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root/group/trunk/OOPSE-2.0/src/brains/SimInfo.cpp
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Comparing trunk/OOPSE-2.0/src/brains/SimInfo.cpp (file contents):
Revision 2097 by tim, Wed Mar 9 17:30:29 2005 UTC vs.
Revision 2116 by tim, Fri Mar 11 15:00:20 2005 UTC

# Line 367 | Line 367 | void SimInfo::addExcludePairs(Molecule* mol) {
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 >    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 >
396   }
397  
398   void SimInfo::removeExcludePairs(Molecule* mol) {
# Line 412 | Line 437 | void SimInfo::removeExcludePairs(Molecule* mol) {
437          exclude_.removePair(c, d);        
438      }
439  
440 +    Molecule::RigidBodyIterator rbIter;
441 +    RigidBody* rb;
442 +    for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
443 +        std::vector<Atom*> atoms = rb->getAtoms();
444 +        for (int i = 0; i < atoms.size() -1 ; ++i) {
445 +            for (int j = i + 1; j < atoms.size(); ++j) {
446 +                a = atoms[i]->getGlobalIndex();
447 +                b = atoms[j]->getGlobalIndex();
448 +                exclude_.removePair(a, b);
449 +            }
450 +        }
451 +    }        
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 +    }  
465 +
466   }
467  
468  
# Line 646 | Line 697 | void SimInfo::setupFortranSim() {
697      }
698      
699      //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
700      int nGlobalExcludes = 0;
701      int* globalExcludes = NULL;
702      int* excludeList = exclude_.getExcludeList();
# Line 836 | Line 884 | void SimInfo::setSnapshotManager(SnapshotManager* sman
884   }
885  
886   void SimInfo::setSnapshotManager(SnapshotManager* sman) {
887 <    //if (sman_ == sman_) {
888 <    //    return;
889 <    //}
890 <    
843 <    //delete sman_;
887 >    if (sman_ == sman) {
888 >        return;
889 >    }    
890 >    delete sman_;
891      sman_ = sman;
892  
893      Molecule* mol;

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