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root/OpenMD/trunk/src/brains/SimInfo.cpp
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Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 1277 by gezelter, Mon Jul 14 12:35:58 2008 UTC vs.
Revision 1386 by gezelter, Fri Oct 23 18:41:09 2009 UTC

# Line 202 | Line 202 | namespace oopse {
202        nCutoffGroups_ += mol->getNCutoffGroups();
203        nConstraints_ += mol->getNConstraintPairs();
204  
205 <      addExcludePairs(mol);
206 <        
205 >      addInteractionPairs(mol);
206 >  
207        return true;
208      } else {
209        return false;
# Line 228 | Line 228 | namespace oopse {
228        nCutoffGroups_ -= mol->getNCutoffGroups();
229        nConstraints_ -= mol->getNConstraintPairs();
230  
231 <      removeExcludePairs(mol);
231 >      removeInteractionPairs(mol);
232        molecules_.erase(mol->getGlobalIndex());
233  
234        delete mol;
# Line 354 | Line 354 | namespace oopse {
354  
355    }
356  
357 <  void SimInfo::addExcludePairs(Molecule* mol) {
357 >  void SimInfo::addInteractionPairs(Molecule* mol) {
358 >    ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
359      std::vector<Bond*>::iterator bondIter;
360      std::vector<Bend*>::iterator bendIter;
361      std::vector<Torsion*>::iterator torsionIter;
# Line 368 | Line 369 | namespace oopse {
369      int c;
370      int d;
371  
372 <    std::map<int, std::set<int> > atomGroups;
372 >    // atomGroups can be used to add special interaction maps between
373 >    // groups of atoms that are in two separate rigid bodies.
374 >    // However, most site-site interactions between two rigid bodies
375 >    // are probably not special, just the ones between the physically
376 >    // bonded atoms.  Interactions *within* a single rigid body should
377 >    // always be excluded.  These are done at the bottom of this
378 >    // function.
379  
380 +    std::map<int, std::set<int> > atomGroups;
381      Molecule::RigidBodyIterator rbIter;
382      RigidBody* rb;
383      Molecule::IntegrableObjectIterator ii;
384      StuntDouble* integrableObject;
385      
386 <    for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
387 <           integrableObject = mol->nextIntegrableObject(ii)) {
388 <
386 >    for (integrableObject = mol->beginIntegrableObject(ii);
387 >         integrableObject != NULL;
388 >         integrableObject = mol->nextIntegrableObject(ii)) {
389 >      
390        if (integrableObject->isRigidBody()) {
391 <          rb = static_cast<RigidBody*>(integrableObject);
392 <          std::vector<Atom*> atoms = rb->getAtoms();
393 <          std::set<int> rigidAtoms;
394 <          for (int i = 0; i < atoms.size(); ++i) {
395 <            rigidAtoms.insert(atoms[i]->getGlobalIndex());
396 <          }
397 <          for (int i = 0; i < atoms.size(); ++i) {
398 <            atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
399 <          }      
391 >        rb = static_cast<RigidBody*>(integrableObject);
392 >        std::vector<Atom*> atoms = rb->getAtoms();
393 >        std::set<int> rigidAtoms;
394 >        for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
395 >          rigidAtoms.insert(atoms[i]->getGlobalIndex());
396 >        }
397 >        for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
398 >          atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
399 >        }      
400        } else {
401          std::set<int> oneAtomSet;
402          oneAtomSet.insert(integrableObject->getGlobalIndex());
403          atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));        
404        }
405      }  
406 +          
407 +    for (bond= mol->beginBond(bondIter); bond != NULL;
408 +         bond = mol->nextBond(bondIter)) {
409  
398 –    
399 –    
400 –    for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
410        a = bond->getAtomA()->getGlobalIndex();
411 <      b = bond->getAtomB()->getGlobalIndex();        
412 <      exclude_.addPair(a, b);
411 >      b = bond->getAtomB()->getGlobalIndex();  
412 >    
413 >      if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
414 >        oneTwoInteractions_.addPair(a, b);
415 >      } else {
416 >        excludedInteractions_.addPair(a, b);
417 >      }
418      }
419  
420 <    for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
420 >    for (bend= mol->beginBend(bendIter); bend != NULL;
421 >         bend = mol->nextBend(bendIter)) {
422 >
423        a = bend->getAtomA()->getGlobalIndex();
424        b = bend->getAtomB()->getGlobalIndex();        
425        c = bend->getAtomC()->getGlobalIndex();
410 –      std::set<int> rigidSetA = getRigidSet(a, atomGroups);
411 –      std::set<int> rigidSetB = getRigidSet(b, atomGroups);
412 –      std::set<int> rigidSetC = getRigidSet(c, atomGroups);
413 –
414 –      exclude_.addPairs(rigidSetA, rigidSetB);
415 –      exclude_.addPairs(rigidSetA, rigidSetC);
416 –      exclude_.addPairs(rigidSetB, rigidSetC);
426        
427 <      //exclude_.addPair(a, b);
428 <      //exclude_.addPair(a, c);
429 <      //exclude_.addPair(b, c);        
427 >      if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
428 >        oneTwoInteractions_.addPair(a, b);      
429 >        oneTwoInteractions_.addPair(b, c);
430 >      } else {
431 >        excludedInteractions_.addPair(a, b);
432 >        excludedInteractions_.addPair(b, c);
433 >      }
434 >
435 >      if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
436 >        oneThreeInteractions_.addPair(a, c);      
437 >      } else {
438 >        excludedInteractions_.addPair(a, c);
439 >      }
440      }
441  
442 <    for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
442 >    for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
443 >         torsion = mol->nextTorsion(torsionIter)) {
444 >
445        a = torsion->getAtomA()->getGlobalIndex();
446        b = torsion->getAtomB()->getGlobalIndex();        
447        c = torsion->getAtomC()->getGlobalIndex();        
448 <      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);
448 >      d = torsion->getAtomD()->getGlobalIndex();      
449  
450 <      exclude_.addPairs(rigidSetA, rigidSetB);
451 <      exclude_.addPairs(rigidSetA, rigidSetC);
452 <      exclude_.addPairs(rigidSetA, rigidSetD);
453 <      exclude_.addPairs(rigidSetB, rigidSetC);
454 <      exclude_.addPairs(rigidSetB, rigidSetD);
455 <      exclude_.addPairs(rigidSetC, rigidSetD);
450 >      if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
451 >        oneTwoInteractions_.addPair(a, b);      
452 >        oneTwoInteractions_.addPair(b, c);
453 >        oneTwoInteractions_.addPair(c, d);
454 >      } else {
455 >        excludedInteractions_.addPair(a, b);
456 >        excludedInteractions_.addPair(b, c);
457 >        excludedInteractions_.addPair(c, d);
458 >      }
459  
460 <      /*
461 <      exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
462 <      exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
463 <      exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
464 <      exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
465 <      exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
466 <      exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
467 <        
468 <      
469 <      exclude_.addPair(a, b);
470 <      exclude_.addPair(a, c);
471 <      exclude_.addPair(a, d);
472 <      exclude_.addPair(b, c);
453 <      exclude_.addPair(b, d);
454 <      exclude_.addPair(c, d);        
455 <      */
460 >      if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
461 >        oneThreeInteractions_.addPair(a, c);      
462 >        oneThreeInteractions_.addPair(b, d);      
463 >      } else {
464 >        excludedInteractions_.addPair(a, c);
465 >        excludedInteractions_.addPair(b, d);
466 >      }
467 >
468 >      if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
469 >        oneFourInteractions_.addPair(a, d);      
470 >      } else {
471 >        excludedInteractions_.addPair(a, d);
472 >      }
473      }
474  
475      for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
476           inversion = mol->nextInversion(inversionIter)) {
477 +
478        a = inversion->getAtomA()->getGlobalIndex();
479        b = inversion->getAtomB()->getGlobalIndex();        
480        c = inversion->getAtomC()->getGlobalIndex();        
481        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);
467 –      std::set<int> rigidSetD = getRigidSet(d, atomGroups);
482  
483 <      exclude_.addPairs(rigidSetA, rigidSetB);
484 <      exclude_.addPairs(rigidSetA, rigidSetC);
485 <      exclude_.addPairs(rigidSetA, rigidSetD);
486 <      exclude_.addPairs(rigidSetB, rigidSetC);
487 <      exclude_.addPairs(rigidSetB, rigidSetD);
488 <      exclude_.addPairs(rigidSetC, rigidSetD);
483 >      if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
484 >        oneTwoInteractions_.addPair(a, b);      
485 >        oneTwoInteractions_.addPair(a, c);
486 >        oneTwoInteractions_.addPair(a, d);
487 >      } else {
488 >        excludedInteractions_.addPair(a, b);
489 >        excludedInteractions_.addPair(a, c);
490 >        excludedInteractions_.addPair(a, d);
491 >      }
492  
493 <      /*
494 <      exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
495 <      exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
496 <      exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
497 <      exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
498 <      exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
499 <      exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
500 <        
501 <      
485 <      exclude_.addPair(a, b);
486 <      exclude_.addPair(a, c);
487 <      exclude_.addPair(a, d);
488 <      exclude_.addPair(b, c);
489 <      exclude_.addPair(b, d);
490 <      exclude_.addPair(c, d);        
491 <      */
493 >      if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
494 >        oneThreeInteractions_.addPair(b, c);    
495 >        oneThreeInteractions_.addPair(b, d);    
496 >        oneThreeInteractions_.addPair(c, d);      
497 >      } else {
498 >        excludedInteractions_.addPair(b, c);
499 >        excludedInteractions_.addPair(b, d);
500 >        excludedInteractions_.addPair(c, d);
501 >      }
502      }
503  
504 <    for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
504 >    for (rb = mol->beginRigidBody(rbIter); rb != NULL;
505 >         rb = mol->nextRigidBody(rbIter)) {
506        std::vector<Atom*> atoms = rb->getAtoms();
507 <      for (int i = 0; i < atoms.size() -1 ; ++i) {
508 <        for (int j = i + 1; j < atoms.size(); ++j) {
507 >      for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
508 >        for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
509            a = atoms[i]->getGlobalIndex();
510            b = atoms[j]->getGlobalIndex();
511 <          exclude_.addPair(a, b);
511 >          excludedInteractions_.addPair(a, b);
512          }
513        }
514      }        
515  
516    }
517  
518 <  void SimInfo::removeExcludePairs(Molecule* mol) {
518 >  void SimInfo::removeInteractionPairs(Molecule* mol) {
519 >    ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
520      std::vector<Bond*>::iterator bondIter;
521      std::vector<Bend*>::iterator bendIter;
522      std::vector<Torsion*>::iterator torsionIter;
# Line 519 | Line 531 | namespace oopse {
531      int d;
532  
533      std::map<int, std::set<int> > atomGroups;
522 –
534      Molecule::RigidBodyIterator rbIter;
535      RigidBody* rb;
536      Molecule::IntegrableObjectIterator ii;
537      StuntDouble* integrableObject;
538      
539 <    for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
540 <           integrableObject = mol->nextIntegrableObject(ii)) {
541 <
539 >    for (integrableObject = mol->beginIntegrableObject(ii);
540 >         integrableObject != NULL;
541 >         integrableObject = mol->nextIntegrableObject(ii)) {
542 >      
543        if (integrableObject->isRigidBody()) {
544 <          rb = static_cast<RigidBody*>(integrableObject);
545 <          std::vector<Atom*> atoms = rb->getAtoms();
546 <          std::set<int> rigidAtoms;
547 <          for (int i = 0; i < atoms.size(); ++i) {
548 <            rigidAtoms.insert(atoms[i]->getGlobalIndex());
549 <          }
550 <          for (int i = 0; i < atoms.size(); ++i) {
551 <            atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
552 <          }      
544 >        rb = static_cast<RigidBody*>(integrableObject);
545 >        std::vector<Atom*> atoms = rb->getAtoms();
546 >        std::set<int> rigidAtoms;
547 >        for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
548 >          rigidAtoms.insert(atoms[i]->getGlobalIndex());
549 >        }
550 >        for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
551 >          atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
552 >        }      
553        } else {
554          std::set<int> oneAtomSet;
555          oneAtomSet.insert(integrableObject->getGlobalIndex());
# Line 545 | Line 557 | namespace oopse {
557        }
558      }  
559  
560 <    
561 <    for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
560 >    for (bond= mol->beginBond(bondIter); bond != NULL;
561 >         bond = mol->nextBond(bondIter)) {
562 >      
563        a = bond->getAtomA()->getGlobalIndex();
564 <      b = bond->getAtomB()->getGlobalIndex();        
565 <      exclude_.removePair(a, b);
564 >      b = bond->getAtomB()->getGlobalIndex();  
565 >    
566 >      if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
567 >        oneTwoInteractions_.removePair(a, b);
568 >      } else {
569 >        excludedInteractions_.removePair(a, b);
570 >      }
571      }
572  
573 <    for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
573 >    for (bend= mol->beginBend(bendIter); bend != NULL;
574 >         bend = mol->nextBend(bendIter)) {
575 >
576        a = bend->getAtomA()->getGlobalIndex();
577        b = bend->getAtomB()->getGlobalIndex();        
578        c = bend->getAtomC()->getGlobalIndex();
559 –
560 –      std::set<int> rigidSetA = getRigidSet(a, atomGroups);
561 –      std::set<int> rigidSetB = getRigidSet(b, atomGroups);
562 –      std::set<int> rigidSetC = getRigidSet(c, atomGroups);
563 –
564 –      exclude_.removePairs(rigidSetA, rigidSetB);
565 –      exclude_.removePairs(rigidSetA, rigidSetC);
566 –      exclude_.removePairs(rigidSetB, rigidSetC);
579        
580 <      //exclude_.removePair(a, b);
581 <      //exclude_.removePair(a, c);
582 <      //exclude_.removePair(b, c);        
580 >      if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
581 >        oneTwoInteractions_.removePair(a, b);      
582 >        oneTwoInteractions_.removePair(b, c);
583 >      } else {
584 >        excludedInteractions_.removePair(a, b);
585 >        excludedInteractions_.removePair(b, c);
586 >      }
587 >
588 >      if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
589 >        oneThreeInteractions_.removePair(a, c);      
590 >      } else {
591 >        excludedInteractions_.removePair(a, c);
592 >      }
593      }
594  
595 <    for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
595 >    for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
596 >         torsion = mol->nextTorsion(torsionIter)) {
597 >
598        a = torsion->getAtomA()->getGlobalIndex();
599        b = torsion->getAtomB()->getGlobalIndex();        
600        c = torsion->getAtomC()->getGlobalIndex();        
601 <      d = torsion->getAtomD()->getGlobalIndex();        
601 >      d = torsion->getAtomD()->getGlobalIndex();      
602 >  
603 >      if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
604 >        oneTwoInteractions_.removePair(a, b);      
605 >        oneTwoInteractions_.removePair(b, c);
606 >        oneTwoInteractions_.removePair(c, d);
607 >      } else {
608 >        excludedInteractions_.removePair(a, b);
609 >        excludedInteractions_.removePair(b, c);
610 >        excludedInteractions_.removePair(c, d);
611 >      }
612  
613 <      std::set<int> rigidSetA = getRigidSet(a, atomGroups);
614 <      std::set<int> rigidSetB = getRigidSet(b, atomGroups);
615 <      std::set<int> rigidSetC = getRigidSet(c, atomGroups);
616 <      std::set<int> rigidSetD = getRigidSet(d, atomGroups);
613 >      if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
614 >        oneThreeInteractions_.removePair(a, c);      
615 >        oneThreeInteractions_.removePair(b, d);      
616 >      } else {
617 >        excludedInteractions_.removePair(a, c);
618 >        excludedInteractions_.removePair(b, d);
619 >      }
620  
621 <      exclude_.removePairs(rigidSetA, rigidSetB);
622 <      exclude_.removePairs(rigidSetA, rigidSetC);
623 <      exclude_.removePairs(rigidSetA, rigidSetD);
624 <      exclude_.removePairs(rigidSetB, rigidSetC);
625 <      exclude_.removePairs(rigidSetB, rigidSetD);
589 <      exclude_.removePairs(rigidSetC, rigidSetD);
590 <
591 <      /*
592 <      exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
593 <      exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
594 <      exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
595 <      exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
596 <      exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
597 <      exclude_.removePairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
598 <
599 <      
600 <      exclude_.removePair(a, b);
601 <      exclude_.removePair(a, c);
602 <      exclude_.removePair(a, d);
603 <      exclude_.removePair(b, c);
604 <      exclude_.removePair(b, d);
605 <      exclude_.removePair(c, d);        
606 <      */
621 >      if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
622 >        oneFourInteractions_.removePair(a, d);      
623 >      } else {
624 >        excludedInteractions_.removePair(a, d);
625 >      }
626      }
627  
628 <    for (inversion= mol->beginInversion(inversionIter); inversion != NULL; inversion = mol->nextInversion(inversionIter)) {
628 >    for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
629 >         inversion = mol->nextInversion(inversionIter)) {
630 >
631        a = inversion->getAtomA()->getGlobalIndex();
632        b = inversion->getAtomB()->getGlobalIndex();        
633        c = inversion->getAtomC()->getGlobalIndex();        
634        d = inversion->getAtomD()->getGlobalIndex();        
635  
636 <      std::set<int> rigidSetA = getRigidSet(a, atomGroups);
637 <      std::set<int> rigidSetB = getRigidSet(b, atomGroups);
638 <      std::set<int> rigidSetC = getRigidSet(c, atomGroups);
639 <      std::set<int> rigidSetD = getRigidSet(d, atomGroups);
636 >      if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
637 >        oneTwoInteractions_.removePair(a, b);      
638 >        oneTwoInteractions_.removePair(a, c);
639 >        oneTwoInteractions_.removePair(a, d);
640 >      } else {
641 >        excludedInteractions_.removePair(a, b);
642 >        excludedInteractions_.removePair(a, c);
643 >        excludedInteractions_.removePair(a, d);
644 >      }
645  
646 <      exclude_.removePairs(rigidSetA, rigidSetB);
647 <      exclude_.removePairs(rigidSetA, rigidSetC);
648 <      exclude_.removePairs(rigidSetA, rigidSetD);
649 <      exclude_.removePairs(rigidSetB, rigidSetC);
650 <      exclude_.removePairs(rigidSetB, rigidSetD);
651 <      exclude_.removePairs(rigidSetC, rigidSetD);
652 <
653 <      /*
654 <      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 <      */
646 >      if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
647 >        oneThreeInteractions_.removePair(b, c);    
648 >        oneThreeInteractions_.removePair(b, d);    
649 >        oneThreeInteractions_.removePair(c, d);      
650 >      } else {
651 >        excludedInteractions_.removePair(b, c);
652 >        excludedInteractions_.removePair(b, d);
653 >        excludedInteractions_.removePair(c, d);
654 >      }
655      }
656  
657 <    for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
657 >    for (rb = mol->beginRigidBody(rbIter); rb != NULL;
658 >         rb = mol->nextRigidBody(rbIter)) {
659        std::vector<Atom*> atoms = rb->getAtoms();
660 <      for (int i = 0; i < atoms.size() -1 ; ++i) {
661 <        for (int j = i + 1; j < atoms.size(); ++j) {
660 >      for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
661 >        for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
662            a = atoms[i]->getGlobalIndex();
663            b = atoms[j]->getGlobalIndex();
664 <          exclude_.removePair(a, b);
664 >          excludedInteractions_.removePair(a, b);
665          }
666        }
667      }        
668 <
668 >    
669    }
670 <
671 <
670 >  
671 >  
672    void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
673      int curStampId;
674 <
674 >    
675      //index from 0
676      curStampId = moleculeStamps_.size();
677  
# Line 750 | Line 763 | namespace oopse {
763      useRF = 0;
764      useSF = 0;
765      useSP = 0;
766 +    useBoxDipole = 0;
767  
768  
769      if (simParams_->haveElectrostaticSummationMethod()) {
# Line 874 | Line 888 | namespace oopse {
888  
889    void SimInfo::setupFortranSim() {
890      int isError;
891 <    int nExclude;
891 >    int nExclude, nOneTwo, nOneThree, nOneFour;
892      std::vector<int> fortranGlobalGroupMembership;
893      
880 –    nExclude = exclude_.getSize();
894      isError = 0;
895  
896      //globalGroupMembership_ is filled by SimCreator    
# Line 909 | Line 922 | namespace oopse {
922            else
923              mfact.push_back( 1.0 );
924          }
912 –
925        }      
926      }
927  
# Line 933 | Line 945 | namespace oopse {
945      }
946      
947      //setup fortran simulation
948 <    int nGlobalExcludes = 0;
949 <    int* globalExcludes = NULL;
950 <    int* excludeList = exclude_.getExcludeList();
948 >
949 >    nExclude = excludedInteractions_.getSize();
950 >    nOneTwo = oneTwoInteractions_.getSize();
951 >    nOneThree = oneThreeInteractions_.getSize();
952 >    nOneFour = oneFourInteractions_.getSize();
953 >
954 >    int* excludeList = excludedInteractions_.getPairList();
955 >    int* oneTwoList = oneTwoInteractions_.getPairList();
956 >    int* oneThreeList = oneThreeInteractions_.getPairList();
957 >    int* oneFourList = oneFourInteractions_.getPairList();
958 >
959      setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
960 <                   &nExclude, excludeList , &nGlobalExcludes, globalExcludes,
960 >                   &nExclude, excludeList,
961 >                   &nOneTwo, oneTwoList,
962 >                   &nOneThree, oneThreeList,
963 >                   &nOneFour, oneFourList,
964                     &molMembershipArray[0], &mfact[0], &nCutoffGroups_,
965                     &fortranGlobalGroupMembership[0], &isError);
966      
# Line 1030 | Line 1053 | namespace oopse {
1053      int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
1054  
1055      // Set LJ shifting bools to false
1056 <    ljsp_ = false;
1057 <    ljsf_ = false;
1056 >    ljsp_ = 0;
1057 >    ljsf_ = 0;
1058  
1059      std::string myPolicy;
1060      if (forceFieldOptions_.haveCutoffPolicy()){
# Line 1102 | Line 1125 | namespace oopse {
1125          toUpper(myMethod);
1126          
1127          if (myMethod == "SHIFTED_POTENTIAL") {
1128 <          ljsp_ = true;
1128 >          ljsp_ = 1;
1129          } else if (myMethod == "SHIFTED_FORCE") {
1130 <          ljsf_ = true;
1130 >          ljsf_ = 1;
1131          }
1132        }
1133 +
1134        notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1135        
1136      } else {
# Line 1128 | Line 1152 | namespace oopse {
1152        // For the time being, we're tethering the LJ shifted behavior to the
1153        // electrostaticSummationMethod keyword options
1154            if (myMethod == "SHIFTED_POTENTIAL") {
1155 <            ljsp_ = true;
1155 >            ljsp_ = 1;
1156            } else if (myMethod == "SHIFTED_FORCE") {
1157 <            ljsf_ = true;
1157 >            ljsf_ = 1;
1158            }
1159            if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1160              if (simParams_->haveSwitchingRadius()){

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