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root/OpenMD/trunk/src/brains/SimInfo.cpp
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Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 608 by chrisfen, Fri Sep 16 21:07:45 2005 UTC vs.
Revision 1277 by gezelter, Mon Jul 14 12:35:58 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/notifyCutoffs_interface.h"
62 > #include "UseTheForce/DarkSide/neighborLists_interface.h"
63 > #include "UseTheForce/DarkSide/electrostatic_interface.h"
64 > #include "UseTheForce/DarkSide/switcheroo_interface.h"
65   #include "utils/MemoryUtils.hpp"
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 <      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
102 <      int nGroups = 0;          //total cutoff groups defined in meta-data file
102 >      int nGroups = 0;      //total cutoff groups defined in meta-data file
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  
99 –
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  
127          nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
128 +
129          nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;            
130  
131          //calculate atoms in rigid bodies
# Line 114 | 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 123 | Line 142 | namespace oopse {
142          
143        }
144  
145 <      //every free atom (atom does not belong to cutoff groups) is a cutoff group
146 <      //therefore the total number of cutoff groups in the system is equal to
147 <      //the total number of atoms minus number of atoms belong to cutoff group defined in meta-data
148 <      //file plus the number of cutoff groups defined in meta-data file
145 >      //every free atom (atom does not belong to cutoff groups) is a cutoff
146 >      //group therefore the total number of cutoff groups in the system is
147 >      //equal to the total number of atoms minus number of atoms belong to
148 >      //cutoff group defined in meta-data file plus the number of cutoff
149 >      //groups defined in meta-data file
150        nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
151  
152 <      //every free atom (atom does not belong to rigid bodies) is an integrable object
153 <      //therefore the total number of  integrable objects in the system is equal to
154 <      //the total number of atoms minus number of atoms belong to  rigid body defined in meta-data
155 <      //file plus the number of  rigid bodies defined in meta-data file
156 <      nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_;
157 <
152 >      //every free atom (atom does not belong to rigid bodies) is an
153 >      //integrable object therefore the total number of integrable objects
154 >      //in the system is equal to the total number of atoms minus number of
155 >      //atoms belong to rigid body defined in meta-data file plus the number
156 >      //of rigid bodies defined in meta-data file
157 >      nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
158 >                                                + nGlobalRigidBodies_;
159 >  
160        nGlobalMols_ = molStampIds_.size();
139 –
140 – #ifdef IS_MPI    
161        molToProcMap_.resize(nGlobalMols_);
142 – #endif
143 –
162      }
163  
164    SimInfo::~SimInfo() {
# Line 150 | Line 168 | namespace oopse {
168      }
169      molecules_.clear();
170        
153 –    delete stamps_;
171      delete sman_;
172      delete simParams_;
173      delete forceField_;
# Line 179 | 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();
# Line 204 | 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();
# Line 257 | 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 275 | 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 330 | Line 358 | namespace oopse {
358      std::vector<Bond*>::iterator bondIter;
359      std::vector<Bend*>::iterator bendIter;
360      std::vector<Torsion*>::iterator torsionIter;
361 +    std::vector<Inversion*>::iterator inversionIter;
362      Bond* bond;
363      Bend* bend;
364      Torsion* torsion;
365 +    Inversion* inversion;
366      int a;
367      int b;
368      int c;
369      int d;
370 +
371 +    std::map<int, std::set<int> > atomGroups;
372 +
373 +    Molecule::RigidBodyIterator rbIter;
374 +    RigidBody* rb;
375 +    Molecule::IntegrableObjectIterator ii;
376 +    StuntDouble* integrableObject;
377      
378 +    for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
379 +           integrableObject = mol->nextIntegrableObject(ii)) {
380 +
381 +      if (integrableObject->isRigidBody()) {
382 +          rb = static_cast<RigidBody*>(integrableObject);
383 +          std::vector<Atom*> atoms = rb->getAtoms();
384 +          std::set<int> rigidAtoms;
385 +          for (int i = 0; i < atoms.size(); ++i) {
386 +            rigidAtoms.insert(atoms[i]->getGlobalIndex());
387 +          }
388 +          for (int i = 0; i < atoms.size(); ++i) {
389 +            atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
390 +          }      
391 +      } else {
392 +        std::set<int> oneAtomSet;
393 +        oneAtomSet.insert(integrableObject->getGlobalIndex());
394 +        atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));        
395 +      }
396 +    }  
397 +
398 +    
399 +    
400      for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
401        a = bond->getAtomA()->getGlobalIndex();
402        b = bond->getAtomB()->getGlobalIndex();        
# Line 348 | Line 407 | namespace oopse {
407        a = bend->getAtomA()->getGlobalIndex();
408        b = bend->getAtomB()->getGlobalIndex();        
409        c = bend->getAtomC()->getGlobalIndex();
410 +      std::set<int> rigidSetA = getRigidSet(a, atomGroups);
411 +      std::set<int> rigidSetB = getRigidSet(b, atomGroups);
412 +      std::set<int> rigidSetC = getRigidSet(c, atomGroups);
413  
414 <      exclude_.addPair(a, b);
415 <      exclude_.addPair(a, c);
416 <      exclude_.addPair(b, c);        
414 >      exclude_.addPairs(rigidSetA, rigidSetB);
415 >      exclude_.addPairs(rigidSetA, rigidSetC);
416 >      exclude_.addPairs(rigidSetB, rigidSetC);
417 >      
418 >      //exclude_.addPair(a, b);
419 >      //exclude_.addPair(a, c);
420 >      //exclude_.addPair(b, c);        
421      }
422  
423      for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
# Line 359 | Line 425 | namespace oopse {
425        b = torsion->getAtomB()->getGlobalIndex();        
426        c = torsion->getAtomC()->getGlobalIndex();        
427        d = torsion->getAtomD()->getGlobalIndex();        
428 +      std::set<int> rigidSetA = getRigidSet(a, atomGroups);
429 +      std::set<int> rigidSetB = getRigidSet(b, atomGroups);
430 +      std::set<int> rigidSetC = getRigidSet(c, atomGroups);
431 +      std::set<int> rigidSetD = getRigidSet(d, atomGroups);
432  
433 +      exclude_.addPairs(rigidSetA, rigidSetB);
434 +      exclude_.addPairs(rigidSetA, rigidSetC);
435 +      exclude_.addPairs(rigidSetA, rigidSetD);
436 +      exclude_.addPairs(rigidSetB, rigidSetC);
437 +      exclude_.addPairs(rigidSetB, rigidSetD);
438 +      exclude_.addPairs(rigidSetC, rigidSetD);
439 +
440 +      /*
441 +      exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
442 +      exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
443 +      exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
444 +      exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
445 +      exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
446 +      exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
447 +        
448 +      
449        exclude_.addPair(a, b);
450        exclude_.addPair(a, c);
451        exclude_.addPair(a, d);
452        exclude_.addPair(b, c);
453        exclude_.addPair(b, d);
454        exclude_.addPair(c, d);        
455 +      */
456      }
457  
458 <    Molecule::RigidBodyIterator rbIter;
459 <    RigidBody* rb;
458 >    for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
459 >         inversion = mol->nextInversion(inversionIter)) {
460 >      a = inversion->getAtomA()->getGlobalIndex();
461 >      b = inversion->getAtomB()->getGlobalIndex();        
462 >      c = inversion->getAtomC()->getGlobalIndex();        
463 >      d = inversion->getAtomD()->getGlobalIndex();        
464 >      std::set<int> rigidSetA = getRigidSet(a, atomGroups);
465 >      std::set<int> rigidSetB = getRigidSet(b, atomGroups);
466 >      std::set<int> rigidSetC = getRigidSet(c, atomGroups);
467 >      std::set<int> rigidSetD = getRigidSet(d, atomGroups);
468 >
469 >      exclude_.addPairs(rigidSetA, rigidSetB);
470 >      exclude_.addPairs(rigidSetA, rigidSetC);
471 >      exclude_.addPairs(rigidSetA, rigidSetD);
472 >      exclude_.addPairs(rigidSetB, rigidSetC);
473 >      exclude_.addPairs(rigidSetB, rigidSetD);
474 >      exclude_.addPairs(rigidSetC, rigidSetD);
475 >
476 >      /*
477 >      exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
478 >      exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
479 >      exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
480 >      exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
481 >      exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
482 >      exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
483 >        
484 >      
485 >      exclude_.addPair(a, b);
486 >      exclude_.addPair(a, c);
487 >      exclude_.addPair(a, d);
488 >      exclude_.addPair(b, c);
489 >      exclude_.addPair(b, d);
490 >      exclude_.addPair(c, d);        
491 >      */
492 >    }
493 >
494      for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
495        std::vector<Atom*> atoms = rb->getAtoms();
496        for (int i = 0; i < atoms.size() -1 ; ++i) {
# Line 387 | Line 508 | namespace oopse {
508      std::vector<Bond*>::iterator bondIter;
509      std::vector<Bend*>::iterator bendIter;
510      std::vector<Torsion*>::iterator torsionIter;
511 +    std::vector<Inversion*>::iterator inversionIter;
512      Bond* bond;
513      Bend* bend;
514      Torsion* torsion;
515 +    Inversion* inversion;
516      int a;
517      int b;
518      int c;
519      int d;
520 +
521 +    std::map<int, std::set<int> > atomGroups;
522 +
523 +    Molecule::RigidBodyIterator rbIter;
524 +    RigidBody* rb;
525 +    Molecule::IntegrableObjectIterator ii;
526 +    StuntDouble* integrableObject;
527      
528 +    for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
529 +           integrableObject = mol->nextIntegrableObject(ii)) {
530 +
531 +      if (integrableObject->isRigidBody()) {
532 +          rb = static_cast<RigidBody*>(integrableObject);
533 +          std::vector<Atom*> atoms = rb->getAtoms();
534 +          std::set<int> rigidAtoms;
535 +          for (int i = 0; i < atoms.size(); ++i) {
536 +            rigidAtoms.insert(atoms[i]->getGlobalIndex());
537 +          }
538 +          for (int i = 0; i < atoms.size(); ++i) {
539 +            atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
540 +          }      
541 +      } else {
542 +        std::set<int> oneAtomSet;
543 +        oneAtomSet.insert(integrableObject->getGlobalIndex());
544 +        atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));        
545 +      }
546 +    }  
547 +
548 +    
549      for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
550        a = bond->getAtomA()->getGlobalIndex();
551        b = bond->getAtomB()->getGlobalIndex();        
# Line 406 | Line 557 | namespace oopse {
557        b = bend->getAtomB()->getGlobalIndex();        
558        c = bend->getAtomC()->getGlobalIndex();
559  
560 <      exclude_.removePair(a, b);
561 <      exclude_.removePair(a, c);
562 <      exclude_.removePair(b, c);        
560 >      std::set<int> rigidSetA = getRigidSet(a, atomGroups);
561 >      std::set<int> rigidSetB = getRigidSet(b, atomGroups);
562 >      std::set<int> rigidSetC = getRigidSet(c, atomGroups);
563 >
564 >      exclude_.removePairs(rigidSetA, rigidSetB);
565 >      exclude_.removePairs(rigidSetA, rigidSetC);
566 >      exclude_.removePairs(rigidSetB, rigidSetC);
567 >      
568 >      //exclude_.removePair(a, b);
569 >      //exclude_.removePair(a, c);
570 >      //exclude_.removePair(b, c);        
571      }
572  
573      for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
# Line 417 | Line 576 | namespace oopse {
576        c = torsion->getAtomC()->getGlobalIndex();        
577        d = torsion->getAtomD()->getGlobalIndex();        
578  
579 +      std::set<int> rigidSetA = getRigidSet(a, atomGroups);
580 +      std::set<int> rigidSetB = getRigidSet(b, atomGroups);
581 +      std::set<int> rigidSetC = getRigidSet(c, atomGroups);
582 +      std::set<int> rigidSetD = getRigidSet(d, atomGroups);
583 +
584 +      exclude_.removePairs(rigidSetA, rigidSetB);
585 +      exclude_.removePairs(rigidSetA, rigidSetC);
586 +      exclude_.removePairs(rigidSetA, rigidSetD);
587 +      exclude_.removePairs(rigidSetB, rigidSetC);
588 +      exclude_.removePairs(rigidSetB, rigidSetD);
589 +      exclude_.removePairs(rigidSetC, rigidSetD);
590 +
591 +      /*
592 +      exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
593 +      exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
594 +      exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
595 +      exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
596 +      exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
597 +      exclude_.removePairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
598 +
599 +      
600        exclude_.removePair(a, b);
601        exclude_.removePair(a, c);
602        exclude_.removePair(a, d);
603        exclude_.removePair(b, c);
604        exclude_.removePair(b, d);
605        exclude_.removePair(c, d);        
606 +      */
607      }
608  
609 <    Molecule::RigidBodyIterator rbIter;
610 <    RigidBody* rb;
609 >    for (inversion= mol->beginInversion(inversionIter); inversion != NULL; inversion = mol->nextInversion(inversionIter)) {
610 >      a = inversion->getAtomA()->getGlobalIndex();
611 >      b = inversion->getAtomB()->getGlobalIndex();        
612 >      c = inversion->getAtomC()->getGlobalIndex();        
613 >      d = inversion->getAtomD()->getGlobalIndex();        
614 >
615 >      std::set<int> rigidSetA = getRigidSet(a, atomGroups);
616 >      std::set<int> rigidSetB = getRigidSet(b, atomGroups);
617 >      std::set<int> rigidSetC = getRigidSet(c, atomGroups);
618 >      std::set<int> rigidSetD = getRigidSet(d, atomGroups);
619 >
620 >      exclude_.removePairs(rigidSetA, rigidSetB);
621 >      exclude_.removePairs(rigidSetA, rigidSetC);
622 >      exclude_.removePairs(rigidSetA, rigidSetD);
623 >      exclude_.removePairs(rigidSetB, rigidSetC);
624 >      exclude_.removePairs(rigidSetB, rigidSetD);
625 >      exclude_.removePairs(rigidSetC, rigidSetD);
626 >
627 >      /*
628 >      exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
629 >      exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
630 >      exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
631 >      exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
632 >      exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
633 >      exclude_.removePairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
634 >
635 >      
636 >      exclude_.removePair(a, b);
637 >      exclude_.removePair(a, c);
638 >      exclude_.removePair(a, d);
639 >      exclude_.removePair(b, c);
640 >      exclude_.removePair(b, d);
641 >      exclude_.removePair(c, d);        
642 >      */
643 >    }
644 >
645      for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
646        std::vector<Atom*> atoms = rb->getAtoms();
647        for (int i = 0; i < atoms.size() -1 ; ++i) {
# Line 465 | Line 680 | namespace oopse {
680      /** @deprecate */    
681      int isError = 0;
682      
683 +    setupCutoff();
684 +    
685      setupElectrostaticSummationMethod( isError );
686 +    setupSwitchingFunction();
687 +    setupAccumulateBoxDipole();
688  
689      if(isError){
690        sprintf( painCave.errMsg,
# Line 473 | Line 692 | namespace oopse {
692        painCave.isFatal = 1;
693        simError();
694      }
476 –  
477 –    
478 –    setupCutoff();
695  
696      calcNdf();
697      calcNdfRaw();
# Line 510 | Line 726 | namespace oopse {
726      int useLennardJones = 0;
727      int useElectrostatic = 0;
728      int useEAM = 0;
729 +    int useSC = 0;
730      int useCharge = 0;
731      int useDirectional = 0;
732      int useDipole = 0;
# Line 521 | Line 738 | namespace oopse {
738      int useDirectionalAtom = 0;    
739      int useElectrostatics = 0;
740      //usePBC and useRF are from simParams
741 <    int usePBC = simParams_->getPBC();
741 >    int usePBC = simParams_->getUsePeriodicBoundaryConditions();
742 >    int useRF;
743 >    int useSF;
744 >    int useSP;
745 >    int useBoxDipole;
746  
747 +    std::string myMethod;
748 +
749 +    // set the useRF logical
750 +    useRF = 0;
751 +    useSF = 0;
752 +    useSP = 0;
753 +
754 +
755 +    if (simParams_->haveElectrostaticSummationMethod()) {
756 +      std::string myMethod = simParams_->getElectrostaticSummationMethod();
757 +      toUpper(myMethod);
758 +      if (myMethod == "REACTION_FIELD"){
759 +        useRF = 1;
760 +      } else if (myMethod == "SHIFTED_FORCE"){
761 +        useSF = 1;
762 +      } else if (myMethod == "SHIFTED_POTENTIAL"){
763 +        useSP = 1;
764 +      }
765 +    }
766 +    
767 +    if (simParams_->haveAccumulateBoxDipole())
768 +      if (simParams_->getAccumulateBoxDipole())
769 +        useBoxDipole = 1;
770 +
771 +    useAtomicVirial_ = simParams_->getUseAtomicVirial();
772 +
773      //loop over all of the atom types
774      for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
775        useLennardJones |= (*i)->isLennardJones();
776        useElectrostatic |= (*i)->isElectrostatic();
777        useEAM |= (*i)->isEAM();
778 +      useSC |= (*i)->isSC();
779        useCharge |= (*i)->isCharge();
780        useDirectional |= (*i)->isDirectional();
781        useDipole |= (*i)->isDipole();
# Line 578 | Line 826 | namespace oopse {
826      temp = useEAM;
827      MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
828  
829 +    temp = useSC;
830 +    MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
831 +    
832      temp = useShape;
833      MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);  
834  
835      temp = useFLARB;
836      MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
837  
838 +    temp = useRF;
839 +    MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
840 +
841 +    temp = useSF;
842 +    MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);  
843 +
844 +    temp = useSP;
845 +    MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
846 +
847 +    temp = useBoxDipole;
848 +    MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
849 +
850 +    temp = useAtomicVirial_;
851 +    MPI_Allreduce(&temp, &useAtomicVirial_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
852 +
853   #endif
854  
855      fInfo_.SIM_uses_PBC = usePBC;    
# Line 596 | Line 862 | namespace oopse {
862      fInfo_.SIM_uses_StickyPower = useStickyPower;
863      fInfo_.SIM_uses_GayBerne = useGayBerne;
864      fInfo_.SIM_uses_EAM = useEAM;
865 +    fInfo_.SIM_uses_SC = useSC;
866      fInfo_.SIM_uses_Shapes = useShape;
867      fInfo_.SIM_uses_FLARB = useFLARB;
868 <
869 <    if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) {
870 <
871 <      if (simParams_->haveDielectric()) {
872 <        fInfo_.dielect = simParams_->getDielectric();
606 <      } else {
607 <        sprintf(painCave.errMsg,
608 <                "SimSetup Error: No Dielectric constant was set.\n"
609 <                "\tYou are trying to use Reaction Field without"
610 <                "\tsetting a dielectric constant!\n");
611 <        painCave.isFatal = 1;
612 <        simError();
613 <      }
614 <        
615 <    } else {
616 <      fInfo_.dielect = 0.0;
617 <    }
618 <
868 >    fInfo_.SIM_uses_RF = useRF;
869 >    fInfo_.SIM_uses_SF = useSF;
870 >    fInfo_.SIM_uses_SP = useSP;
871 >    fInfo_.SIM_uses_BoxDipole = useBoxDipole;
872 >    fInfo_.SIM_uses_AtomicVirial = useAtomicVirial_;
873    }
874  
875    void SimInfo::setupFortranSim() {
# Line 632 | Line 886 | namespace oopse {
886      }
887  
888      //calculate mass ratio of cutoff group
889 <    std::vector<double> mfact;
889 >    std::vector<RealType> mfact;
890      SimInfo::MoleculeIterator mi;
891      Molecule* mol;
892      Molecule::CutoffGroupIterator ci;
893      CutoffGroup* cg;
894      Molecule::AtomIterator ai;
895      Atom* atom;
896 <    double totalMass;
896 >    RealType totalMass;
897  
898      //to avoid memory reallocation, reserve enough space for mfact
899      mfact.reserve(getNCutoffGroups());
# Line 649 | Line 903 | namespace oopse {
903  
904          totalMass = cg->getMass();
905          for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
906 <          mfact.push_back(atom->getMass()/totalMass);
906 >          // Check for massless groups - set mfact to 1 if true
907 >          if (totalMass != 0)
908 >            mfact.push_back(atom->getMass()/totalMass);
909 >          else
910 >            mfact.push_back( 1.0 );
911          }
912  
913        }      
# Line 678 | Line 936 | namespace oopse {
936      int nGlobalExcludes = 0;
937      int* globalExcludes = NULL;
938      int* excludeList = exclude_.getExcludeList();
939 <    setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
940 <                   &nGlobalExcludes, globalExcludes, &molMembershipArray[0],
941 <                   &mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
942 <
939 >    setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
940 >                   &nExclude, excludeList , &nGlobalExcludes, globalExcludes,
941 >                   &molMembershipArray[0], &mfact[0], &nCutoffGroups_,
942 >                   &fortranGlobalGroupMembership[0], &isError);
943 >    
944      if( isError ){
945 <
945 >      
946        sprintf( painCave.errMsg,
947                 "There was an error setting the simulation information in fortran.\n" );
948        painCave.isFatal = 1;
949        painCave.severity = OOPSE_ERROR;
950        simError();
951      }
952 <
953 < #ifdef IS_MPI
952 >    
953 >    
954      sprintf( checkPointMsg,
955               "succesfully sent the simulation information to fortran.\n");
956 <    MPIcheckPoint();
957 < #endif // is_mpi
956 >    
957 >    errorCheckPoint();
958 >    
959 >    // Setup number of neighbors in neighbor list if present
960 >    if (simParams_->haveNeighborListNeighbors()) {
961 >      int nlistNeighbors = simParams_->getNeighborListNeighbors();
962 >      setNeighbors(&nlistNeighbors);
963 >    }
964 >  
965 >
966    }
967  
968  
702 – #ifdef IS_MPI
969    void SimInfo::setupFortranParallel() {
970 <    
970 > #ifdef IS_MPI    
971      //SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
972      std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
973      std::vector<int> localToGlobalCutoffGroupIndex;
# Line 751 | Line 1017 | namespace oopse {
1017      }
1018  
1019      sprintf(checkPointMsg, " mpiRefresh successful.\n");
1020 <    MPIcheckPoint();
1020 >    errorCheckPoint();
1021  
1022 <
1022 > #endif
1023    }
1024  
1025 < #endif
1025 >  void SimInfo::setupCutoff() {          
1026 >    
1027 >    ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
1028  
1029 <  double SimInfo::calcMaxCutoffRadius() {
1029 >    // Check the cutoff policy
1030 >    int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
1031  
1032 <
1033 <    std::set<AtomType*> atomTypes;
1034 <    std::set<AtomType*>::iterator i;
766 <    std::vector<double> cutoffRadius;
767 <
768 <    //get the unique atom types
769 <    atomTypes = getUniqueAtomTypes();
1032 >    // Set LJ shifting bools to false
1033 >    ljsp_ = false;
1034 >    ljsf_ = false;
1035  
1036 <    //query the max cutoff radius among these atom types
1037 <    for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
1038 <      cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
1036 >    std::string myPolicy;
1037 >    if (forceFieldOptions_.haveCutoffPolicy()){
1038 >      myPolicy = forceFieldOptions_.getCutoffPolicy();
1039 >    }else if (simParams_->haveCutoffPolicy()) {
1040 >      myPolicy = simParams_->getCutoffPolicy();
1041      }
1042  
1043 <    double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
1044 < #ifdef IS_MPI
778 <    //pick the max cutoff radius among the processors
779 < #endif
780 <
781 <    return maxCutoffRadius;
782 <  }
783 <
784 <  void SimInfo::getCutoff(double& rcut, double& rsw) {
785 <    
786 <    if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
787 <        
788 <      if (!simParams_->haveRcut()){
789 <        sprintf(painCave.errMsg,
790 <                "SimCreator Warning: No value was set for the cutoffRadius.\n"
791 <                "\tOOPSE will use a default value of 15.0 angstroms"
792 <                "\tfor the cutoffRadius.\n");
793 <        painCave.isFatal = 0;
794 <        simError();
795 <        rcut = 15.0;
796 <      } else{
797 <        rcut = simParams_->getRcut();
798 <      }
799 <
800 <      if (!simParams_->haveRsw()){
801 <        sprintf(painCave.errMsg,
802 <                "SimCreator Warning: No value was set for switchingRadius.\n"
803 <                "\tOOPSE will use a default value of\n"
804 <                "\t0.95 * cutoffRadius for the switchingRadius\n");
805 <        painCave.isFatal = 0;
806 <        simError();
807 <        rsw = 0.95 * rcut;
808 <      } else{
809 <        rsw = simParams_->getRsw();
810 <      }
811 <
812 <    } else {
813 <      // if charge, dipole or reaction field is not used and the cutofff radius is not specified in
814 <      //meta-data file, the maximum cutoff radius calculated from forcefiled will be used
815 <        
816 <      if (simParams_->haveRcut()) {
817 <        rcut = simParams_->getRcut();
818 <      } else {
819 <        //set cutoff radius to the maximum cutoff radius based on atom types in the whole system
820 <        rcut = calcMaxCutoffRadius();
821 <      }
822 <
823 <      if (simParams_->haveRsw()) {
824 <        rsw  = simParams_->getRsw();
825 <      } else {
826 <        rsw = rcut;
827 <      }
828 <    
829 <    }
830 <  }
831 <
832 <  void SimInfo::setupCutoff() {    
833 <    getCutoff(rcut_, rsw_);    
834 <    double rnblist = rcut_ + 1; // skin of neighbor list
835 <
836 <    //Pass these cutoff radius etc. to fortran. This function should be called once and only once
837 <    
838 <    int cp =  TRADITIONAL_CUTOFF_POLICY;
839 <    if (simParams_->haveCutoffPolicy()) {
840 <      std::string myPolicy = simParams_->getCutoffPolicy();
1043 >    if (!myPolicy.empty()){
1044 >      toUpper(myPolicy);
1045        if (myPolicy == "MIX") {
1046          cp = MIX_CUTOFF_POLICY;
1047        } else {
# Line 855 | Line 1059 | namespace oopse {
1059            }    
1060          }          
1061        }
1062 +    }          
1063 +    notifyFortranCutoffPolicy(&cp);
1064 +
1065 +    // Check the Skin Thickness for neighborlists
1066 +    RealType skin;
1067 +    if (simParams_->haveSkinThickness()) {
1068 +      skin = simParams_->getSkinThickness();
1069 +      notifyFortranSkinThickness(&skin);
1070 +    }            
1071 +        
1072 +    // Check if the cutoff was set explicitly:
1073 +    if (simParams_->haveCutoffRadius()) {
1074 +      rcut_ = simParams_->getCutoffRadius();
1075 +      if (simParams_->haveSwitchingRadius()) {
1076 +        rsw_  = simParams_->getSwitchingRadius();
1077 +      } else {
1078 +        if (fInfo_.SIM_uses_Charges |
1079 +            fInfo_.SIM_uses_Dipoles |
1080 +            fInfo_.SIM_uses_RF) {
1081 +          
1082 +          rsw_ = 0.85 * rcut_;
1083 +          sprintf(painCave.errMsg,
1084 +                  "SimCreator Warning: No value was set for the switchingRadius.\n"
1085 +                  "\tOOPSE will use a default value of 85 percent of the cutoffRadius.\n"
1086 +                  "\tswitchingRadius = %f. for this simulation\n", rsw_);
1087 +        painCave.isFatal = 0;
1088 +        simError();
1089 +        } else {
1090 +          rsw_ = rcut_;
1091 +          sprintf(painCave.errMsg,
1092 +                  "SimCreator Warning: No value was set for the switchingRadius.\n"
1093 +                  "\tOOPSE will use the same value as the cutoffRadius.\n"
1094 +                  "\tswitchingRadius = %f. for this simulation\n", rsw_);
1095 +          painCave.isFatal = 0;
1096 +          simError();
1097 +        }
1098 +      }
1099 +
1100 +      if (simParams_->haveElectrostaticSummationMethod()) {
1101 +        std::string myMethod = simParams_->getElectrostaticSummationMethod();
1102 +        toUpper(myMethod);
1103 +        
1104 +        if (myMethod == "SHIFTED_POTENTIAL") {
1105 +          ljsp_ = true;
1106 +        } else if (myMethod == "SHIFTED_FORCE") {
1107 +          ljsf_ = true;
1108 +        }
1109 +      }
1110 +      notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1111 +      
1112 +    } else {
1113 +      
1114 +      // For electrostatic atoms, we'll assume a large safe value:
1115 +      if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
1116 +        sprintf(painCave.errMsg,
1117 +                "SimCreator Warning: No value was set for the cutoffRadius.\n"
1118 +                "\tOOPSE will use a default value of 15.0 angstroms"
1119 +                "\tfor the cutoffRadius.\n");
1120 +        painCave.isFatal = 0;
1121 +        simError();
1122 +        rcut_ = 15.0;
1123 +      
1124 +        if (simParams_->haveElectrostaticSummationMethod()) {
1125 +          std::string myMethod = simParams_->getElectrostaticSummationMethod();
1126 +          toUpper(myMethod);
1127 +      
1128 +      // For the time being, we're tethering the LJ shifted behavior to the
1129 +      // electrostaticSummationMethod keyword options
1130 +          if (myMethod == "SHIFTED_POTENTIAL") {
1131 +            ljsp_ = true;
1132 +          } else if (myMethod == "SHIFTED_FORCE") {
1133 +            ljsf_ = true;
1134 +          }
1135 +          if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1136 +            if (simParams_->haveSwitchingRadius()){
1137 +              sprintf(painCave.errMsg,
1138 +                      "SimInfo Warning: A value was set for the switchingRadius\n"
1139 +                      "\teven though the electrostaticSummationMethod was\n"
1140 +                      "\tset to %s\n", myMethod.c_str());
1141 +              painCave.isFatal = 1;
1142 +              simError();            
1143 +            }
1144 +          }
1145 +        }
1146 +      
1147 +        if (simParams_->haveSwitchingRadius()){
1148 +          rsw_ = simParams_->getSwitchingRadius();
1149 +        } else {        
1150 +          sprintf(painCave.errMsg,
1151 +                  "SimCreator Warning: No value was set for switchingRadius.\n"
1152 +                  "\tOOPSE will use a default value of\n"
1153 +                  "\t0.85 * cutoffRadius for the switchingRadius\n");
1154 +          painCave.isFatal = 0;
1155 +          simError();
1156 +          rsw_ = 0.85 * rcut_;
1157 +        }
1158 +
1159 +        notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1160 +
1161 +      } else {
1162 +        // We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1163 +        // We'll punt and let fortran figure out the cutoffs later.
1164 +        
1165 +        notifyFortranYouAreOnYourOwn();
1166 +
1167 +      }
1168      }
859 –    notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp);
1169    }
1170  
1171    void SimInfo::setupElectrostaticSummationMethod( int isError ) {    
1172      
1173      int errorOut;
1174      int esm =  NONE;
1175 <    double alphaVal;
1176 <
1175 >    int sm = UNDAMPED;
1176 >    RealType alphaVal;
1177 >    RealType dielectric;
1178 >    
1179      errorOut = isError;
1180  
1181      if (simParams_->haveElectrostaticSummationMethod()) {
1182        std::string myMethod = simParams_->getElectrostaticSummationMethod();
1183 +      toUpper(myMethod);
1184        if (myMethod == "NONE") {
1185          esm = NONE;
1186        } else {
1187 <        if (myMethod == "UNDAMPED_WOLF") {
1188 <          esm = UNDAMPED_WOLF;
1187 >        if (myMethod == "SWITCHING_FUNCTION") {
1188 >          esm = SWITCHING_FUNCTION;
1189          } else {
1190 <          if (myMethod == "DAMPED_WOLF") {            
1191 <            esm = DAMPED_WOLF;
1192 <            if (!simParams_->haveDampingAlpha()) {
1193 <              //throw error
1194 <              sprintf( painCave.errMsg,
883 <                       "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.", simParams_->getDampingAlpha());
884 <              painCave.isFatal = 0;
885 <              simError();
886 <            }
887 <            alphaVal = simParams_->getDampingAlpha();
888 <          } else {
889 <            if (myMethod == "REACTION_FIELD") {
890 <              esm = REACTION_FIELD;
1190 >          if (myMethod == "SHIFTED_POTENTIAL") {
1191 >            esm = SHIFTED_POTENTIAL;
1192 >          } else {
1193 >            if (myMethod == "SHIFTED_FORCE") {            
1194 >              esm = SHIFTED_FORCE;
1195              } else {
1196 <              // throw error        
1197 <              sprintf( painCave.errMsg,
1198 <                       "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() );
1199 <              painCave.isFatal = 1;
1200 <              simError();
1201 <            }    
1202 <          }          
1196 >              if (myMethod == "REACTION_FIELD") {
1197 >                esm = REACTION_FIELD;
1198 >                dielectric = simParams_->getDielectric();
1199 >                if (!simParams_->haveDielectric()) {
1200 >                  // throw warning
1201 >                  sprintf( painCave.errMsg,
1202 >                           "SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
1203 >                           "\tA default value of %f will be used for the dielectric.\n", dielectric);
1204 >                  painCave.isFatal = 0;
1205 >                  simError();
1206 >                }
1207 >              } else {
1208 >                // throw error        
1209 >                sprintf( painCave.errMsg,
1210 >                         "SimInfo error: Unknown electrostaticSummationMethod.\n"
1211 >                         "\t(Input file specified %s .)\n"
1212 >                         "\telectrostaticSummationMethod must be one of: \"none\",\n"
1213 >                         "\t\"shifted_potential\", \"shifted_force\", or \n"
1214 >                         "\t\"reaction_field\".\n", myMethod.c_str() );
1215 >                painCave.isFatal = 1;
1216 >                simError();
1217 >              }    
1218 >            }          
1219 >          }
1220          }
1221        }
1222      }
1223 <    initFortranFF( &esm, &alphaVal, &errorOut );
1223 >    
1224 >    if (simParams_->haveElectrostaticScreeningMethod()) {
1225 >      std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1226 >      toUpper(myScreen);
1227 >      if (myScreen == "UNDAMPED") {
1228 >        sm = UNDAMPED;
1229 >      } else {
1230 >        if (myScreen == "DAMPED") {
1231 >          sm = DAMPED;
1232 >          if (!simParams_->haveDampingAlpha()) {
1233 >            // first set a cutoff dependent alpha value
1234 >            // we assume alpha depends linearly with rcut from 0 to 20.5 ang
1235 >            alphaVal = 0.5125 - rcut_* 0.025;
1236 >            // for values rcut > 20.5, alpha is zero
1237 >            if (alphaVal < 0) alphaVal = 0;
1238 >
1239 >            // throw warning
1240 >            sprintf( painCave.errMsg,
1241 >                     "SimInfo warning: dampingAlpha was not specified in the input file.\n"
1242 >                     "\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1243 >            painCave.isFatal = 0;
1244 >            simError();
1245 >          } else {
1246 >            alphaVal = simParams_->getDampingAlpha();
1247 >          }
1248 >          
1249 >        } else {
1250 >          // throw error        
1251 >          sprintf( painCave.errMsg,
1252 >                   "SimInfo error: Unknown electrostaticScreeningMethod.\n"
1253 >                   "\t(Input file specified %s .)\n"
1254 >                   "\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1255 >                   "or \"damped\".\n", myScreen.c_str() );
1256 >          painCave.isFatal = 1;
1257 >          simError();
1258 >        }
1259 >      }
1260 >    }
1261 >    
1262 >    // let's pass some summation method variables to fortran
1263 >    setElectrostaticSummationMethod( &esm );
1264 >    setFortranElectrostaticMethod( &esm );
1265 >    setScreeningMethod( &sm );
1266 >    setDampingAlpha( &alphaVal );
1267 >    setReactionFieldDielectric( &dielectric );
1268 >    initFortranFF( &errorOut );
1269    }
1270  
1271 +  void SimInfo::setupSwitchingFunction() {    
1272 +    int ft = CUBIC;
1273 +
1274 +    if (simParams_->haveSwitchingFunctionType()) {
1275 +      std::string funcType = simParams_->getSwitchingFunctionType();
1276 +      toUpper(funcType);
1277 +      if (funcType == "CUBIC") {
1278 +        ft = CUBIC;
1279 +      } else {
1280 +        if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1281 +          ft = FIFTH_ORDER_POLY;
1282 +        } else {
1283 +          // throw error        
1284 +          sprintf( painCave.errMsg,
1285 +                   "SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1286 +          painCave.isFatal = 1;
1287 +          simError();
1288 +        }          
1289 +      }
1290 +    }
1291 +
1292 +    // send switching function notification to switcheroo
1293 +    setFunctionType(&ft);
1294 +
1295 +  }
1296 +
1297 +  void SimInfo::setupAccumulateBoxDipole() {    
1298 +
1299 +    // we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1300 +    if ( simParams_->haveAccumulateBoxDipole() )
1301 +      if ( simParams_->getAccumulateBoxDipole() ) {
1302 +        setAccumulateBoxDipole();
1303 +        calcBoxDipole_ = true;
1304 +      }
1305 +
1306 +  }
1307 +
1308    void SimInfo::addProperty(GenericData* genData) {
1309      properties_.addProperty(genData);  
1310    }
# Line 958 | Line 1361 | namespace oopse {
1361      Molecule* mol;
1362  
1363      Vector3d comVel(0.0);
1364 <    double totalMass = 0.0;
1364 >    RealType totalMass = 0.0;
1365      
1366  
1367      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1368 <      double mass = mol->getMass();
1368 >      RealType mass = mol->getMass();
1369        totalMass += mass;
1370        comVel += mass * mol->getComVel();
1371      }  
1372  
1373   #ifdef IS_MPI
1374 <    double tmpMass = totalMass;
1374 >    RealType tmpMass = totalMass;
1375      Vector3d tmpComVel(comVel);    
1376 <    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1377 <    MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1376 >    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1377 >    MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1378   #endif
1379  
1380      comVel /= totalMass;
# Line 984 | Line 1387 | namespace oopse {
1387      Molecule* mol;
1388  
1389      Vector3d com(0.0);
1390 <    double totalMass = 0.0;
1390 >    RealType totalMass = 0.0;
1391      
1392      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1393 <      double mass = mol->getMass();
1393 >      RealType mass = mol->getMass();
1394        totalMass += mass;
1395        com += mass * mol->getCom();
1396      }  
1397  
1398   #ifdef IS_MPI
1399 <    double tmpMass = totalMass;
1399 >    RealType tmpMass = totalMass;
1400      Vector3d tmpCom(com);    
1401 <    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1402 <    MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1401 >    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1402 >    MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1403   #endif
1404  
1405      com /= totalMass;
# Line 1020 | Line 1423 | namespace oopse {
1423        Molecule* mol;
1424        
1425      
1426 <      double totalMass = 0.0;
1426 >      RealType totalMass = 0.0;
1427      
1428  
1429        for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1430 <         double mass = mol->getMass();
1430 >         RealType mass = mol->getMass();
1431           totalMass += mass;
1432           com += mass * mol->getCom();
1433           comVel += mass * mol->getComVel();          
1434        }  
1435        
1436   #ifdef IS_MPI
1437 <      double tmpMass = totalMass;
1437 >      RealType tmpMass = totalMass;
1438        Vector3d tmpCom(com);  
1439        Vector3d tmpComVel(comVel);
1440 <      MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1441 <      MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1442 <      MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1440 >      MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1441 >      MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1442 >      MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1443   #endif
1444        
1445        com /= totalMass;
# Line 1055 | Line 1458 | namespace oopse {
1458     void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1459        
1460  
1461 <      double xx = 0.0;
1462 <      double yy = 0.0;
1463 <      double zz = 0.0;
1464 <      double xy = 0.0;
1465 <      double xz = 0.0;
1466 <      double yz = 0.0;
1461 >      RealType xx = 0.0;
1462 >      RealType yy = 0.0;
1463 >      RealType zz = 0.0;
1464 >      RealType xy = 0.0;
1465 >      RealType xz = 0.0;
1466 >      RealType yz = 0.0;
1467        Vector3d com(0.0);
1468        Vector3d comVel(0.0);
1469        
# Line 1072 | Line 1475 | namespace oopse {
1475        Vector3d thisq(0.0);
1476        Vector3d thisv(0.0);
1477  
1478 <      double thisMass = 0.0;
1478 >      RealType thisMass = 0.0;
1479      
1480        
1481        
# Line 1110 | Line 1513 | namespace oopse {
1513   #ifdef IS_MPI
1514        Mat3x3d tmpI(inertiaTensor);
1515        Vector3d tmpAngMom;
1516 <      MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1517 <      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1516 >      MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1517 >      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1518   #endif
1519                
1520        return;
# Line 1132 | Line 1535 | namespace oopse {
1535        Vector3d thisr(0.0);
1536        Vector3d thisp(0.0);
1537        
1538 <      double thisMass;
1538 >      RealType thisMass;
1539        
1540        for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {        
1541          thisMass = mol->getMass();
# Line 1145 | Line 1548 | namespace oopse {
1548        
1549   #ifdef IS_MPI
1550        Vector3d tmpAngMom;
1551 <      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1551 >      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1552   #endif
1553        
1554        return angularMomentum;
1555     }
1556    
1557 <  
1557 >  StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1558 >    return IOIndexToIntegrableObject.at(index);
1559 >  }
1560 >  
1561 >  void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1562 >    IOIndexToIntegrableObject= v;
1563 >  }
1564 >
1565 >  /* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1566 >     based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1567 >     where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1568 >     V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1569 >  */
1570 >  void SimInfo::getGyrationalVolume(RealType &volume){
1571 >    Mat3x3d intTensor;
1572 >    RealType det;
1573 >    Vector3d dummyAngMom;
1574 >    RealType sysconstants;
1575 >    RealType geomCnst;
1576 >
1577 >    geomCnst = 3.0/2.0;
1578 >    /* Get the inertial tensor and angular momentum for free*/
1579 >    getInertiaTensor(intTensor,dummyAngMom);
1580 >    
1581 >    det = intTensor.determinant();
1582 >    sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1583 >    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1584 >    return;
1585 >  }
1586 >
1587 >  void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1588 >    Mat3x3d intTensor;
1589 >    Vector3d dummyAngMom;
1590 >    RealType sysconstants;
1591 >    RealType geomCnst;
1592 >
1593 >    geomCnst = 3.0/2.0;
1594 >    /* Get the inertial tensor and angular momentum for free*/
1595 >    getInertiaTensor(intTensor,dummyAngMom);
1596 >    
1597 >    detI = intTensor.determinant();
1598 >    sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1599 >    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1600 >    return;
1601 >  }
1602 > /*
1603 >   void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1604 >      assert( v.size() == nAtoms_ + nRigidBodies_);
1605 >      sdByGlobalIndex_ = v;
1606 >    }
1607 >
1608 >    StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1609 >      //assert(index < nAtoms_ + nRigidBodies_);
1610 >      return sdByGlobalIndex_.at(index);
1611 >    }  
1612 > */  
1613   }//end namespace oopse
1614  

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