| 65 |
|
|
| 66 |
|
namespace oopse { |
| 67 |
|
|
| 68 |
< |
SimInfo::SimInfo(std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs, |
| 68 |
> |
SimInfo::SimInfo(MakeStamps* stamps, std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs, |
| 69 |
|
ForceField* ff, Globals* simParams) : |
| 70 |
< |
forceField_(ff), simParams_(simParams), |
| 70 |
> |
stamps_(stamps), forceField_(ff), simParams_(simParams), |
| 71 |
|
ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0), |
| 72 |
|
nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0), |
| 73 |
|
nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0), |
| 147 |
|
delete i->second; |
| 148 |
|
} |
| 149 |
|
molecules_.clear(); |
| 150 |
< |
|
| 151 |
< |
MemoryUtils::deletePointers(moleculeStamps_); |
| 152 |
< |
|
| 150 |
> |
|
| 151 |
> |
delete stamps_; |
| 152 |
|
delete sman_; |
| 153 |
|
delete simParams_; |
| 154 |
|
delete forceField_; |
| 379 |
|
} |
| 380 |
|
} |
| 381 |
|
|
| 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 |
– |
|
| 382 |
|
} |
| 383 |
|
|
| 384 |
|
void SimInfo::removeExcludePairs(Molecule* mol) { |
| 436 |
|
} |
| 437 |
|
} |
| 438 |
|
|
| 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 |
– |
} |
| 465 |
– |
|
| 439 |
|
} |
| 440 |
|
|
| 441 |
|
|
| 670 |
|
} |
| 671 |
|
|
| 672 |
|
//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 |
| 673 |
|
int nGlobalExcludes = 0; |
| 674 |
|
int* globalExcludes = NULL; |
| 675 |
|
int* excludeList = exclude_.getExcludeList(); |
| 857 |
|
} |
| 858 |
|
|
| 859 |
|
void SimInfo::setSnapshotManager(SnapshotManager* sman) { |
| 860 |
< |
//if (sman_ == sman_) { |
| 861 |
< |
// return; |
| 862 |
< |
//} |
| 863 |
< |
|
| 894 |
< |
//delete sman_; |
| 860 |
> |
if (sman_ == sman) { |
| 861 |
> |
return; |
| 862 |
> |
} |
| 863 |
> |
delete sman_; |
| 864 |
|
sman_ = sman; |
| 865 |
|
|
| 866 |
|
Molecule* mol; |
