| 334 |
+ |
|
| 335 |
+ |
//Setup Parallel Data and pass the index arrays to fortran |
| 336 |
+ |
parallelData.nMolGlobal = getNMolGlobal(); |
| 337 |
+ |
parallelData.nMolLocal = ; |
| 338 |
+ |
parallelData.nAtomsGlobal = ; |
| 339 |
+ |
parallelData.nAtomsLocal = ; |
| 340 |
+ |
parallelData.nGroupsGlobal = ; |
| 341 |
+ |
parallelData.nGroupsLocal = ; |
| 342 |
+ |
parallelData.myNode = worldRank; |
| 343 |
+ |
MPI_Comm_size(MPI_COMM_WORLD, &(parallelData->nProcessors)); |
| 344 |
+ |
|
| 345 |
+ |
setFsimParallel(parallelData, &(parallelData->nAtomsLocal), |
| 346 |
+ |
&localToGlobalAtomIndex[0], &(parallelData->nGroupsLocal), |
| 347 |
+ |
&localToGlobalCutoffGroupIndex[0], &isError); |
| 348 |
+ |
|
| 349 |
+ |
if (isError) { |
| 350 |
+ |
sprintf(painCave.errMsg, |
| 351 |
+ |
"mpiRefresh errror: fortran didn't like something we gave it.\n"); |
| 352 |
+ |
painCave.isFatal = 1; |
| 353 |
+ |
simError(); |
| 354 |
+ |
} |
| 355 |
+ |
|
| 356 |
+ |
sprintf(checkPointMsg, " mpiRefresh successful.\n"); |
| 357 |
+ |
MPIcheckPoint(); |
| 358 |
+ |
|
| 359 |
+ |
|
| 360 |
+ |
} |
| 361 |
+ |
|
| 362 |
|
std::ostream& operator <<(ostream& o, SimInfo& info) { |
| 363 |
|
|
| 364 |
|
return o; |
