| 234 |
|
|
| 235 |
|
SimInfo* SimCreator::createSim(const std::string & mdFileName, |
| 236 |
|
bool loadInitCoords) { |
| 237 |
< |
|
| 237 |
> |
|
| 238 |
|
const int bufferSize = 65535; |
| 239 |
|
char buffer[bufferSize]; |
| 240 |
|
int lineNo = 0; |
| 369 |
|
} |
| 370 |
|
|
| 371 |
|
ff->parse(forcefieldFileName); |
| 372 |
– |
ff->setFortranForceOptions(); |
| 372 |
|
//create SimInfo |
| 373 |
|
SimInfo * info = new SimInfo(ff, simParams); |
| 374 |
|
|
| 386 |
|
//create the molecules |
| 387 |
|
createMolecules(info); |
| 388 |
|
|
| 390 |
– |
|
| 389 |
|
//allocate memory for DataStorage(circular reference, need to |
| 390 |
|
//break it) |
| 391 |
|
info->setSnapshotManager(new SimSnapshotManager(info)); |
| 411 |
|
|
| 412 |
|
if (loadInitCoords) |
| 413 |
|
loadCoordinates(info, mdFileName); |
| 416 |
– |
|
| 414 |
|
return info; |
| 415 |
|
} |
| 416 |
|
|
| 589 |
|
MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD); |
| 590 |
|
} |
| 591 |
|
|
| 592 |
+ |
cerr << "molToProcMap:\n"; |
| 593 |
+ |
for (int i = 0; i < molToProcMap.size(); i++) { |
| 594 |
+ |
cerr << "m = " << i << " mtpr[m] = " << molToProcMap[i] <<"\n"; |
| 595 |
+ |
} |
| 596 |
+ |
|
| 597 |
|
info->setMolToProcMap(molToProcMap); |
| 598 |
|
sprintf(checkPointMsg, |
| 599 |
|
"Successfully divided the molecules among the processors.\n"); |
| 713 |
|
} |
| 714 |
|
|
| 715 |
|
//fill globalGroupMembership |
| 716 |
< |
std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0); |
| 716 |
> |
std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), -1); |
| 717 |
|
for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { |
| 718 |
|
for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
| 719 |
|
|
| 723 |
|
|
| 724 |
|
} |
| 725 |
|
} |
| 726 |
< |
|
| 726 |
> |
|
| 727 |
|
#ifdef IS_MPI |
| 728 |
|
// Since the globalGroupMembership has been zero filled and we've only |
| 729 |
|
// poked values into the atoms we know, we can do an Allreduce |
| 732 |
|
// docs said we could. |
| 733 |
|
std::vector<int> tmpGroupMembership(info->getNGlobalAtoms(), 0); |
| 734 |
|
MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms, |
| 735 |
< |
MPI_INT, MPI_SUM, MPI_COMM_WORLD); |
| 735 |
> |
MPI_INT, MPI_MAX, MPI_COMM_WORLD); |
| 736 |
|
info->setGlobalGroupMembership(tmpGroupMembership); |
| 737 |
+ |
|
| 738 |
+ |
cerr << "ggm:\n"; |
| 739 |
+ |
for (int i = 0; i < tmpGroupMembership.size(); i++) |
| 740 |
+ |
cerr << "i = " << i << "\t ggm(i) = " << tmpGroupMembership[i] << "\n"; |
| 741 |
+ |
|
| 742 |
|
#else |
| 743 |
|
info->setGlobalGroupMembership(globalGroupMembership); |
| 744 |
|
#endif |
| 798 |
|
globalIO++; |
| 799 |
|
} |
| 800 |
|
} |
| 801 |
< |
|
| 801 |
> |
cerr << "ioi2io:\n"; |
| 802 |
> |
for (int i = 0; i < IOIndexToIntegrableObject.size(); i++) { |
| 803 |
> |
if (IOIndexToIntegrableObject[i] != NULL) { |
| 804 |
> |
cerr << "i = " << i << "globalIOindex = " << IOIndexToIntegrableObject[i]->getGlobalIntegrableObjectIndex() << "\n"; |
| 805 |
> |
} |
| 806 |
> |
} |
| 807 |
> |
|
| 808 |
|
info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject); |
| 809 |
|
|
| 810 |
|
} |
| 811 |
|
|
| 812 |
|
void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) { |
| 813 |
|
Globals* simParams; |
| 814 |
+ |
|
| 815 |
|
simParams = info->getSimParams(); |
| 816 |
|
|
| 803 |
– |
|
| 817 |
|
DumpReader reader(info, mdFileName); |
| 818 |
|
int nframes = reader.getNFrames(); |
| 819 |
< |
|
| 819 |
> |
|
| 820 |
|
if (nframes > 0) { |
| 821 |
|
reader.readFrame(nframes - 1); |
| 822 |
|
} else { |
| 827 |
|
painCave.isFatal = 1; |
| 828 |
|
simError(); |
| 829 |
|
} |
| 817 |
– |
|
| 830 |
|
//copy the current snapshot to previous snapshot |
| 831 |
|
info->getSnapshotManager()->advance(); |
| 832 |
|
} |
