| 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 |
|
|
| 609 |
|
#endif |
| 610 |
|
|
| 611 |
|
stampId = info->getMoleculeStampId(i); |
| 612 |
< |
Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId), |
| 613 |
< |
stampId, i, info->getLocalIndexManager()); |
| 612 |
> |
Molecule * mol = molCreator.createMolecule(info->getForceField(), |
| 613 |
> |
info->getMoleculeStamp(stampId), |
| 614 |
> |
stampId, i, |
| 615 |
> |
info->getLocalIndexManager()); |
| 616 |
|
|
| 617 |
|
info->addMolecule(mol); |
| 618 |
|
|
| 639 |
|
int beginRigidBodyIndex; |
| 640 |
|
int beginCutoffGroupIndex; |
| 641 |
|
int nGlobalAtoms = info->getNGlobalAtoms(); |
| 643 |
– |
|
| 644 |
– |
/**@todo fixme */ |
| 645 |
– |
#ifndef IS_MPI |
| 642 |
|
|
| 643 |
|
beginAtomIndex = 0; |
| 644 |
|
beginRigidBodyIndex = 0; |
| 645 |
|
beginCutoffGroupIndex = 0; |
| 646 |
< |
|
| 647 |
< |
#else |
| 652 |
< |
|
| 653 |
< |
int nproc; |
| 654 |
< |
int myNode; |
| 655 |
< |
|
| 656 |
< |
myNode = worldRank; |
| 657 |
< |
MPI_Comm_size(MPI_COMM_WORLD, &nproc); |
| 658 |
< |
|
| 659 |
< |
std::vector < int > tmpAtomsInProc(nproc, 0); |
| 660 |
< |
std::vector < int > tmpRigidBodiesInProc(nproc, 0); |
| 661 |
< |
std::vector < int > tmpCutoffGroupsInProc(nproc, 0); |
| 662 |
< |
std::vector < int > NumAtomsInProc(nproc, 0); |
| 663 |
< |
std::vector < int > NumRigidBodiesInProc(nproc, 0); |
| 664 |
< |
std::vector < int > NumCutoffGroupsInProc(nproc, 0); |
| 665 |
< |
|
| 666 |
< |
tmpAtomsInProc[myNode] = info->getNAtoms(); |
| 667 |
< |
tmpRigidBodiesInProc[myNode] = info->getNRigidBodies(); |
| 668 |
< |
tmpCutoffGroupsInProc[myNode] = info->getNCutoffGroups(); |
| 669 |
< |
|
| 670 |
< |
//do MPI_ALLREDUCE to exchange the total number of atoms, rigidbodies and cutoff groups |
| 671 |
< |
MPI_Allreduce(&tmpAtomsInProc[0], &NumAtomsInProc[0], nproc, MPI_INT, |
| 672 |
< |
MPI_SUM, MPI_COMM_WORLD); |
| 673 |
< |
MPI_Allreduce(&tmpRigidBodiesInProc[0], &NumRigidBodiesInProc[0], nproc, |
| 674 |
< |
MPI_INT, MPI_SUM, MPI_COMM_WORLD); |
| 675 |
< |
MPI_Allreduce(&tmpCutoffGroupsInProc[0], &NumCutoffGroupsInProc[0], nproc, |
| 676 |
< |
MPI_INT, MPI_SUM, MPI_COMM_WORLD); |
| 677 |
< |
|
| 678 |
< |
beginAtomIndex = 0; |
| 679 |
< |
beginRigidBodyIndex = 0; |
| 680 |
< |
beginCutoffGroupIndex = 0; |
| 681 |
< |
|
| 682 |
< |
for(int i = 0; i < myNode; i++) { |
| 683 |
< |
beginAtomIndex += NumAtomsInProc[i]; |
| 684 |
< |
beginRigidBodyIndex += NumRigidBodiesInProc[i]; |
| 685 |
< |
beginCutoffGroupIndex += NumCutoffGroupsInProc[i]; |
| 686 |
< |
} |
| 687 |
< |
|
| 688 |
< |
#endif |
| 689 |
< |
|
| 690 |
< |
//rigidbody's index begins right after atom's |
| 691 |
< |
beginRigidBodyIndex += info->getNGlobalAtoms(); |
| 692 |
< |
|
| 693 |
< |
for(mol = info->beginMolecule(mi); mol != NULL; |
| 694 |
< |
mol = info->nextMolecule(mi)) { |
| 695 |
< |
|
| 696 |
< |
//local index(index in DataStorge) of atom is important |
| 697 |
< |
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
| 698 |
< |
atom->setGlobalIndex(beginAtomIndex++); |
| 699 |
< |
} |
| 646 |
> |
|
| 647 |
> |
for(int i = 0; i < info->getNGlobalMolecules(); i++) { |
| 648 |
|
|
| 649 |
< |
for(rb = mol->beginRigidBody(ri); rb != NULL; |
| 650 |
< |
rb = mol->nextRigidBody(ri)) { |
| 651 |
< |
rb->setGlobalIndex(beginRigidBodyIndex++); |
| 649 |
> |
#ifdef IS_MPI |
| 650 |
> |
if (info->getMolToProc(i) == worldRank) { |
| 651 |
> |
#endif |
| 652 |
> |
// stuff to do if I own this molecule |
| 653 |
> |
mol = info->getMoleculeByGlobalIndex(i); |
| 654 |
> |
|
| 655 |
> |
//local index(index in DataStorge) of atom is important |
| 656 |
> |
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
| 657 |
> |
atom->setGlobalIndex(beginAtomIndex++); |
| 658 |
> |
} |
| 659 |
> |
|
| 660 |
> |
for(rb = mol->beginRigidBody(ri); rb != NULL; |
| 661 |
> |
rb = mol->nextRigidBody(ri)) { |
| 662 |
> |
rb->setGlobalIndex(beginRigidBodyIndex++); |
| 663 |
> |
} |
| 664 |
> |
|
| 665 |
> |
//local index of cutoff group is trivial, it only depends on |
| 666 |
> |
//the order of travesing |
| 667 |
> |
for(cg = mol->beginCutoffGroup(ci); cg != NULL; |
| 668 |
> |
cg = mol->nextCutoffGroup(ci)) { |
| 669 |
> |
cg->setGlobalIndex(beginCutoffGroupIndex++); |
| 670 |
> |
} |
| 671 |
> |
|
| 672 |
> |
#ifdef IS_MPI |
| 673 |
> |
} else { |
| 674 |
> |
|
| 675 |
> |
// stuff to do if I don't own this molecule |
| 676 |
> |
|
| 677 |
> |
int stampId = info->getMoleculeStampId(i); |
| 678 |
> |
MoleculeStamp* stamp = info->getMoleculeStamp(stampId); |
| 679 |
> |
|
| 680 |
> |
beginAtomIndex += stamp->getNAtoms(); |
| 681 |
> |
beginRigidBodyIndex += stamp->getNRigidBodies(); |
| 682 |
> |
beginCutoffGroupIndex += stamp->getNCutoffGroups() + stamp->getNFreeAtoms(); |
| 683 |
|
} |
| 684 |
< |
|
| 685 |
< |
//local index of cutoff group is trivial, it only depends on the order of travesing |
| 686 |
< |
for(cg = mol->beginCutoffGroup(ci); cg != NULL; |
| 687 |
< |
cg = mol->nextCutoffGroup(ci)) { |
| 709 |
< |
cg->setGlobalIndex(beginCutoffGroupIndex++); |
| 710 |
< |
} |
| 711 |
< |
} |
| 712 |
< |
|
| 684 |
> |
#endif |
| 685 |
> |
|
| 686 |
> |
} //end for(int i=0) |
| 687 |
> |
|
| 688 |
|
//fill globalGroupMembership |
| 689 |
|
std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0); |
| 690 |
|
for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { |
| 696 |
|
|
| 697 |
|
} |
| 698 |
|
} |
| 699 |
< |
|
| 699 |
> |
|
| 700 |
|
#ifdef IS_MPI |
| 701 |
|
// Since the globalGroupMembership has been zero filled and we've only |
| 702 |
|
// poked values into the atoms we know, we can do an Allreduce |
| 766 |
|
globalIO++; |
| 767 |
|
} |
| 768 |
|
} |
| 769 |
< |
|
| 769 |
> |
|
| 770 |
|
info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject); |
| 771 |
|
|
| 772 |
|
} |
| 773 |
|
|
| 774 |
|
void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) { |
| 775 |
|
Globals* simParams; |
| 776 |
+ |
|
| 777 |
|
simParams = info->getSimParams(); |
| 778 |
|
|
| 803 |
– |
|
| 779 |
|
DumpReader reader(info, mdFileName); |
| 780 |
|
int nframes = reader.getNFrames(); |
| 781 |
< |
|
| 781 |
> |
|
| 782 |
|
if (nframes > 0) { |
| 783 |
|
reader.readFrame(nframes - 1); |
| 784 |
|
} else { |
| 789 |
|
painCave.isFatal = 1; |
| 790 |
|
simError(); |
| 791 |
|
} |
| 817 |
– |
|
| 792 |
|
//copy the current snapshot to previous snapshot |
| 793 |
|
info->getSnapshotManager()->advance(); |
| 794 |
|
} |
