380 |
|
} |
381 |
|
} |
382 |
|
|
383 |
– |
Molecule::CutoffGroupIterator cgIter; |
384 |
– |
CutoffGroup* cg; |
385 |
– |
for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) { |
386 |
– |
std::vector<Atom*> atoms = cg->getAtoms(); |
387 |
– |
for (int i = 0; i < atoms.size() -1 ; ++i) { |
388 |
– |
for (int j = i + 1; j < atoms.size(); ++j) { |
389 |
– |
a = atoms[i]->getGlobalIndex(); |
390 |
– |
b = atoms[j]->getGlobalIndex(); |
391 |
– |
exclude_.addPair(a, b); |
392 |
– |
} |
393 |
– |
} |
394 |
– |
} |
395 |
– |
|
383 |
|
} |
384 |
|
|
385 |
|
void SimInfo::removeExcludePairs(Molecule* mol) { |
436 |
|
} |
437 |
|
} |
438 |
|
} |
452 |
– |
|
453 |
– |
Molecule::CutoffGroupIterator cgIter; |
454 |
– |
CutoffGroup* cg; |
455 |
– |
for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) { |
456 |
– |
std::vector<Atom*> atoms = cg->getAtoms(); |
457 |
– |
for (int i = 0; i < atoms.size() -1 ; ++i) { |
458 |
– |
for (int j = i + 1; j < atoms.size(); ++j) { |
459 |
– |
a = atoms[i]->getGlobalIndex(); |
460 |
– |
b = atoms[j]->getGlobalIndex(); |
461 |
– |
exclude_.removePair(a, b); |
462 |
– |
} |
463 |
– |
} |
464 |
– |
} |
439 |
|
|
440 |
|
} |
441 |
|
|
671 |
|
} |
672 |
|
|
673 |
|
//setup fortran simulation |
700 |
– |
//gloalExcludes and molMembershipArray should go away (They are never used) |
701 |
– |
//why the hell fortran need to know molecule? |
702 |
– |
//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 |
< |
|
894 |
< |
//delete sman_; |
861 |
> |
if (sman_ == sman) { |
862 |
> |
return; |
863 |
> |
} |
864 |
> |
delete sman_; |
865 |
|
sman_ = sman; |
866 |
|
|
867 |
|
Molecule* mol; |