# | Line 65 | Line 65 | namespace oopse { | |
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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), | |
# | Line 147 | Line 147 | SimInfo::~SimInfo() { | |
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_; | |
# | Line 380 | Line 379 | void SimInfo::addExcludePairs(Molecule* mol) { | |
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) { | |
# | Line 450 | Line 436 | 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 | ||
# | Line 697 | Line 670 | void SimInfo::setupFortranSim() { | |
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(); | |
# | Line 887 | Line 857 | void SimInfo::setSnapshotManager(SnapshotManager* sman | |
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; |
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< | Changed lines |
> | Changed lines |