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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 645 by chrisfen, Tue Oct 4 19:34:03 2005 UTC vs.
Revision 1290 by cli2, Wed Sep 10 19:51:45 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  
81 –            
82 –      std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
99        MoleculeStamp* molStamp;
100        int nMolWithSameStamp;
101        int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
# Line 87 | 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  
100 –
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 116 | 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 141 | Line 158 | namespace oopse {
158                                                  + nGlobalRigidBodies_;
159    
160        nGlobalMols_ = molStampIds_.size();
144 –
145 – #ifdef IS_MPI    
161        molToProcMap_.resize(nGlobalMols_);
147 – #endif
148 –
162      }
163  
164    SimInfo::~SimInfo() {
# Line 155 | Line 168 | namespace oopse {
168      }
169      molecules_.clear();
170        
158 –    delete stamps_;
171      delete sman_;
172      delete simParams_;
173      delete forceField_;
# Line 184 | 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 209 | 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 262 | 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 280 | 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 331 | 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 <      exclude_.addPair(a, b);
451 <      exclude_.addPair(a, c);
452 <      exclude_.addPair(a, d);
453 <      exclude_.addPair(b, c);
454 <      exclude_.addPair(b, d);
455 <      exclude_.addPair(c, d);        
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 >      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)) {
540 <      a = bond->getAtomA()->getGlobalIndex();
541 <      b = bond->getAtomB()->getGlobalIndex();        
542 <      exclude_.removePair(a, b);
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 >    
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 470 | 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 478 | Line 705 | namespace oopse {
705        painCave.isFatal = 1;
706        simError();
707      }
481 –  
482 –    
483 –    setupCutoff();
708  
709      calcNdf();
710      calcNdfRaw();
# Line 515 | 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 526 | Line 751 | namespace oopse {
751      int useDirectionalAtom = 0;    
752      int useElectrostatics = 0;
753      //usePBC and useRF are from simParams
754 <    int usePBC = simParams_->getPBC();
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 <    std::string myMethod = simParams_->getElectrostaticSummationMethod();
764 <    if (myMethod == "REACTION_FIELD")
765 <      useRF = 1;
536 <    else
537 <      useRF = 0;
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 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 591 | 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 600 | Line 851 | namespace oopse {
851      temp = useRF;
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);  
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 612 | 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 <
883 <    if( fInfo_.SIM_uses_Dipoles && myMethod == "REACTION_FIELD") {
884 <
885 <      if (simParams_->haveDielectric()) {
622 <        fInfo_.dielect = simParams_->getDielectric();
623 <      } else {
624 <        sprintf(painCave.errMsg,
625 <                "SimSetup Error: No Dielectric constant was set.\n"
626 <                "\tYou are trying to use Reaction Field without"
627 <                "\tsetting a dielectric constant!\n");
628 <        painCave.isFatal = 1;
629 <        simError();
630 <      }
631 <        
632 <    } else {
633 <      fInfo_.dielect = 0.0;
634 <    }
635 <
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      
643 –    nExclude = exclude_.getSize();
893      isError = 0;
894  
895      //globalGroupMembership_ is filled by SimCreator    
# Line 649 | 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 672 | Line 921 | namespace oopse {
921            else
922              mfact.push_back( 1.0 );
923          }
675 –
924        }      
925      }
926  
# Line 696 | Line 944 | namespace oopse {
944      }
945      
946      //setup fortran simulation
699 –    int nGlobalExcludes = 0;
700 –    int* globalExcludes = NULL;
701 –    int* excludeList = exclude_.getExcludeList();
702 –    setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
703 –                   &nGlobalExcludes, globalExcludes, &molMembershipArray[0],
704 –                   &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  
723 – #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 772 | Line 1044 | namespace oopse {
1044      }
1045  
1046      sprintf(checkPointMsg, " mpiRefresh successful.\n");
1047 <    MPIcheckPoint();
1047 >    errorCheckPoint();
1048  
777 –
778 –  }
779 –
1049   #endif
781 –
782 –  double SimInfo::calcMaxCutoffRadius() {
783 –
784 –
785 –    std::set<AtomType*> atomTypes;
786 –    std::set<AtomType*>::iterator i;
787 –    std::vector<double> cutoffRadius;
788 –
789 –    //get the unique atom types
790 –    atomTypes = getUniqueAtomTypes();
791 –
792 –    //query the max cutoff radius among these atom types
793 –    for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
794 –      cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
795 –    }
796 –
797 –    double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
798 – #ifdef IS_MPI
799 –    //pick the max cutoff radius among the processors
800 – #endif
801 –
802 –    return maxCutoffRadius;
1050    }
1051  
1052 <  void SimInfo::getCutoff(double& rcut, double& rsw) {
1052 >  void SimInfo::setupCutoff() {          
1053      
1054 <    if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
808 <        
809 <      if (!simParams_->haveRcut()){
810 <        sprintf(painCave.errMsg,
811 <                "SimCreator Warning: No value was set for the cutoffRadius.\n"
812 <                "\tOOPSE will use a default value of 15.0 angstroms"
813 <                "\tfor the cutoffRadius.\n");
814 <        painCave.isFatal = 0;
815 <        simError();
816 <        rcut = 15.0;
817 <      } else{
818 <        rcut = simParams_->getRcut();
819 <      }
1054 >    ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
1055  
1056 <      if (!simParams_->haveRsw()){
1057 <        sprintf(painCave.errMsg,
823 <                "SimCreator Warning: No value was set for switchingRadius.\n"
824 <                "\tOOPSE will use a default value of\n"
825 <                "\t0.95 * cutoffRadius for the switchingRadius\n");
826 <        painCave.isFatal = 0;
827 <        simError();
828 <        rsw = 0.95 * rcut;
829 <      } else{
830 <        rsw = simParams_->getRsw();
831 <      }
1056 >    // Check the cutoff policy
1057 >    int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
1058  
1059 <    } else {
1060 <      // if charge, dipole or reaction field is not used and the cutofff radius is not specified in
1061 <      //meta-data file, the maximum cutoff radius calculated from forcefiled will be used
836 <        
837 <      if (simParams_->haveRcut()) {
838 <        rcut = simParams_->getRcut();
839 <      } else {
840 <        //set cutoff radius to the maximum cutoff radius based on atom types in the whole system
841 <        rcut = calcMaxCutoffRadius();
842 <      }
1059 >    // Set LJ shifting bools to false
1060 >    ljsp_ = false;
1061 >    ljsf_ = false;
1062  
1063 <      if (simParams_->haveRsw()) {
1064 <        rsw  = simParams_->getRsw();
1065 <      } else {
1066 <        rsw = rcut;
1067 <      }
849 <    
1063 >    std::string myPolicy;
1064 >    if (forceFieldOptions_.haveCutoffPolicy()){
1065 >      myPolicy = forceFieldOptions_.getCutoffPolicy();
1066 >    }else if (simParams_->haveCutoffPolicy()) {
1067 >      myPolicy = simParams_->getCutoffPolicy();
1068      }
851 –  }
1069  
1070 <  void SimInfo::setupCutoff() {    
1071 <    getCutoff(rcut_, rsw_);    
855 <    double rnblist = rcut_ + 1; // skin of neighbor list
856 <
857 <    //Pass these cutoff radius etc. to fortran. This function should be called once and only once
858 <    
859 <    int cp =  TRADITIONAL_CUTOFF_POLICY;
860 <    if (simParams_->haveCutoffPolicy()) {
861 <      std::string myPolicy = simParams_->getCutoffPolicy();
1070 >    if (!myPolicy.empty()){
1071 >      toUpper(myPolicy);
1072        if (myPolicy == "MIX") {
1073          cp = MIX_CUTOFF_POLICY;
1074        } else {
# Line 876 | Line 1086 | namespace oopse {
1086            }    
1087          }          
1088        }
1089 <    }
1089 >    }          
1090 >    notifyFortranCutoffPolicy(&cp);
1091  
1092 <
1092 >    // Check the Skin Thickness for neighborlists
1093 >    RealType skin;
1094      if (simParams_->haveSkinThickness()) {
1095 <      double skinThickness = simParams_->getSkinThickness();
1096 <    }
1095 >      skin = simParams_->getSkinThickness();
1096 >      notifyFortranSkinThickness(&skin);
1097 >    }            
1098 >        
1099 >    // Check if the cutoff was set explicitly:
1100 >    if (simParams_->haveCutoffRadius()) {
1101 >      rcut_ = simParams_->getCutoffRadius();
1102 >      if (simParams_->haveSwitchingRadius()) {
1103 >        rsw_  = simParams_->getSwitchingRadius();
1104 >      } else {
1105 >        if (fInfo_.SIM_uses_Charges |
1106 >            fInfo_.SIM_uses_Dipoles |
1107 >            fInfo_.SIM_uses_RF) {
1108 >          
1109 >          rsw_ = 0.85 * rcut_;
1110 >          sprintf(painCave.errMsg,
1111 >                  "SimCreator Warning: No value was set for the switchingRadius.\n"
1112 >                  "\tOOPSE will use a default value of 85 percent of the cutoffRadius.\n"
1113 >                  "\tswitchingRadius = %f. for this simulation\n", rsw_);
1114 >        painCave.isFatal = 0;
1115 >        simError();
1116 >        } else {
1117 >          rsw_ = rcut_;
1118 >          sprintf(painCave.errMsg,
1119 >                  "SimCreator Warning: No value was set for the switchingRadius.\n"
1120 >                  "\tOOPSE will use the same value as the cutoffRadius.\n"
1121 >                  "\tswitchingRadius = %f. for this simulation\n", rsw_);
1122 >          painCave.isFatal = 0;
1123 >          simError();
1124 >        }
1125 >      }
1126  
1127 <    notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp);
1128 <    // also send cutoff notification to electrostatics
1129 <    setElectrostaticCutoffRadius(&rcut_);
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 >      
1141 >      // For electrostatic atoms, we'll assume a large safe value:
1142 >      if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
1143 >        sprintf(painCave.errMsg,
1144 >                "SimCreator Warning: No value was set for the cutoffRadius.\n"
1145 >                "\tOOPSE will use a default value of 15.0 angstroms"
1146 >                "\tfor the cutoffRadius.\n");
1147 >        painCave.isFatal = 0;
1148 >        simError();
1149 >        rcut_ = 15.0;
1150 >      
1151 >        if (simParams_->haveElectrostaticSummationMethod()) {
1152 >          std::string myMethod = simParams_->getElectrostaticSummationMethod();
1153 >          toUpper(myMethod);
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"
1166 >                      "\teven though the electrostaticSummationMethod was\n"
1167 >                      "\tset to %s\n", myMethod.c_str());
1168 >              painCave.isFatal = 1;
1169 >              simError();            
1170 >            }
1171 >          }
1172 >        }
1173 >      
1174 >        if (simParams_->haveSwitchingRadius()){
1175 >          rsw_ = simParams_->getSwitchingRadius();
1176 >        } else {        
1177 >          sprintf(painCave.errMsg,
1178 >                  "SimCreator Warning: No value was set for switchingRadius.\n"
1179 >                  "\tOOPSE will use a default value of\n"
1180 >                  "\t0.85 * cutoffRadius for the switchingRadius\n");
1181 >          painCave.isFatal = 0;
1182 >          simError();
1183 >          rsw_ = 0.85 * rcut_;
1184 >        }
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.
1191 >        
1192 >        notifyFortranYouAreOnYourOwn();
1193 >
1194 >      }
1195 >    }
1196    }
1197  
1198    void SimInfo::setupElectrostaticSummationMethod( int isError ) {    
1199      
1200      int errorOut;
1201      int esm =  NONE;
1202 <    double alphaVal;
1203 <    double dielectric;
1204 <
1202 >    int sm = UNDAMPED;
1203 >    RealType alphaVal;
1204 >    RealType dielectric;
1205 >    
1206      errorOut = isError;
899 –    alphaVal = simParams_->getDampingAlpha();
900 –    dielectric = simParams_->getDielectric();
1207  
1208      if (simParams_->haveElectrostaticSummationMethod()) {
1209        std::string myMethod = simParams_->getElectrostaticSummationMethod();
1210 +      toUpper(myMethod);
1211        if (myMethod == "NONE") {
1212          esm = NONE;
1213        } else {
1214 <        if (myMethod == "UNDAMPED_WOLF") {
1215 <          esm = UNDAMPED_WOLF;
1216 <        } else {
1217 <          if (myMethod == "DAMPED_WOLF") {            
1218 <            esm = DAMPED_WOLF;
1219 <            if (!simParams_->haveDampingAlpha()) {
1220 <              //throw error
1221 <              sprintf( painCave.errMsg,
915 <                       "SimInfo warning: dampingAlpha was not specified in the input file. A default value of %f (1/ang) will be used for the Damped Wolf Method.", alphaVal);
916 <              painCave.isFatal = 0;
917 <              simError();
918 <            }
919 <          } else {
920 <            if (myMethod == "REACTION_FIELD") {
921 <              esm = REACTION_FIELD;
1214 >        if (myMethod == "SWITCHING_FUNCTION") {
1215 >          esm = SWITCHING_FUNCTION;
1216 >        } else {
1217 >          if (myMethod == "SHIFTED_POTENTIAL") {
1218 >            esm = SHIFTED_POTENTIAL;
1219 >          } else {
1220 >            if (myMethod == "SHIFTED_FORCE") {            
1221 >              esm = SHIFTED_FORCE;
1222              } else {
1223 <              // throw error        
1224 <              sprintf( painCave.errMsg,
1225 <                       "SimInfo error: Unknown electrostaticSummationMethod. (Input file specified %s .)\n\telectrostaticSummationMethod must be one of: \"none\", \"undamped_wolf\", \"damped_wolf\", or \"reaction_field\".", myMethod.c_str() );
1226 <              painCave.isFatal = 1;
1227 <              simError();
1228 <            }    
1229 <          }          
1223 >              if (myMethod == "REACTION_FIELD") {
1224 >                esm = REACTION_FIELD;
1225 >                dielectric = simParams_->getDielectric();
1226 >                if (!simParams_->haveDielectric()) {
1227 >                  // throw warning
1228 >                  sprintf( painCave.errMsg,
1229 >                           "SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
1230 >                           "\tA default value of %f will be used for the dielectric.\n", dielectric);
1231 >                  painCave.isFatal = 0;
1232 >                  simError();
1233 >                }
1234 >              } else {
1235 >                // throw error        
1236 >                sprintf( painCave.errMsg,
1237 >                         "SimInfo error: Unknown electrostaticSummationMethod.\n"
1238 >                         "\t(Input file specified %s .)\n"
1239 >                         "\telectrostaticSummationMethod must be one of: \"none\",\n"
1240 >                         "\t\"shifted_potential\", \"shifted_force\", or \n"
1241 >                         "\t\"reaction_field\".\n", myMethod.c_str() );
1242 >                painCave.isFatal = 1;
1243 >                simError();
1244 >              }    
1245 >            }          
1246 >          }
1247          }
1248        }
1249      }
1250 +    
1251 +    if (simParams_->haveElectrostaticScreeningMethod()) {
1252 +      std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1253 +      toUpper(myScreen);
1254 +      if (myScreen == "UNDAMPED") {
1255 +        sm = UNDAMPED;
1256 +      } else {
1257 +        if (myScreen == "DAMPED") {
1258 +          sm = DAMPED;
1259 +          if (!simParams_->haveDampingAlpha()) {
1260 +            // first set a cutoff dependent alpha value
1261 +            // we assume alpha depends linearly with rcut from 0 to 20.5 ang
1262 +            alphaVal = 0.5125 - rcut_* 0.025;
1263 +            // for values rcut > 20.5, alpha is zero
1264 +            if (alphaVal < 0) alphaVal = 0;
1265 +
1266 +            // throw warning
1267 +            sprintf( painCave.errMsg,
1268 +                     "SimInfo warning: dampingAlpha was not specified in the input file.\n"
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,
1279 +                   "SimInfo error: Unknown electrostaticScreeningMethod.\n"
1280 +                   "\t(Input file specified %s .)\n"
1281 +                   "\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1282 +                   "or \"damped\".\n", myScreen.c_str() );
1283 +          painCave.isFatal = 1;
1284 +          simError();
1285 +        }
1286 +      }
1287 +    }
1288 +    
1289      // let's pass some summation method variables to fortran
1290      setElectrostaticSummationMethod( &esm );
1291 <    setDampedWolfAlpha( &alphaVal );
1291 >    setFortranElectrostaticMethod( &esm );
1292 >    setScreeningMethod( &sm );
1293 >    setDampingAlpha( &alphaVal );
1294      setReactionFieldDielectric( &dielectric );
1295 <    initFortranFF( &esm, &errorOut );
1295 >    initFortranFF( &errorOut );
1296    }
1297  
1298 +  void SimInfo::setupSwitchingFunction() {    
1299 +    int ft = CUBIC;
1300 +
1301 +    if (simParams_->haveSwitchingFunctionType()) {
1302 +      std::string funcType = simParams_->getSwitchingFunctionType();
1303 +      toUpper(funcType);
1304 +      if (funcType == "CUBIC") {
1305 +        ft = CUBIC;
1306 +      } else {
1307 +        if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1308 +          ft = FIFTH_ORDER_POLY;
1309 +        } else {
1310 +          // throw error        
1311 +          sprintf( painCave.errMsg,
1312 +                   "SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1313 +          painCave.isFatal = 1;
1314 +          simError();
1315 +        }          
1316 +      }
1317 +    }
1318 +
1319 +    // send switching function notification to switcheroo
1320 +    setFunctionType(&ft);
1321 +
1322 +  }
1323 +
1324 +  void SimInfo::setupAccumulateBoxDipole() {    
1325 +
1326 +    // we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1327 +    if ( simParams_->haveAccumulateBoxDipole() )
1328 +      if ( simParams_->getAccumulateBoxDipole() ) {
1329 +        setAccumulateBoxDipole();
1330 +        calcBoxDipole_ = true;
1331 +      }
1332 +
1333 +  }
1334 +
1335    void SimInfo::addProperty(GenericData* genData) {
1336      properties_.addProperty(genData);  
1337    }
# Line 993 | Line 1388 | namespace oopse {
1388      Molecule* mol;
1389  
1390      Vector3d comVel(0.0);
1391 <    double totalMass = 0.0;
1391 >    RealType totalMass = 0.0;
1392      
1393  
1394      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1395 <      double mass = mol->getMass();
1395 >      RealType mass = mol->getMass();
1396        totalMass += mass;
1397        comVel += mass * mol->getComVel();
1398      }  
1399  
1400   #ifdef IS_MPI
1401 <    double tmpMass = totalMass;
1401 >    RealType tmpMass = totalMass;
1402      Vector3d tmpComVel(comVel);    
1403 <    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1404 <    MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1403 >    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1404 >    MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1405   #endif
1406  
1407      comVel /= totalMass;
# Line 1019 | Line 1414 | namespace oopse {
1414      Molecule* mol;
1415  
1416      Vector3d com(0.0);
1417 <    double totalMass = 0.0;
1417 >    RealType totalMass = 0.0;
1418      
1419      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1420 <      double mass = mol->getMass();
1420 >      RealType mass = mol->getMass();
1421        totalMass += mass;
1422        com += mass * mol->getCom();
1423      }  
1424  
1425   #ifdef IS_MPI
1426 <    double tmpMass = totalMass;
1426 >    RealType tmpMass = totalMass;
1427      Vector3d tmpCom(com);    
1428 <    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1429 <    MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1428 >    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1429 >    MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1430   #endif
1431  
1432      com /= totalMass;
# Line 1055 | Line 1450 | namespace oopse {
1450        Molecule* mol;
1451        
1452      
1453 <      double totalMass = 0.0;
1453 >      RealType totalMass = 0.0;
1454      
1455  
1456        for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1457 <         double mass = mol->getMass();
1457 >         RealType mass = mol->getMass();
1458           totalMass += mass;
1459           com += mass * mol->getCom();
1460           comVel += mass * mol->getComVel();          
1461        }  
1462        
1463   #ifdef IS_MPI
1464 <      double tmpMass = totalMass;
1464 >      RealType tmpMass = totalMass;
1465        Vector3d tmpCom(com);  
1466        Vector3d tmpComVel(comVel);
1467 <      MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1468 <      MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1469 <      MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1467 >      MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1468 >      MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1469 >      MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1470   #endif
1471        
1472        com /= totalMass;
# Line 1090 | Line 1485 | namespace oopse {
1485     void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1486        
1487  
1488 <      double xx = 0.0;
1489 <      double yy = 0.0;
1490 <      double zz = 0.0;
1491 <      double xy = 0.0;
1492 <      double xz = 0.0;
1493 <      double yz = 0.0;
1488 >      RealType xx = 0.0;
1489 >      RealType yy = 0.0;
1490 >      RealType zz = 0.0;
1491 >      RealType xy = 0.0;
1492 >      RealType xz = 0.0;
1493 >      RealType yz = 0.0;
1494        Vector3d com(0.0);
1495        Vector3d comVel(0.0);
1496        
# Line 1107 | Line 1502 | namespace oopse {
1502        Vector3d thisq(0.0);
1503        Vector3d thisv(0.0);
1504  
1505 <      double thisMass = 0.0;
1505 >      RealType thisMass = 0.0;
1506      
1507        
1508        
# Line 1145 | Line 1540 | namespace oopse {
1540   #ifdef IS_MPI
1541        Mat3x3d tmpI(inertiaTensor);
1542        Vector3d tmpAngMom;
1543 <      MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1544 <      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1543 >      MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1544 >      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1545   #endif
1546                
1547        return;
# Line 1167 | Line 1562 | namespace oopse {
1562        Vector3d thisr(0.0);
1563        Vector3d thisp(0.0);
1564        
1565 <      double thisMass;
1565 >      RealType thisMass;
1566        
1567        for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {        
1568          thisMass = mol->getMass();
# Line 1180 | Line 1575 | namespace oopse {
1575        
1576   #ifdef IS_MPI
1577        Vector3d tmpAngMom;
1578 <      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1578 >      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1579   #endif
1580        
1581        return angularMomentum;
1582     }
1583    
1584 <  
1584 >  StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1585 >    return IOIndexToIntegrableObject.at(index);
1586 >  }
1587 >  
1588 >  void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
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_);
1632 >      sdByGlobalIndex_ = v;
1633 >    }
1634 >
1635 >    StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1636 >      //assert(index < nAtoms_ + nRigidBodies_);
1637 >      return sdByGlobalIndex_.at(index);
1638 >    }  
1639 > */  
1640   }//end namespace oopse
1641  

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