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root/OpenMD/branches/development/src/brains/SimInfo.cpp
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Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 1241 by gezelter, Fri Apr 25 15:14:47 2008 UTC vs.
Revision 1277 by gezelter, Mon Jul 14 12:35:58 2008 UTC

# Line 90 | Line 90 | namespace oopse {
90      ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
91      nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
92      nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
93 <    nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nRigidBodies_(0),
94 <    nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
95 <    sman_(NULL), fortranInitialized_(false), calcBoxDipole_(false),
96 <    useAtomicVirial_(true) {
93 >    nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
94 >    nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
95 >    nConstraints_(0), sman_(NULL), fortranInitialized_(false),
96 >    calcBoxDipole_(false), useAtomicVirial_(true) {
97  
98 +
99        MoleculeStamp* molStamp;
100        int nMolWithSameStamp;
101        int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
# Line 102 | Line 103 | namespace oopse {
103        CutoffGroupStamp* cgStamp;    
104        RigidBodyStamp* rbStamp;
105        int nRigidAtoms = 0;
106 +
107        std::vector<Component*> components = simParams->getComponents();
108        
109        for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
# Line 194 | Line 196 | namespace oopse {
196        nBonds_ += mol->getNBonds();
197        nBends_ += mol->getNBends();
198        nTorsions_ += mol->getNTorsions();
199 +      nInversions_ += mol->getNInversions();
200        nRigidBodies_ += mol->getNRigidBodies();
201        nIntegrableObjects_ += mol->getNIntegrableObjects();
202        nCutoffGroups_ += mol->getNCutoffGroups();
# Line 219 | Line 222 | namespace oopse {
222        nBonds_ -= mol->getNBonds();
223        nBends_ -= mol->getNBends();
224        nTorsions_ -= mol->getNTorsions();
225 +      nInversions_ -= mol->getNInversions();
226        nRigidBodies_ -= mol->getNRigidBodies();
227        nIntegrableObjects_ -= mol->getNIntegrableObjects();
228        nCutoffGroups_ -= mol->getNCutoffGroups();
# Line 354 | Line 358 | namespace oopse {
358      std::vector<Bond*>::iterator bondIter;
359      std::vector<Bend*>::iterator bendIter;
360      std::vector<Torsion*>::iterator torsionIter;
361 +    std::vector<Inversion*>::iterator inversionIter;
362      Bond* bond;
363      Bend* bend;
364      Torsion* torsion;
365 +    Inversion* inversion;
366      int a;
367      int b;
368      int c;
# Line 419 | Line 425 | namespace oopse {
425        b = torsion->getAtomB()->getGlobalIndex();        
426        c = torsion->getAtomC()->getGlobalIndex();        
427        d = torsion->getAtomD()->getGlobalIndex();        
428 +      std::set<int> rigidSetA = getRigidSet(a, atomGroups);
429 +      std::set<int> rigidSetB = getRigidSet(b, atomGroups);
430 +      std::set<int> rigidSetC = getRigidSet(c, atomGroups);
431 +      std::set<int> rigidSetD = getRigidSet(d, atomGroups);
432 +
433 +      exclude_.addPairs(rigidSetA, rigidSetB);
434 +      exclude_.addPairs(rigidSetA, rigidSetC);
435 +      exclude_.addPairs(rigidSetA, rigidSetD);
436 +      exclude_.addPairs(rigidSetB, rigidSetC);
437 +      exclude_.addPairs(rigidSetB, rigidSetD);
438 +      exclude_.addPairs(rigidSetC, rigidSetD);
439 +
440 +      /*
441 +      exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
442 +      exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
443 +      exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
444 +      exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
445 +      exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
446 +      exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
447 +        
448 +      
449 +      exclude_.addPair(a, b);
450 +      exclude_.addPair(a, c);
451 +      exclude_.addPair(a, d);
452 +      exclude_.addPair(b, c);
453 +      exclude_.addPair(b, d);
454 +      exclude_.addPair(c, d);        
455 +      */
456 +    }
457 +
458 +    for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
459 +         inversion = mol->nextInversion(inversionIter)) {
460 +      a = inversion->getAtomA()->getGlobalIndex();
461 +      b = inversion->getAtomB()->getGlobalIndex();        
462 +      c = inversion->getAtomC()->getGlobalIndex();        
463 +      d = inversion->getAtomD()->getGlobalIndex();        
464        std::set<int> rigidSetA = getRigidSet(a, atomGroups);
465        std::set<int> rigidSetB = getRigidSet(b, atomGroups);
466        std::set<int> rigidSetC = getRigidSet(c, atomGroups);
# Line 466 | Line 508 | namespace oopse {
508      std::vector<Bond*>::iterator bondIter;
509      std::vector<Bend*>::iterator bendIter;
510      std::vector<Torsion*>::iterator torsionIter;
511 +    std::vector<Inversion*>::iterator inversionIter;
512      Bond* bond;
513      Bend* bend;
514      Torsion* torsion;
515 +    Inversion* inversion;
516      int a;
517      int b;
518      int c;
# Line 562 | Line 606 | namespace oopse {
606        */
607      }
608  
609 +    for (inversion= mol->beginInversion(inversionIter); inversion != NULL; inversion = mol->nextInversion(inversionIter)) {
610 +      a = inversion->getAtomA()->getGlobalIndex();
611 +      b = inversion->getAtomB()->getGlobalIndex();        
612 +      c = inversion->getAtomC()->getGlobalIndex();        
613 +      d = inversion->getAtomD()->getGlobalIndex();        
614 +
615 +      std::set<int> rigidSetA = getRigidSet(a, atomGroups);
616 +      std::set<int> rigidSetB = getRigidSet(b, atomGroups);
617 +      std::set<int> rigidSetC = getRigidSet(c, atomGroups);
618 +      std::set<int> rigidSetD = getRigidSet(d, atomGroups);
619 +
620 +      exclude_.removePairs(rigidSetA, rigidSetB);
621 +      exclude_.removePairs(rigidSetA, rigidSetC);
622 +      exclude_.removePairs(rigidSetA, rigidSetD);
623 +      exclude_.removePairs(rigidSetB, rigidSetC);
624 +      exclude_.removePairs(rigidSetB, rigidSetD);
625 +      exclude_.removePairs(rigidSetC, rigidSetD);
626 +
627 +      /*
628 +      exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
629 +      exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
630 +      exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
631 +      exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
632 +      exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
633 +      exclude_.removePairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
634 +
635 +      
636 +      exclude_.removePair(a, b);
637 +      exclude_.removePair(a, c);
638 +      exclude_.removePair(a, d);
639 +      exclude_.removePair(b, c);
640 +      exclude_.removePair(b, d);
641 +      exclude_.removePair(c, d);        
642 +      */
643 +    }
644 +
645      for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
646        std::vector<Atom*> atoms = rb->getAtoms();
647        for (int i = 0; i < atoms.size() -1 ; ++i) {

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