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root/OpenMD/trunk/src/brains/SimInfo.cpp
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Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 413 by tim, Wed Mar 9 17:30:29 2005 UTC vs.
Revision 435 by tim, Fri Mar 11 15:55:17 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   }
384  
385   void SimInfo::removeExcludePairs(Molecule* mol) {
# Line 412 | Line 424 | 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  
# Line 646 | Line 671 | void SimInfo::setupFortranSim() {
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();
# Line 836 | Line 858 | void SimInfo::setSnapshotManager(SnapshotManager* sman
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;

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