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root/OpenMD/trunk/src/brains/SimInfo.cpp
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Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 1126 by gezelter, Fri Apr 6 21:53:43 2007 UTC vs.
Revision 1290 by cli2, Wed Sep 10 19:51:45 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 156 | Line 158 | namespace oopse {
158                                                  + nGlobalRigidBodies_;
159    
160        nGlobalMols_ = molStampIds_.size();
159 –
160 – #ifdef IS_MPI    
161        molToProcMap_.resize(nGlobalMols_);
162 – #endif
163 –
162      }
163  
164    SimInfo::~SimInfo() {
# Line 198 | 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();
203        nConstraints_ += mol->getNConstraintPairs();
204  
205 <      addExcludePairs(mol);
206 <        
205 >      addInteractionPairs(mol);
206 >  
207        return true;
208      } else {
209        return false;
# Line 223 | 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();
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;
362 +    std::vector<Inversion*>::iterator inversionIter;
363      Bond* bond;
364      Bend* bend;
365      Torsion* torsion;
366 +    Inversion* inversion;
367      int a;
368      int b;
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  
396 –    
397 –    
398 –    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();
408 –      std::set<int> rigidSetA = getRigidSet(a, atomGroups);
409 –      std::set<int> rigidSetB = getRigidSet(b, atomGroups);
410 –      std::set<int> rigidSetC = getRigidSet(c, atomGroups);
411 –
412 –      exclude_.addPairs(rigidSetA, rigidSetB);
413 –      exclude_.addPairs(rigidSetA, rigidSetC);
414 –      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();        
426 <      std::set<int> rigidSetA = getRigidSet(a, atomGroups);
427 <      std::set<int> rigidSetB = getRigidSet(b, atomGroups);
428 <      std::set<int> rigidSetC = getRigidSet(c, atomGroups);
429 <      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);
451 <      exclude_.addPair(b, d);
452 <      exclude_.addPair(c, d);        
453 <      */
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 (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
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();        
482 >
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 >      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;
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;
523 +    std::vector<Inversion*>::iterator inversionIter;
524      Bond* bond;
525      Bend* bend;
526      Torsion* torsion;
527 +    Inversion* inversion;
528      int a;
529      int b;
530      int c;
531      int d;
532  
533      std::map<int, std::set<int> > atomGroups;
482 –
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 505 | 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();
519 –
520 –      std::set<int> rigidSetA = getRigidSet(a, atomGroups);
521 –      std::set<int> rigidSetB = getRigidSet(b, atomGroups);
522 –      std::set<int> rigidSetC = getRigidSet(c, atomGroups);
523 –
524 –      exclude_.removePairs(rigidSetA, rigidSetB);
525 –      exclude_.removePairs(rigidSetA, rigidSetC);
526 –      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);
626 <      exclude_.removePairs(rigidSetC, rigidSetD);
621 >      if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
622 >        oneFourInteractions_.removePair(a, d);      
623 >      } else {
624 >        excludedInteractions_.removePair(a, d);
625 >      }
626 >    }
627  
628 <      /*
629 <      exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
553 <      exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
554 <      exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
555 <      exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
556 <      exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
557 <      exclude_.removePairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
628 >    for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
629 >         inversion = mol->nextInversion(inversionIter)) {
630  
631 <      
632 <      exclude_.removePair(a, b);
633 <      exclude_.removePair(a, c);
634 <      exclude_.removePair(a, d);
563 <      exclude_.removePair(b, c);
564 <      exclude_.removePair(b, d);
565 <      exclude_.removePair(c, d);        
566 <      */
567 <    }
631 >      a = inversion->getAtomA()->getGlobalIndex();
632 >      b = inversion->getAtomB()->getGlobalIndex();        
633 >      c = inversion->getAtomC()->getGlobalIndex();        
634 >      d = inversion->getAtomD()->getGlobalIndex();        
635  
636 <    for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
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 >      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;
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 798 | Line 887 | namespace oopse {
887  
888    void SimInfo::setupFortranSim() {
889      int isError;
890 <    int nExclude;
890 >    int nExclude, nOneTwo, nOneThree, nOneFour;
891      std::vector<int> fortranGlobalGroupMembership;
892      
804 –    nExclude = exclude_.getSize();
893      isError = 0;
894  
895      //globalGroupMembership_ is filled by SimCreator    
# Line 833 | Line 921 | namespace oopse {
921            else
922              mfact.push_back( 1.0 );
923          }
836 –
924        }      
925      }
926  
# Line 857 | Line 944 | namespace oopse {
944      }
945      
946      //setup fortran simulation
860 –    int nGlobalExcludes = 0;
861 –    int* globalExcludes = NULL;
862 –    int* excludeList = exclude_.getExcludeList();
863 –    setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
864 –                   &nGlobalExcludes, globalExcludes, &molMembershipArray[0],
865 –                   &mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
947  
948 <    if( isError ){
948 >    nExclude = excludedInteractions_.getSize();
949 >    nOneTwo = oneTwoInteractions_.getSize();
950 >    nOneThree = oneThreeInteractions_.getSize();
951 >    nOneFour = oneFourInteractions_.getSize();
952  
953 +    std::cerr << "excludedInteractions contains: " << excludedInteractions_.getSize() << " pairs \n";
954 +    std::cerr << "oneTwoInteractions contains: " << oneTwoInteractions_.getSize() << " pairs \n";
955 +    std::cerr << "oneThreeInteractions contains: " << oneThreeInteractions_.getSize() << " pairs \n";
956 +    std::cerr << "oneFourInteractions contains: " << oneFourInteractions_.getSize() << " pairs \n";
957 +
958 +    int* excludeList = excludedInteractions_.getPairList();
959 +    int* oneTwoList = oneTwoInteractions_.getPairList();
960 +    int* oneThreeList = oneThreeInteractions_.getPairList();
961 +    int* oneFourList = oneFourInteractions_.getPairList();
962 +
963 +    setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
964 +                   &nExclude, excludeList,
965 +                   &nOneTwo, oneTwoList,
966 +                   &nOneThree, oneThreeList,
967 +                   &nOneFour, oneFourList,
968 +                   &molMembershipArray[0], &mfact[0], &nCutoffGroups_,
969 +                   &fortranGlobalGroupMembership[0], &isError);
970 +    
971 +    if( isError ){
972 +      
973        sprintf( painCave.errMsg,
974                 "There was an error setting the simulation information in fortran.\n" );
975        painCave.isFatal = 1;
976        painCave.severity = OOPSE_ERROR;
977        simError();
978      }
979 <
980 < #ifdef IS_MPI
979 >    
980 >    
981      sprintf( checkPointMsg,
982               "succesfully sent the simulation information to fortran.\n");
983 <    MPIcheckPoint();
984 < #endif // is_mpi
985 <
983 >    
984 >    errorCheckPoint();
985 >    
986      // Setup number of neighbors in neighbor list if present
987      if (simParams_->haveNeighborListNeighbors()) {
988        int nlistNeighbors = simParams_->getNeighborListNeighbors();
# Line 889 | Line 993 | namespace oopse {
993    }
994  
995  
892 – #ifdef IS_MPI
996    void SimInfo::setupFortranParallel() {
997 <    
997 > #ifdef IS_MPI    
998      //SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
999      std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
1000      std::vector<int> localToGlobalCutoffGroupIndex;
# Line 941 | Line 1044 | namespace oopse {
1044      }
1045  
1046      sprintf(checkPointMsg, " mpiRefresh successful.\n");
1047 <    MPIcheckPoint();
1047 >    errorCheckPoint();
1048  
1049 <
1049 > #endif
1050    }
1051  
949 – #endif
950 –
1052    void SimInfo::setupCutoff() {          
1053      
1054      ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
# Line 955 | Line 1056 | namespace oopse {
1056      // Check the cutoff policy
1057      int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
1058  
1059 +    // Set LJ shifting bools to false
1060 +    ljsp_ = false;
1061 +    ljsf_ = false;
1062 +
1063      std::string myPolicy;
1064      if (forceFieldOptions_.haveCutoffPolicy()){
1065        myPolicy = forceFieldOptions_.getCutoffPolicy();
# Line 1018 | Line 1123 | namespace oopse {
1123            simError();
1124          }
1125        }
1126 <      
1127 <      notifyFortranCutoffs(&rcut_, &rsw_);
1126 >
1127 >      if (simParams_->haveElectrostaticSummationMethod()) {
1128 >        std::string myMethod = simParams_->getElectrostaticSummationMethod();
1129 >        toUpper(myMethod);
1130 >        
1131 >        if (myMethod == "SHIFTED_POTENTIAL") {
1132 >          ljsp_ = true;
1133 >        } else if (myMethod == "SHIFTED_FORCE") {
1134 >          ljsf_ = true;
1135 >        }
1136 >      }
1137 >      notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1138        
1139      } else {
1140        
# Line 1036 | Line 1151 | namespace oopse {
1151          if (simParams_->haveElectrostaticSummationMethod()) {
1152            std::string myMethod = simParams_->getElectrostaticSummationMethod();
1153            toUpper(myMethod);
1154 <          if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1154 >      
1155 >      // For the time being, we're tethering the LJ shifted behavior to the
1156 >      // electrostaticSummationMethod keyword options
1157 >          if (myMethod == "SHIFTED_POTENTIAL") {
1158 >            ljsp_ = true;
1159 >          } else if (myMethod == "SHIFTED_FORCE") {
1160 >            ljsf_ = true;
1161 >          }
1162 >          if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1163              if (simParams_->haveSwitchingRadius()){
1164                sprintf(painCave.errMsg,
1165                        "SimInfo Warning: A value was set for the switchingRadius\n"
# Line 1059 | Line 1182 | namespace oopse {
1182            simError();
1183            rsw_ = 0.85 * rcut_;
1184          }
1185 <        notifyFortranCutoffs(&rcut_, &rsw_);
1185 >
1186 >        notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1187 >
1188        } else {
1189          // We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1190          // We'll punt and let fortran figure out the cutoffs later.

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