| 35 |
|
|
| 36 |
|
namespace oopse { |
| 37 |
|
|
| 38 |
< |
void SimSetup::parseFile(const std::string& mdFileName, MakeStamps *stamps, Globals *globals) { |
| 38 |
> |
void SimCreator::parseFile(const std::string& mdFileName, MakeStamps *stamps, Globals *globals) { |
| 39 |
|
|
| 40 |
|
#ifdef IS_MPI |
| 41 |
|
|
| 81 |
|
//create the force field |
| 82 |
|
ForceFiled * ff = ForceFieldFactory::getInstance()->createObject( |
| 83 |
|
globals->getForceField()); |
| 84 |
< |
|
| 84 |
> |
|
| 85 |
|
if (ff == NULL) { |
| 86 |
|
sprintf(painCave.errMsg, "ForceFiled Factory can not create %s force field\n", |
| 87 |
|
globals->getForceField()); |
| 88 |
|
painCave.isFatal = 1; |
| 89 |
|
simError(); |
| 90 |
|
} |
| 91 |
+ |
ff->parse(); |
| 92 |
|
|
| 93 |
|
//extract the molecule stamps |
| 94 |
|
std::vector < std::pair<MoleculeStamp *, int> > moleculeStampPairs; |
| 514 |
|
} |
| 515 |
|
} |
| 516 |
|
|
| 517 |
+ |
//fill globalGroupMembership |
| 518 |
|
std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0); |
| 519 |
|
for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
| 520 |
|
for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
| 525 |
|
|
| 526 |
|
} |
| 527 |
|
} |
| 528 |
< |
|
| 528 |
> |
|
| 529 |
> |
#ifdef IS_MPI |
| 530 |
|
// Since the globalGroupMembership has been zero filled and we've only |
| 531 |
|
// poked values into the atoms we know, we can do an Allreduce |
| 532 |
|
// to get the full globalGroupMembership array (We think). |
| 537 |
|
info->getGlobalGroupMembershipPointer(), |
| 538 |
|
info->getNGlobalAtoms(), |
| 539 |
|
MPI_INT, MPI_SUM, MPI_COMM_WORLD); |
| 540 |
+ |
#else |
| 541 |
+ |
std::copy(globalGroupMembership.begin(), globalGroupMembership.end(), |
| 542 |
+ |
info->getGlobalGroupMembershipPointer()); |
| 543 |
+ |
#endif |
| 544 |
|
|
| 545 |
|
//fill molMembership |
| 546 |
|
std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0); |
| 551 |
|
globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex(); |
| 552 |
|
} |
| 553 |
|
|
| 554 |
+ |
#ifdef IS_MPI |
| 555 |
|
MPI_Allreduce(&globalMolMembership[0], |
| 556 |
|
info->getGlobalMolMembershipPointer(), |
| 557 |
|
info->getNGlobalAtoms(), |
| 558 |
|
MPI_INT, MPI_SUM, MPI_COMM_WORLD); |
| 559 |
< |
|
| 560 |
< |
} |
| 561 |
< |
|
| 554 |
< |
|
| 555 |
< |
void SimCreator::initFortran(SimInfo* info) { |
| 556 |
< |
info->update(); |
| 557 |
< |
|
| 558 |
< |
std::vector<AtomType*> atomTypes; |
| 559 |
< |
std::vector<AtomType*>::iterator i; |
| 560 |
< |
std::vector<double> cutoffRadius; |
| 561 |
< |
ForceField* ff; |
| 562 |
< |
|
| 563 |
< |
//get the unique atom types |
| 564 |
< |
atomTypes = info->getUniqueAtomTypes(); |
| 565 |
< |
|
| 566 |
< |
ff = info->getForceField(); |
| 567 |
< |
|
| 568 |
< |
//query the max cutoff radius among these atom types |
| 569 |
< |
for (i = atomTypes.begin(); i != atomTypes.end(); ++i) { |
| 570 |
< |
cutoffRadius.push_back(ff->(*i)); |
| 571 |
< |
} |
| 572 |
< |
|
| 573 |
< |
double maxCutoffRadius = std::max_element(cutoffRadius.begin(), cutoffRadius.end()); |
| 574 |
< |
|
| 575 |
< |
#ifdef IS_MPI |
| 576 |
< |
//pick the max cutoff radius among the processors |
| 559 |
> |
#else |
| 560 |
> |
std::copy(globalMolMembership.begin(), globalMolMembership.end(), |
| 561 |
> |
info->getGlobalMolMembershipPointer()); |
| 562 |
|
#endif |
| 563 |
|
|
| 579 |
– |
|
| 580 |
– |
|
| 564 |
|
} |
| 565 |
|
|
| 566 |
|
void SimCreator::loadCoordinates(SimInfo* info) { |
| 580 |
|
if (nframes > 0) { |
| 581 |
|
reader.readFrame(info, nframes - 1); |
| 582 |
|
} else { |
| 583 |
< |
//invalid initial coordinate file |
| 583 |
> |
//invalid initial coordinate file |
| 584 |
|
sprintf(painCave.errMsg, "Initial configuration file %s should at least contain one frame\n", |
| 585 |
|
globals->getInitialConfig()); |
| 586 |
|
painCave.isFatal = 1; |
