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root/OpenMD/trunk/src/brains/SimInfo.cpp
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Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 1050 by chrisfen, Fri Sep 22 22:19:59 2006 UTC vs.
Revision 1290 by cli2, Wed Sep 10 19:51:45 2008 UTC

# Line 59 | Line 59
59   #include "UseTheForce/DarkSide/fElectrostaticScreeningMethod.h"
60   #include "UseTheForce/DarkSide/fSwitchingFunctionType.h"
61   #include "UseTheForce/doForces_interface.h"
62 + #include "UseTheForce/DarkSide/neighborLists_interface.h"
63   #include "UseTheForce/DarkSide/electrostatic_interface.h"
64   #include "UseTheForce/DarkSide/switcheroo_interface.h"
65   #include "utils/MemoryUtils.hpp"
# Line 67 | Line 68
68   #include "io/ForceFieldOptions.hpp"
69   #include "UseTheForce/ForceField.hpp"
70  
71 +
72   #ifdef IS_MPI
73   #include "UseTheForce/mpiComponentPlan.h"
74   #include "UseTheForce/DarkSide/simParallel_interface.h"
# Line 88 | 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) {
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 99 | 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 153 | Line 158 | namespace oopse {
158                                                  + nGlobalRigidBodies_;
159    
160        nGlobalMols_ = molStampIds_.size();
156 –
157 – #ifdef IS_MPI    
161        molToProcMap_.resize(nGlobalMols_);
159 – #endif
160 –
162      }
163  
164    SimInfo::~SimInfo() {
# Line 195 | 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 220 | 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 351 | 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  
393 –    
394 –    
395 –    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();
405 –      std::set<int> rigidSetA = getRigidSet(a, atomGroups);
406 –      std::set<int> rigidSetB = getRigidSet(b, atomGroups);
407 –      std::set<int> rigidSetC = getRigidSet(c, atomGroups);
408 –
409 –      exclude_.addPairs(rigidSetA, rigidSetB);
410 –      exclude_.addPairs(rigidSetA, rigidSetC);
411 –      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();        
423 <      std::set<int> rigidSetA = getRigidSet(a, atomGroups);
424 <      std::set<int> rigidSetB = getRigidSet(b, atomGroups);
425 <      std::set<int> rigidSetC = getRigidSet(c, atomGroups);
426 <      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);
448 <      exclude_.addPair(b, d);
449 <      exclude_.addPair(c, d);        
450 <      */
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;
479 –
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 502 | 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();
516 –
517 –      std::set<int> rigidSetA = getRigidSet(a, atomGroups);
518 –      std::set<int> rigidSetB = getRigidSet(b, atomGroups);
519 –      std::set<int> rigidSetC = getRigidSet(c, atomGroups);
520 –
521 –      exclude_.removePairs(rigidSetA, rigidSetB);
522 –      exclude_.removePairs(rigidSetA, rigidSetC);
523 –      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());
550 <      exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
551 <      exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
552 <      exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
553 <      exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
554 <      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);
635 <      exclude_.removePair(b, c);
636 <      exclude_.removePair(b, d);
637 <      exclude_.removePair(c, d);        
638 <      */
631 >      a = inversion->getAtomA()->getGlobalIndex();
632 >      b = inversion->getAtomB()->getGlobalIndex();        
633 >      c = inversion->getAtomC()->getGlobalIndex();        
634 >      d = inversion->getAtomD()->getGlobalIndex();        
635 >
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; 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 664 | Line 756 | namespace oopse {
756      int useSF;
757      int useSP;
758      int useBoxDipole;
759 +
760      std::string myMethod;
761  
762      // set the useRF logical
763      useRF = 0;
764      useSF = 0;
765 +    useSP = 0;
766  
767  
768      if (simParams_->haveElectrostaticSummationMethod()) {
769        std::string myMethod = simParams_->getElectrostaticSummationMethod();
770        toUpper(myMethod);
771        if (myMethod == "REACTION_FIELD"){
772 <        useRF=1;
772 >        useRF = 1;
773        } else if (myMethod == "SHIFTED_FORCE"){
774          useSF = 1;
775        } else if (myMethod == "SHIFTED_POTENTIAL"){
# Line 687 | Line 781 | namespace oopse {
781        if (simParams_->getAccumulateBoxDipole())
782          useBoxDipole = 1;
783  
784 +    useAtomicVirial_ = simParams_->getUseAtomicVirial();
785 +
786      //loop over all of the atom types
787      for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
788        useLennardJones |= (*i)->isLennardJones();
# Line 763 | Line 859 | namespace oopse {
859  
860      temp = useBoxDipole;
861      MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
862 +
863 +    temp = useAtomicVirial_;
864 +    MPI_Allreduce(&temp, &useAtomicVirial_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
865  
866   #endif
867  
# Line 783 | Line 882 | namespace oopse {
882      fInfo_.SIM_uses_SF = useSF;
883      fInfo_.SIM_uses_SP = useSP;
884      fInfo_.SIM_uses_BoxDipole = useBoxDipole;
885 +    fInfo_.SIM_uses_AtomicVirial = useAtomicVirial_;
886    }
887  
888    void SimInfo::setupFortranSim() {
889      int isError;
890 <    int nExclude;
890 >    int nExclude, nOneTwo, nOneThree, nOneFour;
891      std::vector<int> fortranGlobalGroupMembership;
892      
793 –    nExclude = exclude_.getSize();
893      isError = 0;
894  
895      //globalGroupMembership_ is filled by SimCreator    
# Line 822 | Line 921 | namespace oopse {
921            else
922              mfact.push_back( 1.0 );
923          }
825 –
924        }      
925      }
926  
# Line 846 | Line 944 | namespace oopse {
944      }
945      
946      //setup fortran simulation
849 –    int nGlobalExcludes = 0;
850 –    int* globalExcludes = NULL;
851 –    int* excludeList = exclude_.getExcludeList();
852 –    setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
853 –                   &nGlobalExcludes, globalExcludes, &molMembershipArray[0],
854 –                   &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
983 >    
984 >    errorCheckPoint();
985 >    
986 >    // Setup number of neighbors in neighbor list if present
987 >    if (simParams_->haveNeighborListNeighbors()) {
988 >      int nlistNeighbors = simParams_->getNeighborListNeighbors();
989 >      setNeighbors(&nlistNeighbors);
990 >    }
991 >  
992 >
993    }
994  
995  
873 – #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 922 | Line 1044 | namespace oopse {
1044      }
1045  
1046      sprintf(checkPointMsg, " mpiRefresh successful.\n");
1047 <    MPIcheckPoint();
1047 >    errorCheckPoint();
1048  
1049 <
1049 > #endif
1050    }
1051  
930 – #endif
931 –
1052    void SimInfo::setupCutoff() {          
1053      
1054      ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
# Line 936 | 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 999 | 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 1017 | 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 1040 | 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.
# Line 1125 | Line 1269 | namespace oopse {
1269                       "\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1270              painCave.isFatal = 0;
1271              simError();
1272 +          } else {
1273 +            alphaVal = simParams_->getDampingAlpha();
1274            }
1275 +          
1276          } else {
1277            // throw error        
1278            sprintf( painCave.errMsg,
# Line 1442 | Line 1589 | namespace oopse {
1589      IOIndexToIntegrableObject= v;
1590    }
1591  
1592 +  /* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1593 +     based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1594 +     where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1595 +     V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1596 +  */
1597 +  void SimInfo::getGyrationalVolume(RealType &volume){
1598 +    Mat3x3d intTensor;
1599 +    RealType det;
1600 +    Vector3d dummyAngMom;
1601 +    RealType sysconstants;
1602 +    RealType geomCnst;
1603 +
1604 +    geomCnst = 3.0/2.0;
1605 +    /* Get the inertial tensor and angular momentum for free*/
1606 +    getInertiaTensor(intTensor,dummyAngMom);
1607 +    
1608 +    det = intTensor.determinant();
1609 +    sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1610 +    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1611 +    return;
1612 +  }
1613 +
1614 +  void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1615 +    Mat3x3d intTensor;
1616 +    Vector3d dummyAngMom;
1617 +    RealType sysconstants;
1618 +    RealType geomCnst;
1619 +
1620 +    geomCnst = 3.0/2.0;
1621 +    /* Get the inertial tensor and angular momentum for free*/
1622 +    getInertiaTensor(intTensor,dummyAngMom);
1623 +    
1624 +    detI = intTensor.determinant();
1625 +    sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1626 +    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1627 +    return;
1628 +  }
1629   /*
1630     void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1631        assert( v.size() == nAtoms_ + nRigidBodies_);

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