| 35 |
|
* |
| 36 |
|
* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
| 37 |
|
* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
| 38 |
< |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
| 38 |
> |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008). |
| 39 |
|
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
|
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
|
*/ |
| 310 |
|
SimInfo::MoleculeIterator mi; |
| 311 |
|
Molecule::IntegrableObjectIterator ii; |
| 312 |
|
RigidBody::AtomIterator ai; |
| 313 |
– |
Atom* atom; |
| 313 |
|
|
| 314 |
|
#ifndef IS_MPI |
| 315 |
|
os << " <Snapshot>\n"; |
| 317 |
|
writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot()); |
| 318 |
|
|
| 319 |
|
os << " <StuntDoubles>\n"; |
| 320 |
< |
for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
| 321 |
< |
|
| 320 |
> |
for (mol = info_->beginMolecule(mi); mol != NULL; |
| 321 |
> |
mol = info_->nextMolecule(mi)) { |
| 322 |
|
|
| 323 |
|
for (sd = mol->beginIntegrableObject(ii); sd != NULL; |
| 324 |
|
sd = mol->nextIntegrableObject(ii)) { |
| 334 |
|
mol = info_->nextMolecule(mi)) { |
| 335 |
|
|
| 336 |
|
for (sd = mol->beginIntegrableObject(ii); sd != NULL; |
| 337 |
< |
sd = mol->nextIntegrableObject(ii)) { |
| 338 |
< |
|
| 337 |
> |
sd = mol->nextIntegrableObject(ii)) { |
| 338 |
> |
|
| 339 |
|
int ioIndex = sd->getGlobalIntegrableObjectIndex(); |
| 340 |
|
// do one for the IO itself |
| 341 |
|
os << prepareSiteLine(sd, ioIndex, 0); |
| 344 |
|
|
| 345 |
|
RigidBody* rb = static_cast<RigidBody*>(sd); |
| 346 |
|
int siteIndex = 0; |
| 347 |
< |
for (atom = rb->beginAtom(ai); atom != NULL; |
| 347 |
> |
for (Atom* atom = rb->beginAtom(ai); atom != NULL; |
| 348 |
|
atom = rb->nextAtom(ai)) { |
| 349 |
|
os << prepareSiteLine(atom, ioIndex, siteIndex); |
| 350 |
|
siteIndex++; |
| 419 |
|
// send our buffer: |
| 420 |
|
MPI::COMM_WORLD.Send((void *)buffer.c_str(), sendBufferLength, |
| 421 |
|
MPI::CHAR, masterNode, 0); |
| 422 |
+ |
|
| 423 |
|
} |
| 424 |
|
} |
| 425 |
|
} |
| 447 |
|
|
| 448 |
|
RigidBody* rb = static_cast<RigidBody*>(sd); |
| 449 |
|
int siteIndex = 0; |
| 450 |
< |
for (atom = rb->beginAtom(ai); atom != NULL; |
| 450 |
> |
for (Atom* atom = rb->beginAtom(ai); atom != NULL; |
| 451 |
|
atom = rb->nextAtom(ai)) { |
| 452 |
|
buffer += prepareSiteLine(atom, ioIndex, siteIndex); |
| 453 |
|
siteIndex++; |
| 726 |
|
#ifdef IS_MPI |
| 727 |
|
if (worldRank == 0) { |
| 728 |
|
#endif // is_mpi |
| 729 |
< |
|
| 729 |
> |
|
| 730 |
|
eorStream = createOStream(eorFilename_); |
| 731 |
|
|
| 732 |
|
#ifdef IS_MPI |
| 733 |
|
} |
| 734 |
< |
#endif // is_mpi |
| 735 |
< |
|
| 734 |
> |
#endif |
| 735 |
> |
|
| 736 |
|
writeFrame(*eorStream); |
| 737 |
< |
|
| 737 |
> |
|
| 738 |
|
#ifdef IS_MPI |
| 739 |
|
if (worldRank == 0) { |
| 740 |
< |
#endif // is_mpi |
| 740 |
> |
#endif |
| 741 |
> |
|
| 742 |
|
writeClosing(*eorStream); |
| 743 |
|
delete eorStream; |
| 744 |
+ |
|
| 745 |
|
#ifdef IS_MPI |
| 746 |
|
} |
| 747 |
|
#endif // is_mpi |
