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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 720 by chrisfen, Tue Nov 8 13:32:06 2005 UTC vs.
Revision 1287 by gezelter, Wed Sep 10 18:11:32 2008 UTC

# Line 48 | Line 48
48  
49   #include <algorithm>
50   #include <set>
51 + #include <map>
52  
53   #include "brains/SimInfo.hpp"
54   #include "math/Vector3.hpp"
55   #include "primitives/Molecule.hpp"
56 + #include "primitives/StuntDouble.hpp"
57   #include "UseTheForce/fCutoffPolicy.h"
58   #include "UseTheForce/DarkSide/fElectrostaticSummationMethod.h"
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/notifyCutoffs_interface.h"
64 > #include "UseTheForce/DarkSide/switcheroo_interface.h"
65   #include "utils/MemoryUtils.hpp"
66   #include "utils/simError.h"
67   #include "selection/SelectionManager.hpp"
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"
75   #endif
76  
77   namespace oopse {
78 +  std::set<int> getRigidSet(int index, std::map<int, std::set<int> >& container) {
79 +    std::map<int, std::set<int> >::iterator i = container.find(index);
80 +    std::set<int> result;
81 +    if (i != container.end()) {
82 +        result = i->second;
83 +    }
84  
85 <  SimInfo::SimInfo(MakeStamps* stamps, std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
86 <                   ForceField* ff, Globals* simParams) :
87 <    stamps_(stamps), forceField_(ff), simParams_(simParams),
88 <    ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
85 >    return result;
86 >  }
87 >  
88 >  SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
89 >    forceField_(ff), simParams_(simParams),
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) {
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 <            
83 <      std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
98 >
99        MoleculeStamp* molStamp;
100        int nMolWithSameStamp;
101        int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
# Line 88 | Line 103 | namespace oopse {
103        CutoffGroupStamp* cgStamp;    
104        RigidBodyStamp* rbStamp;
105        int nRigidAtoms = 0;
106 <    
107 <      for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
108 <        molStamp = i->first;
109 <        nMolWithSameStamp = i->second;
106 >
107 >      std::vector<Component*> components = simParams->getComponents();
108 >      
109 >      for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
110 >        molStamp = (*i)->getMoleculeStamp();
111 >        nMolWithSameStamp = (*i)->getNMol();
112          
113          addMoleculeStamp(molStamp, nMolWithSameStamp);
114  
115          //calculate atoms in molecules
116          nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;  
117  
101 –
118          //calculate atoms in cutoff groups
119          int nAtomsInGroups = 0;
120          int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
121          
122          for (int j=0; j < nCutoffGroupsInStamp; j++) {
123 <          cgStamp = molStamp->getCutoffGroup(j);
123 >          cgStamp = molStamp->getCutoffGroupStamp(j);
124            nAtomsInGroups += cgStamp->getNMembers();
125          }
126  
# Line 117 | Line 133 | namespace oopse {
133          int nRigidBodiesInStamp = molStamp->getNRigidBodies();
134          
135          for (int j=0; j < nRigidBodiesInStamp; j++) {
136 <          rbStamp = molStamp->getRigidBody(j);
136 >          rbStamp = molStamp->getRigidBodyStamp(j);
137            nAtomsInRigidBodies += rbStamp->getNMembers();
138          }
139  
# Line 142 | Line 158 | namespace oopse {
158                                                  + nGlobalRigidBodies_;
159    
160        nGlobalMols_ = molStampIds_.size();
145 –
146 – #ifdef IS_MPI    
161        molToProcMap_.resize(nGlobalMols_);
148 – #endif
149 –
162      }
163  
164    SimInfo::~SimInfo() {
# Line 156 | Line 168 | namespace oopse {
168      }
169      molecules_.clear();
170        
159 –    delete stamps_;
171      delete sman_;
172      delete simParams_;
173      delete forceField_;
# Line 185 | 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 210 | 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 263 | Line 276 | namespace oopse {
276            }
277          }
278              
279 <      }//end for (integrableObject)
280 <    }// end for (mol)
279 >      }
280 >    }
281      
282      // n_constraints is local, so subtract them on each processor
283      ndf_local -= nConstraints_;
# Line 281 | Line 294 | namespace oopse {
294  
295    }
296  
297 +  int SimInfo::getFdf() {
298 + #ifdef IS_MPI
299 +    MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
300 + #else
301 +    fdf_ = fdf_local;
302 + #endif
303 +    return fdf_;
304 +  }
305 +    
306    void SimInfo::calcNdfRaw() {
307      int ndfRaw_local;
308  
# Line 332 | 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 +    // 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 (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
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 < 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 >
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();
426 +      
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 <      exclude_.addPair(a, b);
436 <      exclude_.addPair(a, c);
437 <      exclude_.addPair(b, c);        
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();        
448 >      d = torsion->getAtomD()->getGlobalIndex();      
449 >  
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 <      exclude_.addPair(a, b);
461 <      exclude_.addPair(a, c);
462 <      exclude_.addPair(a, d);
463 <      exclude_.addPair(b, c);
464 <      exclude_.addPair(b, d);
465 <      exclude_.addPair(c, d);        
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 <    Molecule::RigidBodyIterator rbIter;
476 <    RigidBody* rb;
477 <    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;
534 +    Molecule::RigidBodyIterator rbIter;
535 +    RigidBody* rb;
536 +    Molecule::IntegrableObjectIterator ii;
537 +    StuntDouble* integrableObject;
538      
539 <    for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
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 < 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());
556 >        atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));        
557 >      }
558 >    }  
559 >
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();
579 +      
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 <      exclude_.removePair(a, b);
589 <      exclude_.removePair(a, c);
590 <      exclude_.removePair(b, c);        
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 <      exclude_.removePair(a, b);
614 <      exclude_.removePair(a, c);
615 <      exclude_.removePair(a, d);
616 <      exclude_.removePair(b, c);
617 <      exclude_.removePair(b, d);
618 <      exclude_.removePair(c, d);        
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 >      if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
622 >        oneFourInteractions_.removePair(a, d);      
623 >      } else {
624 >        excludedInteractions_.removePair(a, d);
625 >      }
626      }
627  
628 <    Molecule::RigidBodyIterator rbIter;
629 <    RigidBody* rb;
630 <    for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
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 >      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 471 | Line 693 | namespace oopse {
693      /** @deprecate */    
694      int isError = 0;
695      
696 +    setupCutoff();
697 +    
698      setupElectrostaticSummationMethod( isError );
699 +    setupSwitchingFunction();
700 +    setupAccumulateBoxDipole();
701  
702      if(isError){
703        sprintf( painCave.errMsg,
# Line 479 | Line 705 | namespace oopse {
705        painCave.isFatal = 1;
706        simError();
707      }
482 –  
483 –    
484 –    setupCutoff();
708  
709      calcNdf();
710      calcNdfRaw();
# Line 516 | Line 739 | namespace oopse {
739      int useLennardJones = 0;
740      int useElectrostatic = 0;
741      int useEAM = 0;
742 +    int useSC = 0;
743      int useCharge = 0;
744      int useDirectional = 0;
745      int useDipole = 0;
# Line 530 | Line 754 | namespace oopse {
754      int usePBC = simParams_->getUsePeriodicBoundaryConditions();
755      int useRF;
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;
773 <      } else {
774 <        if (myMethod == "SHIFTED_FORCE") {
775 <          useSF = 1;
776 <        }
771 >      if (myMethod == "REACTION_FIELD"){
772 >        useRF = 1;
773 >      } else if (myMethod == "SHIFTED_FORCE"){
774 >        useSF = 1;
775 >      } else if (myMethod == "SHIFTED_POTENTIAL"){
776 >        useSP = 1;
777        }
778      }
779 +    
780 +    if (simParams_->haveAccumulateBoxDipole())
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();
789        useElectrostatic |= (*i)->isElectrostatic();
790        useEAM |= (*i)->isEAM();
791 +      useSC |= (*i)->isSC();
792        useCharge |= (*i)->isCharge();
793        useDirectional |= (*i)->isDirectional();
794        useDipole |= (*i)->isDipole();
# Line 604 | Line 839 | namespace oopse {
839      temp = useEAM;
840      MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
841  
842 +    temp = useSC;
843 +    MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
844 +    
845      temp = useShape;
846      MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);  
847  
# Line 614 | Line 852 | namespace oopse {
852      MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
853  
854      temp = useSF;
855 <    MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
855 >    MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);  
856 >
857 >    temp = useSP;
858 >    MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
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  
868      fInfo_.SIM_uses_PBC = usePBC;    
# Line 628 | Line 875 | namespace oopse {
875      fInfo_.SIM_uses_StickyPower = useStickyPower;
876      fInfo_.SIM_uses_GayBerne = useGayBerne;
877      fInfo_.SIM_uses_EAM = useEAM;
878 +    fInfo_.SIM_uses_SC = useSC;
879      fInfo_.SIM_uses_Shapes = useShape;
880      fInfo_.SIM_uses_FLARB = useFLARB;
881      fInfo_.SIM_uses_RF = useRF;
882      fInfo_.SIM_uses_SF = useSF;
883 <
884 <    if( myMethod == "REACTION_FIELD") {
885 <      
638 <      if (simParams_->haveDielectric()) {
639 <        fInfo_.dielect = simParams_->getDielectric();
640 <      } else {
641 <        sprintf(painCave.errMsg,
642 <                "SimSetup Error: No Dielectric constant was set.\n"
643 <                "\tYou are trying to use Reaction Field without"
644 <                "\tsetting a dielectric constant!\n");
645 <        painCave.isFatal = 1;
646 <        simError();
647 <      }      
648 <    }
649 <
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      
657 –    nExclude = exclude_.getSize();
893      isError = 0;
894  
895      //globalGroupMembership_ is filled by SimCreator    
# Line 663 | Line 898 | namespace oopse {
898      }
899  
900      //calculate mass ratio of cutoff group
901 <    std::vector<double> mfact;
901 >    std::vector<RealType> mfact;
902      SimInfo::MoleculeIterator mi;
903      Molecule* mol;
904      Molecule::CutoffGroupIterator ci;
905      CutoffGroup* cg;
906      Molecule::AtomIterator ai;
907      Atom* atom;
908 <    double totalMass;
908 >    RealType totalMass;
909  
910      //to avoid memory reallocation, reserve enough space for mfact
911      mfact.reserve(getNCutoffGroups());
# Line 686 | Line 921 | namespace oopse {
921            else
922              mfact.push_back( 1.0 );
923          }
689 –
924        }      
925      }
926  
# Line 710 | Line 944 | namespace oopse {
944      }
945      
946      //setup fortran simulation
713 –    int nGlobalExcludes = 0;
714 –    int* globalExcludes = NULL;
715 –    int* excludeList = exclude_.getExcludeList();
716 –    setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
717 –                   &nGlobalExcludes, globalExcludes, &molMembershipArray[0],
718 –                   &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 << "exculdes:\n";
954 +    std::cerr << excludedInteractions_;
955 +    std::cerr << "\noneTwo:\n";
956 +    std::cerr << oneTwoInteractions_;
957 +    std::cerr << "\noneThree:\n";
958 +    std::cerr << oneThreeInteractions_;
959 +    std::cerr << "\noneFour:\n";
960 +    std::cerr << oneFourInteractions_;
961 +
962 +    int* excludeList = excludedInteractions_.getPairList();
963 +    int* oneTwoList = oneTwoInteractions_.getPairList();
964 +    int* oneThreeList = oneThreeInteractions_.getPairList();
965 +    int* oneFourList = oneFourInteractions_.getPairList();
966 +
967 +    setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
968 +                   &nExclude, excludeList,
969 +                   &nOneTwo, oneTwoList,
970 +                   &nOneThree, oneThreeList,
971 +                   &nOneFour, oneFourList,
972 +                   &molMembershipArray[0], &mfact[0], &nCutoffGroups_,
973 +                   &fortranGlobalGroupMembership[0], &isError);
974 +    
975 +    if( isError ){
976 +      
977        sprintf( painCave.errMsg,
978                 "There was an error setting the simulation information in fortran.\n" );
979        painCave.isFatal = 1;
980        painCave.severity = OOPSE_ERROR;
981        simError();
982      }
983 <
984 < #ifdef IS_MPI
983 >    
984 >    
985      sprintf( checkPointMsg,
986               "succesfully sent the simulation information to fortran.\n");
987 <    MPIcheckPoint();
988 < #endif // is_mpi
987 >    
988 >    errorCheckPoint();
989 >    
990 >    // Setup number of neighbors in neighbor list if present
991 >    if (simParams_->haveNeighborListNeighbors()) {
992 >      int nlistNeighbors = simParams_->getNeighborListNeighbors();
993 >      setNeighbors(&nlistNeighbors);
994 >    }
995 >  
996 >
997    }
998  
999  
737 – #ifdef IS_MPI
1000    void SimInfo::setupFortranParallel() {
1001 <    
1001 > #ifdef IS_MPI    
1002      //SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
1003      std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
1004      std::vector<int> localToGlobalCutoffGroupIndex;
# Line 786 | Line 1048 | namespace oopse {
1048      }
1049  
1050      sprintf(checkPointMsg, " mpiRefresh successful.\n");
1051 <    MPIcheckPoint();
1051 >    errorCheckPoint();
1052  
791 –
792 –  }
793 –
1053   #endif
795 –
796 –  double SimInfo::calcMaxCutoffRadius() {
797 –
798 –
799 –    std::set<AtomType*> atomTypes;
800 –    std::set<AtomType*>::iterator i;
801 –    std::vector<double> cutoffRadius;
802 –
803 –    //get the unique atom types
804 –    atomTypes = getUniqueAtomTypes();
805 –
806 –    //query the max cutoff radius among these atom types
807 –    for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
808 –      cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
809 –    }
810 –
811 –    double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
812 – #ifdef IS_MPI
813 –    //pick the max cutoff radius among the processors
814 – #endif
815 –
816 –    return maxCutoffRadius;
1054    }
1055  
1056 <  void SimInfo::getCutoff(double& rcut, double& rsw) {
1056 >  void SimInfo::setupCutoff() {          
1057      
1058 <    if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
822 <        
823 <      if (!simParams_->haveCutoffRadius()){
824 <        sprintf(painCave.errMsg,
825 <                "SimCreator Warning: No value was set for the cutoffRadius.\n"
826 <                "\tOOPSE will use a default value of 15.0 angstroms"
827 <                "\tfor the cutoffRadius.\n");
828 <        painCave.isFatal = 0;
829 <        simError();
830 <        rcut = 15.0;
831 <      } else{
832 <        rcut = simParams_->getCutoffRadius();
833 <      }
1058 >    ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
1059  
1060 <      if (!simParams_->haveSwitchingRadius()){
1061 <        sprintf(painCave.errMsg,
837 <                "SimCreator Warning: No value was set for switchingRadius.\n"
838 <                "\tOOPSE will use a default value of\n"
839 <                "\t0.85 * cutoffRadius for the switchingRadius\n");
840 <        painCave.isFatal = 0;
841 <        simError();
842 <        rsw = 0.85 * rcut;
843 <      } else{
844 <        rsw = simParams_->getSwitchingRadius();
845 <      }
1060 >    // Check the cutoff policy
1061 >    int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
1062  
1063 <    } else {
1064 <      // if charge, dipole or reaction field is not used and the cutofff radius is not specified in
1065 <      //meta-data file, the maximum cutoff radius calculated from forcefiled will be used
850 <        
851 <      if (simParams_->haveCutoffRadius()) {
852 <        rcut = simParams_->getCutoffRadius();
853 <      } else {
854 <        //set cutoff radius to the maximum cutoff radius based on atom types in the whole system
855 <        rcut = calcMaxCutoffRadius();
856 <      }
1063 >    // Set LJ shifting bools to false
1064 >    ljsp_ = false;
1065 >    ljsf_ = false;
1066  
1067 <      if (simParams_->haveSwitchingRadius()) {
1068 <        rsw  = simParams_->getSwitchingRadius();
1069 <      } else {
1070 <        rsw = rcut;
1071 <      }
863 <    
1067 >    std::string myPolicy;
1068 >    if (forceFieldOptions_.haveCutoffPolicy()){
1069 >      myPolicy = forceFieldOptions_.getCutoffPolicy();
1070 >    }else if (simParams_->haveCutoffPolicy()) {
1071 >      myPolicy = simParams_->getCutoffPolicy();
1072      }
865 –  }
1073  
1074 <  void SimInfo::setupCutoff() {    
868 <    getCutoff(rcut_, rsw_);    
869 <    double rnblist = rcut_ + 1; // skin of neighbor list
870 <
871 <    //Pass these cutoff radius etc. to fortran. This function should be called once and only once
872 <    
873 <    int cp =  TRADITIONAL_CUTOFF_POLICY;
874 <    if (simParams_->haveCutoffPolicy()) {
875 <      std::string myPolicy = simParams_->getCutoffPolicy();
1074 >    if (!myPolicy.empty()){
1075        toUpper(myPolicy);
1076        if (myPolicy == "MIX") {
1077          cp = MIX_CUTOFF_POLICY;
# Line 891 | Line 1090 | namespace oopse {
1090            }    
1091          }          
1092        }
1093 <    }
1093 >    }          
1094 >    notifyFortranCutoffPolicy(&cp);
1095  
1096 <
1096 >    // Check the Skin Thickness for neighborlists
1097 >    RealType skin;
1098      if (simParams_->haveSkinThickness()) {
1099 <      double skinThickness = simParams_->getSkinThickness();
1100 <    }
1099 >      skin = simParams_->getSkinThickness();
1100 >      notifyFortranSkinThickness(&skin);
1101 >    }            
1102 >        
1103 >    // Check if the cutoff was set explicitly:
1104 >    if (simParams_->haveCutoffRadius()) {
1105 >      rcut_ = simParams_->getCutoffRadius();
1106 >      if (simParams_->haveSwitchingRadius()) {
1107 >        rsw_  = simParams_->getSwitchingRadius();
1108 >      } else {
1109 >        if (fInfo_.SIM_uses_Charges |
1110 >            fInfo_.SIM_uses_Dipoles |
1111 >            fInfo_.SIM_uses_RF) {
1112 >          
1113 >          rsw_ = 0.85 * rcut_;
1114 >          sprintf(painCave.errMsg,
1115 >                  "SimCreator Warning: No value was set for the switchingRadius.\n"
1116 >                  "\tOOPSE will use a default value of 85 percent of the cutoffRadius.\n"
1117 >                  "\tswitchingRadius = %f. for this simulation\n", rsw_);
1118 >        painCave.isFatal = 0;
1119 >        simError();
1120 >        } else {
1121 >          rsw_ = rcut_;
1122 >          sprintf(painCave.errMsg,
1123 >                  "SimCreator Warning: No value was set for the switchingRadius.\n"
1124 >                  "\tOOPSE will use the same value as the cutoffRadius.\n"
1125 >                  "\tswitchingRadius = %f. for this simulation\n", rsw_);
1126 >          painCave.isFatal = 0;
1127 >          simError();
1128 >        }
1129 >      }
1130  
1131 <    notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp);
1132 <    // also send cutoff notification to electrostatics
1133 <    setElectrostaticCutoffRadius(&rcut_, &rsw_);
1131 >      if (simParams_->haveElectrostaticSummationMethod()) {
1132 >        std::string myMethod = simParams_->getElectrostaticSummationMethod();
1133 >        toUpper(myMethod);
1134 >        
1135 >        if (myMethod == "SHIFTED_POTENTIAL") {
1136 >          ljsp_ = true;
1137 >        } else if (myMethod == "SHIFTED_FORCE") {
1138 >          ljsf_ = true;
1139 >        }
1140 >      }
1141 >      notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1142 >      
1143 >    } else {
1144 >      
1145 >      // For electrostatic atoms, we'll assume a large safe value:
1146 >      if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
1147 >        sprintf(painCave.errMsg,
1148 >                "SimCreator Warning: No value was set for the cutoffRadius.\n"
1149 >                "\tOOPSE will use a default value of 15.0 angstroms"
1150 >                "\tfor the cutoffRadius.\n");
1151 >        painCave.isFatal = 0;
1152 >        simError();
1153 >        rcut_ = 15.0;
1154 >      
1155 >        if (simParams_->haveElectrostaticSummationMethod()) {
1156 >          std::string myMethod = simParams_->getElectrostaticSummationMethod();
1157 >          toUpper(myMethod);
1158 >      
1159 >      // For the time being, we're tethering the LJ shifted behavior to the
1160 >      // electrostaticSummationMethod keyword options
1161 >          if (myMethod == "SHIFTED_POTENTIAL") {
1162 >            ljsp_ = true;
1163 >          } else if (myMethod == "SHIFTED_FORCE") {
1164 >            ljsf_ = true;
1165 >          }
1166 >          if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1167 >            if (simParams_->haveSwitchingRadius()){
1168 >              sprintf(painCave.errMsg,
1169 >                      "SimInfo Warning: A value was set for the switchingRadius\n"
1170 >                      "\teven though the electrostaticSummationMethod was\n"
1171 >                      "\tset to %s\n", myMethod.c_str());
1172 >              painCave.isFatal = 1;
1173 >              simError();            
1174 >            }
1175 >          }
1176 >        }
1177 >      
1178 >        if (simParams_->haveSwitchingRadius()){
1179 >          rsw_ = simParams_->getSwitchingRadius();
1180 >        } else {        
1181 >          sprintf(painCave.errMsg,
1182 >                  "SimCreator Warning: No value was set for switchingRadius.\n"
1183 >                  "\tOOPSE will use a default value of\n"
1184 >                  "\t0.85 * cutoffRadius for the switchingRadius\n");
1185 >          painCave.isFatal = 0;
1186 >          simError();
1187 >          rsw_ = 0.85 * rcut_;
1188 >        }
1189 >
1190 >        notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1191 >
1192 >      } else {
1193 >        // We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1194 >        // We'll punt and let fortran figure out the cutoffs later.
1195 >        
1196 >        notifyFortranYouAreOnYourOwn();
1197 >
1198 >      }
1199 >    }
1200    }
1201  
1202    void SimInfo::setupElectrostaticSummationMethod( int isError ) {    
# Line 908 | Line 1204 | namespace oopse {
1204      int errorOut;
1205      int esm =  NONE;
1206      int sm = UNDAMPED;
1207 <    double alphaVal;
1208 <    double dielectric;
1209 <
1207 >    RealType alphaVal;
1208 >    RealType dielectric;
1209 >    
1210      errorOut = isError;
915 –    alphaVal = simParams_->getDampingAlpha();
916 –    dielectric = simParams_->getDielectric();
1211  
1212      if (simParams_->haveElectrostaticSummationMethod()) {
1213        std::string myMethod = simParams_->getElectrostaticSummationMethod();
# Line 930 | Line 1224 | namespace oopse {
1224              if (myMethod == "SHIFTED_FORCE") {            
1225                esm = SHIFTED_FORCE;
1226              } else {
1227 <              if (myMethod == "REACTION_FIELD") {            
1227 >              if (myMethod == "REACTION_FIELD") {
1228                  esm = REACTION_FIELD;
1229 +                dielectric = simParams_->getDielectric();
1230 +                if (!simParams_->haveDielectric()) {
1231 +                  // throw warning
1232 +                  sprintf( painCave.errMsg,
1233 +                           "SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
1234 +                           "\tA default value of %f will be used for the dielectric.\n", dielectric);
1235 +                  painCave.isFatal = 0;
1236 +                  simError();
1237 +                }
1238                } else {
1239                  // throw error        
1240                  sprintf( painCave.errMsg,
1241 <                         "SimInfo error: Unknown electrostaticSummationMethod. (Input file specified %s .)\n\telectrostaticSummationMethod must be one of: \"none\", \"shifted_potential\", \"shifted_force\", or \"reaction_field\".", myMethod.c_str() );
1241 >                         "SimInfo error: Unknown electrostaticSummationMethod.\n"
1242 >                         "\t(Input file specified %s .)\n"
1243 >                         "\telectrostaticSummationMethod must be one of: \"none\",\n"
1244 >                         "\t\"shifted_potential\", \"shifted_force\", or \n"
1245 >                         "\t\"reaction_field\".\n", myMethod.c_str() );
1246                  painCave.isFatal = 1;
1247                  simError();
1248                }    
# Line 954 | Line 1261 | namespace oopse {
1261          if (myScreen == "DAMPED") {
1262            sm = DAMPED;
1263            if (!simParams_->haveDampingAlpha()) {
1264 <            //throw error
1264 >            // first set a cutoff dependent alpha value
1265 >            // we assume alpha depends linearly with rcut from 0 to 20.5 ang
1266 >            alphaVal = 0.5125 - rcut_* 0.025;
1267 >            // for values rcut > 20.5, alpha is zero
1268 >            if (alphaVal < 0) alphaVal = 0;
1269 >
1270 >            // throw warning
1271              sprintf( painCave.errMsg,
1272 <                     "SimInfo warning: dampingAlpha was not specified in the input file. A default value of %f (1/ang) will be used.", alphaVal);
1272 >                     "SimInfo warning: dampingAlpha was not specified in the input file.\n"
1273 >                     "\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1274              painCave.isFatal = 0;
1275              simError();
1276 +          } else {
1277 +            alphaVal = simParams_->getDampingAlpha();
1278            }
1279 +          
1280          } else {
1281            // throw error        
1282            sprintf( painCave.errMsg,
1283 <                   "SimInfo error: Unknown electrostaticScreeningMethod. (Input file specified %s .)\n\telectrostaticScreeningMethod must be one of: \"undamped\" or \"damped\".", myScreen.c_str() );
1283 >                   "SimInfo error: Unknown electrostaticScreeningMethod.\n"
1284 >                   "\t(Input file specified %s .)\n"
1285 >                   "\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1286 >                   "or \"damped\".\n", myScreen.c_str() );
1287            painCave.isFatal = 1;
1288            simError();
1289          }
# Line 972 | Line 1292 | namespace oopse {
1292      
1293      // let's pass some summation method variables to fortran
1294      setElectrostaticSummationMethod( &esm );
1295 +    setFortranElectrostaticMethod( &esm );
1296      setScreeningMethod( &sm );
1297      setDampingAlpha( &alphaVal );
1298      setReactionFieldDielectric( &dielectric );
1299 <    initFortranFF( &esm, &errorOut );
1299 >    initFortranFF( &errorOut );
1300    }
1301  
1302 +  void SimInfo::setupSwitchingFunction() {    
1303 +    int ft = CUBIC;
1304 +
1305 +    if (simParams_->haveSwitchingFunctionType()) {
1306 +      std::string funcType = simParams_->getSwitchingFunctionType();
1307 +      toUpper(funcType);
1308 +      if (funcType == "CUBIC") {
1309 +        ft = CUBIC;
1310 +      } else {
1311 +        if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1312 +          ft = FIFTH_ORDER_POLY;
1313 +        } else {
1314 +          // throw error        
1315 +          sprintf( painCave.errMsg,
1316 +                   "SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1317 +          painCave.isFatal = 1;
1318 +          simError();
1319 +        }          
1320 +      }
1321 +    }
1322 +
1323 +    // send switching function notification to switcheroo
1324 +    setFunctionType(&ft);
1325 +
1326 +  }
1327 +
1328 +  void SimInfo::setupAccumulateBoxDipole() {    
1329 +
1330 +    // we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1331 +    if ( simParams_->haveAccumulateBoxDipole() )
1332 +      if ( simParams_->getAccumulateBoxDipole() ) {
1333 +        setAccumulateBoxDipole();
1334 +        calcBoxDipole_ = true;
1335 +      }
1336 +
1337 +  }
1338 +
1339    void SimInfo::addProperty(GenericData* genData) {
1340      properties_.addProperty(genData);  
1341    }
# Line 1034 | Line 1392 | namespace oopse {
1392      Molecule* mol;
1393  
1394      Vector3d comVel(0.0);
1395 <    double totalMass = 0.0;
1395 >    RealType totalMass = 0.0;
1396      
1397  
1398      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1399 <      double mass = mol->getMass();
1399 >      RealType mass = mol->getMass();
1400        totalMass += mass;
1401        comVel += mass * mol->getComVel();
1402      }  
1403  
1404   #ifdef IS_MPI
1405 <    double tmpMass = totalMass;
1405 >    RealType tmpMass = totalMass;
1406      Vector3d tmpComVel(comVel);    
1407 <    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1408 <    MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1407 >    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1408 >    MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1409   #endif
1410  
1411      comVel /= totalMass;
# Line 1060 | Line 1418 | namespace oopse {
1418      Molecule* mol;
1419  
1420      Vector3d com(0.0);
1421 <    double totalMass = 0.0;
1421 >    RealType totalMass = 0.0;
1422      
1423      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1424 <      double mass = mol->getMass();
1424 >      RealType mass = mol->getMass();
1425        totalMass += mass;
1426        com += mass * mol->getCom();
1427      }  
1428  
1429   #ifdef IS_MPI
1430 <    double tmpMass = totalMass;
1430 >    RealType tmpMass = totalMass;
1431      Vector3d tmpCom(com);    
1432 <    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1433 <    MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1432 >    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1433 >    MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1434   #endif
1435  
1436      com /= totalMass;
# Line 1096 | Line 1454 | namespace oopse {
1454        Molecule* mol;
1455        
1456      
1457 <      double totalMass = 0.0;
1457 >      RealType totalMass = 0.0;
1458      
1459  
1460        for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1461 <         double mass = mol->getMass();
1461 >         RealType mass = mol->getMass();
1462           totalMass += mass;
1463           com += mass * mol->getCom();
1464           comVel += mass * mol->getComVel();          
1465        }  
1466        
1467   #ifdef IS_MPI
1468 <      double tmpMass = totalMass;
1468 >      RealType tmpMass = totalMass;
1469        Vector3d tmpCom(com);  
1470        Vector3d tmpComVel(comVel);
1471 <      MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1472 <      MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1473 <      MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1471 >      MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1472 >      MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1473 >      MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1474   #endif
1475        
1476        com /= totalMass;
# Line 1131 | Line 1489 | namespace oopse {
1489     void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1490        
1491  
1492 <      double xx = 0.0;
1493 <      double yy = 0.0;
1494 <      double zz = 0.0;
1495 <      double xy = 0.0;
1496 <      double xz = 0.0;
1497 <      double yz = 0.0;
1492 >      RealType xx = 0.0;
1493 >      RealType yy = 0.0;
1494 >      RealType zz = 0.0;
1495 >      RealType xy = 0.0;
1496 >      RealType xz = 0.0;
1497 >      RealType yz = 0.0;
1498        Vector3d com(0.0);
1499        Vector3d comVel(0.0);
1500        
# Line 1148 | Line 1506 | namespace oopse {
1506        Vector3d thisq(0.0);
1507        Vector3d thisv(0.0);
1508  
1509 <      double thisMass = 0.0;
1509 >      RealType thisMass = 0.0;
1510      
1511        
1512        
# Line 1186 | Line 1544 | namespace oopse {
1544   #ifdef IS_MPI
1545        Mat3x3d tmpI(inertiaTensor);
1546        Vector3d tmpAngMom;
1547 <      MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1548 <      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1547 >      MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1548 >      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1549   #endif
1550                
1551        return;
# Line 1208 | Line 1566 | namespace oopse {
1566        Vector3d thisr(0.0);
1567        Vector3d thisp(0.0);
1568        
1569 <      double thisMass;
1569 >      RealType thisMass;
1570        
1571        for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {        
1572          thisMass = mol->getMass();
# Line 1221 | Line 1579 | namespace oopse {
1579        
1580   #ifdef IS_MPI
1581        Vector3d tmpAngMom;
1582 <      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1582 >      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1583   #endif
1584        
1585        return angularMomentum;
1586     }
1587    
1588 <  
1588 >  StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1589 >    return IOIndexToIntegrableObject.at(index);
1590 >  }
1591 >  
1592 >  void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1593 >    IOIndexToIntegrableObject= v;
1594 >  }
1595 >
1596 >  /* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1597 >     based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1598 >     where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1599 >     V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1600 >  */
1601 >  void SimInfo::getGyrationalVolume(RealType &volume){
1602 >    Mat3x3d intTensor;
1603 >    RealType det;
1604 >    Vector3d dummyAngMom;
1605 >    RealType sysconstants;
1606 >    RealType geomCnst;
1607 >
1608 >    geomCnst = 3.0/2.0;
1609 >    /* Get the inertial tensor and angular momentum for free*/
1610 >    getInertiaTensor(intTensor,dummyAngMom);
1611 >    
1612 >    det = intTensor.determinant();
1613 >    sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1614 >    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1615 >    return;
1616 >  }
1617 >
1618 >  void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1619 >    Mat3x3d intTensor;
1620 >    Vector3d dummyAngMom;
1621 >    RealType sysconstants;
1622 >    RealType geomCnst;
1623 >
1624 >    geomCnst = 3.0/2.0;
1625 >    /* Get the inertial tensor and angular momentum for free*/
1626 >    getInertiaTensor(intTensor,dummyAngMom);
1627 >    
1628 >    detI = intTensor.determinant();
1629 >    sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1630 >    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1631 >    return;
1632 >  }
1633 > /*
1634 >   void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1635 >      assert( v.size() == nAtoms_ + nRigidBodies_);
1636 >      sdByGlobalIndex_ = v;
1637 >    }
1638 >
1639 >    StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1640 >      //assert(index < nAtoms_ + nRigidBodies_);
1641 >      return sdByGlobalIndex_.at(index);
1642 >    }  
1643 > */  
1644   }//end namespace oopse
1645  

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