| 367 |
|
exclude_.addPair(c, d); |
| 368 |
|
} |
| 369 |
|
|
| 370 |
< |
|
| 370 |
> |
Molecule::RigidBodyIterator rbIter; |
| 371 |
> |
RigidBody* rb; |
| 372 |
> |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
| 373 |
> |
std::vector<Atom*> atoms = rb->getAtoms(); |
| 374 |
> |
for (int i = 0; i < atoms.size() -1 ; ++i) { |
| 375 |
> |
for (int j = i + 1; j < atoms.size(); ++j) { |
| 376 |
> |
a = atoms[i]->getGlobalIndex(); |
| 377 |
> |
b = atoms[j]->getGlobalIndex(); |
| 378 |
> |
exclude_.addPair(a, b); |
| 379 |
> |
} |
| 380 |
> |
} |
| 381 |
> |
} |
| 382 |
> |
|
| 383 |
|
} |
| 384 |
|
|
| 385 |
|
void SimInfo::removeExcludePairs(Molecule* mol) { |
| 424 |
|
exclude_.removePair(c, d); |
| 425 |
|
} |
| 426 |
|
|
| 427 |
+ |
Molecule::RigidBodyIterator rbIter; |
| 428 |
+ |
RigidBody* rb; |
| 429 |
+ |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
| 430 |
+ |
std::vector<Atom*> atoms = rb->getAtoms(); |
| 431 |
+ |
for (int i = 0; i < atoms.size() -1 ; ++i) { |
| 432 |
+ |
for (int j = i + 1; j < atoms.size(); ++j) { |
| 433 |
+ |
a = atoms[i]->getGlobalIndex(); |
| 434 |
+ |
b = atoms[j]->getGlobalIndex(); |
| 435 |
+ |
exclude_.removePair(a, b); |
| 436 |
+ |
} |
| 437 |
+ |
} |
| 438 |
+ |
} |
| 439 |
+ |
|
| 440 |
|
} |
| 441 |
|
|
| 442 |
|
|
| 671 |
|
} |
| 672 |
|
|
| 673 |
|
//setup fortran simulation |
| 649 |
– |
//gloalExcludes and molMembershipArray should go away (They are never used) |
| 650 |
– |
//why the hell fortran need to know molecule? |
| 651 |
– |
//OOPSE = Object-Obfuscated Parallel Simulation Engine |
| 674 |
|
int nGlobalExcludes = 0; |
| 675 |
|
int* globalExcludes = NULL; |
| 676 |
|
int* excludeList = exclude_.getExcludeList(); |
| 858 |
|
} |
| 859 |
|
|
| 860 |
|
void SimInfo::setSnapshotManager(SnapshotManager* sman) { |
| 861 |
< |
//if (sman_ == sman_) { |
| 862 |
< |
// return; |
| 863 |
< |
//} |
| 864 |
< |
|
| 843 |
< |
//delete sman_; |
| 861 |
> |
if (sman_ == sman) { |
| 862 |
> |
return; |
| 863 |
> |
} |
| 864 |
> |
delete sman_; |
| 865 |
|
sman_ = sman; |
| 866 |
|
|
| 867 |
|
Molecule* mol; |
