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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 580 by chrisfen, Tue Aug 30 18:23:50 2005 UTC vs.
Revision 1129 by chrisfen, Fri Apr 20 18:15:48 2007 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) {
95 >    sman_(NULL), fortranInitialized_(false), calcBoxDipole_(false),
96 >    useAtomicVirial_(true) {
97  
78 –            
79 –      std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
98        MoleculeStamp* molStamp;
99        int nMolWithSameStamp;
100        int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
101 <      int nGroups = 0;          //total cutoff groups defined in meta-data file
101 >      int nGroups = 0;      //total cutoff groups defined in meta-data file
102        CutoffGroupStamp* cgStamp;    
103        RigidBodyStamp* rbStamp;
104        int nRigidAtoms = 0;
105 <    
106 <      for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
107 <        molStamp = i->first;
108 <        nMolWithSameStamp = i->second;
105 >      std::vector<Component*> components = simParams->getComponents();
106 >      
107 >      for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
108 >        molStamp = (*i)->getMoleculeStamp();
109 >        nMolWithSameStamp = (*i)->getNMol();
110          
111          addMoleculeStamp(molStamp, nMolWithSameStamp);
112  
113          //calculate atoms in molecules
114          nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;  
115  
97 –
116          //calculate atoms in cutoff groups
117          int nAtomsInGroups = 0;
118          int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
119          
120          for (int j=0; j < nCutoffGroupsInStamp; j++) {
121 <          cgStamp = molStamp->getCutoffGroup(j);
121 >          cgStamp = molStamp->getCutoffGroupStamp(j);
122            nAtomsInGroups += cgStamp->getNMembers();
123          }
124  
125          nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
126 +
127          nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;            
128  
129          //calculate atoms in rigid bodies
# Line 112 | Line 131 | namespace oopse {
131          int nRigidBodiesInStamp = molStamp->getNRigidBodies();
132          
133          for (int j=0; j < nRigidBodiesInStamp; j++) {
134 <          rbStamp = molStamp->getRigidBody(j);
134 >          rbStamp = molStamp->getRigidBodyStamp(j);
135            nAtomsInRigidBodies += rbStamp->getNMembers();
136          }
137  
# Line 121 | Line 140 | namespace oopse {
140          
141        }
142  
143 <      //every free atom (atom does not belong to cutoff groups) is a cutoff group
144 <      //therefore the total number of cutoff groups in the system is equal to
145 <      //the total number of atoms minus number of atoms belong to cutoff group defined in meta-data
146 <      //file plus the number of cutoff groups defined in meta-data file
143 >      //every free atom (atom does not belong to cutoff groups) is a cutoff
144 >      //group therefore the total number of cutoff groups in the system is
145 >      //equal to the total number of atoms minus number of atoms belong to
146 >      //cutoff group defined in meta-data file plus the number of cutoff
147 >      //groups defined in meta-data file
148        nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
149  
150 <      //every free atom (atom does not belong to rigid bodies) is an integrable object
151 <      //therefore the total number of  integrable objects in the system is equal to
152 <      //the total number of atoms minus number of atoms belong to  rigid body defined in meta-data
153 <      //file plus the number of  rigid bodies defined in meta-data file
154 <      nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_;
155 <
150 >      //every free atom (atom does not belong to rigid bodies) is an
151 >      //integrable object therefore the total number of integrable objects
152 >      //in the system is equal to the total number of atoms minus number of
153 >      //atoms belong to rigid body defined in meta-data file plus the number
154 >      //of rigid bodies defined in meta-data file
155 >      nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
156 >                                                + nGlobalRigidBodies_;
157 >  
158        nGlobalMols_ = molStampIds_.size();
159  
160   #ifdef IS_MPI    
# Line 148 | Line 170 | namespace oopse {
170      }
171      molecules_.clear();
172        
151 –    delete stamps_;
173      delete sman_;
174      delete simParams_;
175      delete forceField_;
# Line 255 | 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 273 | 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 335 | Line 365 | namespace oopse {
365      int b;
366      int c;
367      int d;
368 +
369 +    std::map<int, std::set<int> > atomGroups;
370 +
371 +    Molecule::RigidBodyIterator rbIter;
372 +    RigidBody* rb;
373 +    Molecule::IntegrableObjectIterator ii;
374 +    StuntDouble* integrableObject;
375      
376 +    for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
377 +           integrableObject = mol->nextIntegrableObject(ii)) {
378 +
379 +      if (integrableObject->isRigidBody()) {
380 +          rb = static_cast<RigidBody*>(integrableObject);
381 +          std::vector<Atom*> atoms = rb->getAtoms();
382 +          std::set<int> rigidAtoms;
383 +          for (int i = 0; i < atoms.size(); ++i) {
384 +            rigidAtoms.insert(atoms[i]->getGlobalIndex());
385 +          }
386 +          for (int i = 0; i < atoms.size(); ++i) {
387 +            atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
388 +          }      
389 +      } else {
390 +        std::set<int> oneAtomSet;
391 +        oneAtomSet.insert(integrableObject->getGlobalIndex());
392 +        atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));        
393 +      }
394 +    }  
395 +
396 +    
397 +    
398      for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
399        a = bond->getAtomA()->getGlobalIndex();
400        b = bond->getAtomB()->getGlobalIndex();        
# Line 346 | Line 405 | namespace oopse {
405        a = bend->getAtomA()->getGlobalIndex();
406        b = bend->getAtomB()->getGlobalIndex();        
407        c = bend->getAtomC()->getGlobalIndex();
408 +      std::set<int> rigidSetA = getRigidSet(a, atomGroups);
409 +      std::set<int> rigidSetB = getRigidSet(b, atomGroups);
410 +      std::set<int> rigidSetC = getRigidSet(c, atomGroups);
411  
412 <      exclude_.addPair(a, b);
413 <      exclude_.addPair(a, c);
414 <      exclude_.addPair(b, c);        
412 >      exclude_.addPairs(rigidSetA, rigidSetB);
413 >      exclude_.addPairs(rigidSetA, rigidSetC);
414 >      exclude_.addPairs(rigidSetB, rigidSetC);
415 >      
416 >      //exclude_.addPair(a, b);
417 >      //exclude_.addPair(a, c);
418 >      //exclude_.addPair(b, c);        
419      }
420  
421      for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
# Line 357 | Line 423 | namespace oopse {
423        b = torsion->getAtomB()->getGlobalIndex();        
424        c = torsion->getAtomC()->getGlobalIndex();        
425        d = torsion->getAtomD()->getGlobalIndex();        
426 +      std::set<int> rigidSetA = getRigidSet(a, atomGroups);
427 +      std::set<int> rigidSetB = getRigidSet(b, atomGroups);
428 +      std::set<int> rigidSetC = getRigidSet(c, atomGroups);
429 +      std::set<int> rigidSetD = getRigidSet(d, atomGroups);
430  
431 +      exclude_.addPairs(rigidSetA, rigidSetB);
432 +      exclude_.addPairs(rigidSetA, rigidSetC);
433 +      exclude_.addPairs(rigidSetA, rigidSetD);
434 +      exclude_.addPairs(rigidSetB, rigidSetC);
435 +      exclude_.addPairs(rigidSetB, rigidSetD);
436 +      exclude_.addPairs(rigidSetC, rigidSetD);
437 +
438 +      /*
439 +      exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
440 +      exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
441 +      exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
442 +      exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
443 +      exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
444 +      exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
445 +        
446 +      
447        exclude_.addPair(a, b);
448        exclude_.addPair(a, c);
449        exclude_.addPair(a, d);
450        exclude_.addPair(b, c);
451        exclude_.addPair(b, d);
452        exclude_.addPair(c, d);        
453 +      */
454      }
455  
369 –    Molecule::RigidBodyIterator rbIter;
370 –    RigidBody* rb;
456      for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
457        std::vector<Atom*> atoms = rb->getAtoms();
458        for (int i = 0; i < atoms.size() -1 ; ++i) {
# Line 392 | Line 477 | namespace oopse {
477      int b;
478      int c;
479      int d;
480 +
481 +    std::map<int, std::set<int> > atomGroups;
482 +
483 +    Molecule::RigidBodyIterator rbIter;
484 +    RigidBody* rb;
485 +    Molecule::IntegrableObjectIterator ii;
486 +    StuntDouble* integrableObject;
487      
488 +    for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
489 +           integrableObject = mol->nextIntegrableObject(ii)) {
490 +
491 +      if (integrableObject->isRigidBody()) {
492 +          rb = static_cast<RigidBody*>(integrableObject);
493 +          std::vector<Atom*> atoms = rb->getAtoms();
494 +          std::set<int> rigidAtoms;
495 +          for (int i = 0; i < atoms.size(); ++i) {
496 +            rigidAtoms.insert(atoms[i]->getGlobalIndex());
497 +          }
498 +          for (int i = 0; i < atoms.size(); ++i) {
499 +            atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
500 +          }      
501 +      } else {
502 +        std::set<int> oneAtomSet;
503 +        oneAtomSet.insert(integrableObject->getGlobalIndex());
504 +        atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));        
505 +      }
506 +    }  
507 +
508 +    
509      for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
510        a = bond->getAtomA()->getGlobalIndex();
511        b = bond->getAtomB()->getGlobalIndex();        
# Line 404 | Line 517 | namespace oopse {
517        b = bend->getAtomB()->getGlobalIndex();        
518        c = bend->getAtomC()->getGlobalIndex();
519  
520 <      exclude_.removePair(a, b);
521 <      exclude_.removePair(a, c);
522 <      exclude_.removePair(b, c);        
520 >      std::set<int> rigidSetA = getRigidSet(a, atomGroups);
521 >      std::set<int> rigidSetB = getRigidSet(b, atomGroups);
522 >      std::set<int> rigidSetC = getRigidSet(c, atomGroups);
523 >
524 >      exclude_.removePairs(rigidSetA, rigidSetB);
525 >      exclude_.removePairs(rigidSetA, rigidSetC);
526 >      exclude_.removePairs(rigidSetB, rigidSetC);
527 >      
528 >      //exclude_.removePair(a, b);
529 >      //exclude_.removePair(a, c);
530 >      //exclude_.removePair(b, c);        
531      }
532  
533      for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
# Line 415 | Line 536 | namespace oopse {
536        c = torsion->getAtomC()->getGlobalIndex();        
537        d = torsion->getAtomD()->getGlobalIndex();        
538  
539 +      std::set<int> rigidSetA = getRigidSet(a, atomGroups);
540 +      std::set<int> rigidSetB = getRigidSet(b, atomGroups);
541 +      std::set<int> rigidSetC = getRigidSet(c, atomGroups);
542 +      std::set<int> rigidSetD = getRigidSet(d, atomGroups);
543 +
544 +      exclude_.removePairs(rigidSetA, rigidSetB);
545 +      exclude_.removePairs(rigidSetA, rigidSetC);
546 +      exclude_.removePairs(rigidSetA, rigidSetD);
547 +      exclude_.removePairs(rigidSetB, rigidSetC);
548 +      exclude_.removePairs(rigidSetB, rigidSetD);
549 +      exclude_.removePairs(rigidSetC, rigidSetD);
550 +
551 +      /*
552 +      exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
553 +      exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
554 +      exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
555 +      exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
556 +      exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
557 +      exclude_.removePairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
558 +
559 +      
560        exclude_.removePair(a, b);
561        exclude_.removePair(a, c);
562        exclude_.removePair(a, d);
563        exclude_.removePair(b, c);
564        exclude_.removePair(b, d);
565        exclude_.removePair(c, d);        
566 +      */
567      }
568  
426 –    Molecule::RigidBodyIterator rbIter;
427 –    RigidBody* rb;
569      for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
570        std::vector<Atom*> atoms = rb->getAtoms();
571        for (int i = 0; i < atoms.size() -1 ; ++i) {
# Line 462 | Line 603 | namespace oopse {
603      //setup fortran force field
604      /** @deprecate */    
605      int isError = 0;
606 <    initFortranFF( &fInfo_.SIM_uses_RF, &fInfo_.SIM_uses_UW,
607 <                   &fInfo_.SIM_uses_DW, &isError );
606 >    
607 >    setupCutoff();
608 >    
609 >    setupElectrostaticSummationMethod( isError );
610 >    setupSwitchingFunction();
611 >    setupAccumulateBoxDipole();
612 >
613      if(isError){
614        sprintf( painCave.errMsg,
615                 "ForceField error: There was an error initializing the forceField in fortran.\n" );
616        painCave.isFatal = 1;
617        simError();
618      }
473 –  
474 –    
475 –    setupCutoff();
619  
620      calcNdf();
621      calcNdfRaw();
# Line 507 | Line 650 | namespace oopse {
650      int useLennardJones = 0;
651      int useElectrostatic = 0;
652      int useEAM = 0;
653 +    int useSC = 0;
654      int useCharge = 0;
655      int useDirectional = 0;
656      int useDipole = 0;
# Line 518 | Line 662 | namespace oopse {
662      int useDirectionalAtom = 0;    
663      int useElectrostatics = 0;
664      //usePBC and useRF are from simParams
665 <    int usePBC = simParams_->getPBC();
666 <    int useRF = simParams_->getUseRF();
667 <    int useUW = simParams_->getUseUndampedWolf();
668 <    int useDW = simParams_->getUseDampedWolf();
665 >    int usePBC = simParams_->getUsePeriodicBoundaryConditions();
666 >    int useRF;
667 >    int useSF;
668 >    int useSP;
669 >    int useBoxDipole;
670  
671 +    std::string myMethod;
672 +
673 +    // set the useRF logical
674 +    useRF = 0;
675 +    useSF = 0;
676 +    useSP = 0;
677 +
678 +
679 +    if (simParams_->haveElectrostaticSummationMethod()) {
680 +      std::string myMethod = simParams_->getElectrostaticSummationMethod();
681 +      toUpper(myMethod);
682 +      if (myMethod == "REACTION_FIELD"){
683 +        useRF = 1;
684 +      } else if (myMethod == "SHIFTED_FORCE"){
685 +        useSF = 1;
686 +      } else if (myMethod == "SHIFTED_POTENTIAL"){
687 +        useSP = 1;
688 +      }
689 +    }
690 +    
691 +    if (simParams_->haveAccumulateBoxDipole())
692 +      if (simParams_->getAccumulateBoxDipole())
693 +        useBoxDipole = 1;
694 +
695 +    useAtomicVirial_ = simParams_->getUseAtomicVirial();
696 +
697      //loop over all of the atom types
698      for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
699        useLennardJones |= (*i)->isLennardJones();
700        useElectrostatic |= (*i)->isElectrostatic();
701        useEAM |= (*i)->isEAM();
702 +      useSC |= (*i)->isSC();
703        useCharge |= (*i)->isCharge();
704        useDirectional |= (*i)->isDirectional();
705        useDipole |= (*i)->isDipole();
# Line 578 | Line 750 | namespace oopse {
750      temp = useEAM;
751      MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
752  
753 +    temp = useSC;
754 +    MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
755 +    
756      temp = useShape;
757      MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);  
758  
# Line 587 | Line 762 | namespace oopse {
762      temp = useRF;
763      MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
764  
765 <    temp = useUW;
766 <    MPI_Allreduce(&temp, &useUW, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);  
765 >    temp = useSF;
766 >    MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);  
767  
768 <    temp = useDW;
769 <    MPI_Allreduce(&temp, &useDW, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);  
770 <    
768 >    temp = useSP;
769 >    MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
770 >
771 >    temp = useBoxDipole;
772 >    MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
773 >
774 >    temp = useAtomicVirial_;
775 >    MPI_Allreduce(&temp, &useAtomicVirial_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
776 >
777   #endif
778  
779      fInfo_.SIM_uses_PBC = usePBC;    
# Line 605 | Line 786 | namespace oopse {
786      fInfo_.SIM_uses_StickyPower = useStickyPower;
787      fInfo_.SIM_uses_GayBerne = useGayBerne;
788      fInfo_.SIM_uses_EAM = useEAM;
789 +    fInfo_.SIM_uses_SC = useSC;
790      fInfo_.SIM_uses_Shapes = useShape;
791      fInfo_.SIM_uses_FLARB = useFLARB;
792      fInfo_.SIM_uses_RF = useRF;
793 <    fInfo_.SIM_uses_UW = useUW;
794 <    fInfo_.SIM_uses_DW = useDW;
795 <
796 <    if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) {
615 <
616 <      if (simParams_->haveDielectric()) {
617 <        fInfo_.dielect = simParams_->getDielectric();
618 <      } else {
619 <        sprintf(painCave.errMsg,
620 <                "SimSetup Error: No Dielectric constant was set.\n"
621 <                "\tYou are trying to use Reaction Field without"
622 <                "\tsetting a dielectric constant!\n");
623 <        painCave.isFatal = 1;
624 <        simError();
625 <      }
626 <        
627 <    } else {
628 <      fInfo_.dielect = 0.0;
629 <    }
630 <
793 >    fInfo_.SIM_uses_SF = useSF;
794 >    fInfo_.SIM_uses_SP = useSP;
795 >    fInfo_.SIM_uses_BoxDipole = useBoxDipole;
796 >    fInfo_.SIM_uses_AtomicVirial = useAtomicVirial_;
797    }
798  
799    void SimInfo::setupFortranSim() {
# Line 644 | Line 810 | namespace oopse {
810      }
811  
812      //calculate mass ratio of cutoff group
813 <    std::vector<double> mfact;
813 >    std::vector<RealType> mfact;
814      SimInfo::MoleculeIterator mi;
815      Molecule* mol;
816      Molecule::CutoffGroupIterator ci;
817      CutoffGroup* cg;
818      Molecule::AtomIterator ai;
819      Atom* atom;
820 <    double totalMass;
820 >    RealType totalMass;
821  
822      //to avoid memory reallocation, reserve enough space for mfact
823      mfact.reserve(getNCutoffGroups());
# Line 661 | Line 827 | namespace oopse {
827  
828          totalMass = cg->getMass();
829          for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
830 <          mfact.push_back(atom->getMass()/totalMass);
830 >          // Check for massless groups - set mfact to 1 if true
831 >          if (totalMass != 0)
832 >            mfact.push_back(atom->getMass()/totalMass);
833 >          else
834 >            mfact.push_back( 1.0 );
835          }
836  
837        }      
# Line 708 | Line 878 | namespace oopse {
878               "succesfully sent the simulation information to fortran.\n");
879      MPIcheckPoint();
880   #endif // is_mpi
881 +
882 +    // Setup number of neighbors in neighbor list if present
883 +    if (simParams_->haveNeighborListNeighbors()) {
884 +      int nlistNeighbors = simParams_->getNeighborListNeighbors();
885 +      setNeighbors(&nlistNeighbors);
886 +    }
887 +  
888 +
889    }
890  
891  
# Line 770 | Line 948 | namespace oopse {
948  
949   #endif
950  
951 <  double SimInfo::calcMaxCutoffRadius() {
951 >  void SimInfo::setupCutoff() {          
952 >    
953 >    ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
954  
955 +    // Check the cutoff policy
956 +    int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
957  
958 <    std::set<AtomType*> atomTypes;
959 <    std::set<AtomType*>::iterator i;
960 <    std::vector<double> cutoffRadius;
958 >    // Set LJ shifting bools to false
959 >    ljsp_ = false;
960 >    ljsf_ = false;
961  
962 <    //get the unique atom types
963 <    atomTypes = getUniqueAtomTypes();
964 <
965 <    //query the max cutoff radius among these atom types
966 <    for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
785 <      cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
962 >    std::string myPolicy;
963 >    if (forceFieldOptions_.haveCutoffPolicy()){
964 >      myPolicy = forceFieldOptions_.getCutoffPolicy();
965 >    }else if (simParams_->haveCutoffPolicy()) {
966 >      myPolicy = simParams_->getCutoffPolicy();
967      }
968  
969 <    double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
970 < #ifdef IS_MPI
971 <    //pick the max cutoff radius among the processors
972 < #endif
969 >    if (!myPolicy.empty()){
970 >      toUpper(myPolicy);
971 >      if (myPolicy == "MIX") {
972 >        cp = MIX_CUTOFF_POLICY;
973 >      } else {
974 >        if (myPolicy == "MAX") {
975 >          cp = MAX_CUTOFF_POLICY;
976 >        } else {
977 >          if (myPolicy == "TRADITIONAL") {            
978 >            cp = TRADITIONAL_CUTOFF_POLICY;
979 >          } else {
980 >            // throw error        
981 >            sprintf( painCave.errMsg,
982 >                     "SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
983 >            painCave.isFatal = 1;
984 >            simError();
985 >          }    
986 >        }          
987 >      }
988 >    }          
989 >    notifyFortranCutoffPolicy(&cp);
990  
991 <    return maxCutoffRadius;
992 <  }
993 <
994 <  void SimInfo::getCutoff(double& rcut, double& rsw) {
995 <    
996 <    if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
991 >    // Check the Skin Thickness for neighborlists
992 >    RealType skin;
993 >    if (simParams_->haveSkinThickness()) {
994 >      skin = simParams_->getSkinThickness();
995 >      notifyFortranSkinThickness(&skin);
996 >    }            
997          
998 <      if (!simParams_->haveRcut()){
999 <        sprintf(painCave.errMsg,
998 >    // Check if the cutoff was set explicitly:
999 >    if (simParams_->haveCutoffRadius()) {
1000 >      rcut_ = simParams_->getCutoffRadius();
1001 >      if (simParams_->haveSwitchingRadius()) {
1002 >        rsw_  = simParams_->getSwitchingRadius();
1003 >      } else {
1004 >        if (fInfo_.SIM_uses_Charges |
1005 >            fInfo_.SIM_uses_Dipoles |
1006 >            fInfo_.SIM_uses_RF) {
1007 >          
1008 >          rsw_ = 0.85 * rcut_;
1009 >          sprintf(painCave.errMsg,
1010 >                  "SimCreator Warning: No value was set for the switchingRadius.\n"
1011 >                  "\tOOPSE will use a default value of 85 percent of the cutoffRadius.\n"
1012 >                  "\tswitchingRadius = %f. for this simulation\n", rsw_);
1013 >        painCave.isFatal = 0;
1014 >        simError();
1015 >        } else {
1016 >          rsw_ = rcut_;
1017 >          sprintf(painCave.errMsg,
1018 >                  "SimCreator Warning: No value was set for the switchingRadius.\n"
1019 >                  "\tOOPSE will use the same value as the cutoffRadius.\n"
1020 >                  "\tswitchingRadius = %f. for this simulation\n", rsw_);
1021 >          painCave.isFatal = 0;
1022 >          simError();
1023 >        }
1024 >      }
1025 >
1026 >      if (simParams_->haveElectrostaticSummationMethod()) {
1027 >        std::string myMethod = simParams_->getElectrostaticSummationMethod();
1028 >        toUpper(myMethod);
1029 >        
1030 >        if (myMethod == "SHIFTED_POTENTIAL") {
1031 >          ljsp_ = true;
1032 >        } else if (myMethod == "SHIFTED_FORCE") {
1033 >          ljsf_ = true;
1034 >        }
1035 >      }
1036 >      notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1037 >      
1038 >    } else {
1039 >      
1040 >      // For electrostatic atoms, we'll assume a large safe value:
1041 >      if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
1042 >        sprintf(painCave.errMsg,
1043                  "SimCreator Warning: No value was set for the cutoffRadius.\n"
1044                  "\tOOPSE will use a default value of 15.0 angstroms"
1045                  "\tfor the cutoffRadius.\n");
1046 <        painCave.isFatal = 0;
1046 >        painCave.isFatal = 0;
1047          simError();
1048 <        rcut = 15.0;
1049 <      } else{
1050 <        rcut = simParams_->getRcut();
1051 <      }
1048 >        rcut_ = 15.0;
1049 >      
1050 >        if (simParams_->haveElectrostaticSummationMethod()) {
1051 >          std::string myMethod = simParams_->getElectrostaticSummationMethod();
1052 >          toUpper(myMethod);
1053 >      
1054 >      // For the time being, we're tethering the LJ shifted behavior to the
1055 >      // electrostaticSummationMethod keyword options
1056 >          if (myMethod == "SHIFTED_POTENTIAL") {
1057 >            ljsp_ = true;
1058 >          } else if (myMethod == "SHIFTED_FORCE") {
1059 >            ljsf_ = true;
1060 >          }
1061 >          if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1062 >            if (simParams_->haveSwitchingRadius()){
1063 >              sprintf(painCave.errMsg,
1064 >                      "SimInfo Warning: A value was set for the switchingRadius\n"
1065 >                      "\teven though the electrostaticSummationMethod was\n"
1066 >                      "\tset to %s\n", myMethod.c_str());
1067 >              painCave.isFatal = 1;
1068 >              simError();            
1069 >            }
1070 >          }
1071 >        }
1072 >      
1073 >        if (simParams_->haveSwitchingRadius()){
1074 >          rsw_ = simParams_->getSwitchingRadius();
1075 >        } else {        
1076 >          sprintf(painCave.errMsg,
1077 >                  "SimCreator Warning: No value was set for switchingRadius.\n"
1078 >                  "\tOOPSE will use a default value of\n"
1079 >                  "\t0.85 * cutoffRadius for the switchingRadius\n");
1080 >          painCave.isFatal = 0;
1081 >          simError();
1082 >          rsw_ = 0.85 * rcut_;
1083 >        }
1084  
1085 <      if (!simParams_->haveRsw()){
813 <        sprintf(painCave.errMsg,
814 <                "SimCreator Warning: No value was set for switchingRadius.\n"
815 <                "\tOOPSE will use a default value of\n"
816 <                "\t0.95 * cutoffRadius for the switchingRadius\n");
817 <        painCave.isFatal = 0;
818 <        simError();
819 <        rsw = 0.95 * rcut;
820 <      } else{
821 <        rsw = simParams_->getRsw();
822 <      }
1085 >        notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1086  
824 –    } else {
825 –      // if charge, dipole or reaction field is not used and the cutofff radius is not specified in
826 –      //meta-data file, the maximum cutoff radius calculated from forcefiled will be used
827 –        
828 –      if (simParams_->haveRcut()) {
829 –        rcut = simParams_->getRcut();
1087        } else {
1088 <        //set cutoff radius to the maximum cutoff radius based on atom types in the whole system
1089 <        rcut = calcMaxCutoffRadius();
1088 >        // We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1089 >        // We'll punt and let fortran figure out the cutoffs later.
1090 >        
1091 >        notifyFortranYouAreOnYourOwn();
1092 >
1093        }
1094 +    }
1095 +  }
1096  
1097 <      if (simParams_->haveRsw()) {
1098 <        rsw  = simParams_->getRsw();
1097 >  void SimInfo::setupElectrostaticSummationMethod( int isError ) {    
1098 >    
1099 >    int errorOut;
1100 >    int esm =  NONE;
1101 >    int sm = UNDAMPED;
1102 >    RealType alphaVal;
1103 >    RealType dielectric;
1104 >    
1105 >    errorOut = isError;
1106 >
1107 >    if (simParams_->haveElectrostaticSummationMethod()) {
1108 >      std::string myMethod = simParams_->getElectrostaticSummationMethod();
1109 >      toUpper(myMethod);
1110 >      if (myMethod == "NONE") {
1111 >        esm = NONE;
1112        } else {
1113 <        rsw = rcut;
1113 >        if (myMethod == "SWITCHING_FUNCTION") {
1114 >          esm = SWITCHING_FUNCTION;
1115 >        } else {
1116 >          if (myMethod == "SHIFTED_POTENTIAL") {
1117 >            esm = SHIFTED_POTENTIAL;
1118 >          } else {
1119 >            if (myMethod == "SHIFTED_FORCE") {            
1120 >              esm = SHIFTED_FORCE;
1121 >            } else {
1122 >              if (myMethod == "REACTION_FIELD") {
1123 >                esm = REACTION_FIELD;
1124 >                dielectric = simParams_->getDielectric();
1125 >                if (!simParams_->haveDielectric()) {
1126 >                  // throw warning
1127 >                  sprintf( painCave.errMsg,
1128 >                           "SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
1129 >                           "\tA default value of %f will be used for the dielectric.\n", dielectric);
1130 >                  painCave.isFatal = 0;
1131 >                  simError();
1132 >                }
1133 >              } else {
1134 >                // throw error        
1135 >                sprintf( painCave.errMsg,
1136 >                         "SimInfo error: Unknown electrostaticSummationMethod.\n"
1137 >                         "\t(Input file specified %s .)\n"
1138 >                         "\telectrostaticSummationMethod must be one of: \"none\",\n"
1139 >                         "\t\"shifted_potential\", \"shifted_force\", or \n"
1140 >                         "\t\"reaction_field\".\n", myMethod.c_str() );
1141 >                painCave.isFatal = 1;
1142 >                simError();
1143 >              }    
1144 >            }          
1145 >          }
1146 >        }
1147        }
1148 +    }
1149      
1150 +    if (simParams_->haveElectrostaticScreeningMethod()) {
1151 +      std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1152 +      toUpper(myScreen);
1153 +      if (myScreen == "UNDAMPED") {
1154 +        sm = UNDAMPED;
1155 +      } else {
1156 +        if (myScreen == "DAMPED") {
1157 +          sm = DAMPED;
1158 +          if (!simParams_->haveDampingAlpha()) {
1159 +            // first set a cutoff dependent alpha value
1160 +            // we assume alpha depends linearly with rcut from 0 to 20.5 ang
1161 +            alphaVal = 0.5125 - rcut_* 0.025;
1162 +            // for values rcut > 20.5, alpha is zero
1163 +            if (alphaVal < 0) alphaVal = 0;
1164 +
1165 +            // throw warning
1166 +            sprintf( painCave.errMsg,
1167 +                     "SimInfo warning: dampingAlpha was not specified in the input file.\n"
1168 +                     "\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1169 +            painCave.isFatal = 0;
1170 +            simError();
1171 +          } else {
1172 +            alphaVal = simParams_->getDampingAlpha();
1173 +          }
1174 +          
1175 +        } else {
1176 +          // throw error        
1177 +          sprintf( painCave.errMsg,
1178 +                   "SimInfo error: Unknown electrostaticScreeningMethod.\n"
1179 +                   "\t(Input file specified %s .)\n"
1180 +                   "\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1181 +                   "or \"damped\".\n", myScreen.c_str() );
1182 +          painCave.isFatal = 1;
1183 +          simError();
1184 +        }
1185 +      }
1186      }
1187 +    
1188 +    // let's pass some summation method variables to fortran
1189 +    setElectrostaticSummationMethod( &esm );
1190 +    setFortranElectrostaticMethod( &esm );
1191 +    setScreeningMethod( &sm );
1192 +    setDampingAlpha( &alphaVal );
1193 +    setReactionFieldDielectric( &dielectric );
1194 +    initFortranFF( &errorOut );
1195    }
1196  
1197 <  void SimInfo::setupCutoff() {
1198 <    getCutoff(rcut_, rsw_);    
846 <    double rnblist = rcut_ + 1; // skin of neighbor list
1197 >  void SimInfo::setupSwitchingFunction() {    
1198 >    int ft = CUBIC;
1199  
1200 <    //Pass these cutoff radius etc. to fortran. This function should be called once and only once
1201 <    notifyFortranCutoffs(&rcut_, &rsw_, &rnblist);
1200 >    if (simParams_->haveSwitchingFunctionType()) {
1201 >      std::string funcType = simParams_->getSwitchingFunctionType();
1202 >      toUpper(funcType);
1203 >      if (funcType == "CUBIC") {
1204 >        ft = CUBIC;
1205 >      } else {
1206 >        if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1207 >          ft = FIFTH_ORDER_POLY;
1208 >        } else {
1209 >          // throw error        
1210 >          sprintf( painCave.errMsg,
1211 >                   "SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1212 >          painCave.isFatal = 1;
1213 >          simError();
1214 >        }          
1215 >      }
1216 >    }
1217 >
1218 >    // send switching function notification to switcheroo
1219 >    setFunctionType(&ft);
1220 >
1221    }
1222  
1223 +  void SimInfo::setupAccumulateBoxDipole() {    
1224 +
1225 +    // we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1226 +    if ( simParams_->haveAccumulateBoxDipole() )
1227 +      if ( simParams_->getAccumulateBoxDipole() ) {
1228 +        setAccumulateBoxDipole();
1229 +        calcBoxDipole_ = true;
1230 +      }
1231 +
1232 +  }
1233 +
1234    void SimInfo::addProperty(GenericData* genData) {
1235      properties_.addProperty(genData);  
1236    }
# Line 905 | Line 1287 | namespace oopse {
1287      Molecule* mol;
1288  
1289      Vector3d comVel(0.0);
1290 <    double totalMass = 0.0;
1290 >    RealType totalMass = 0.0;
1291      
1292  
1293      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1294 <      double mass = mol->getMass();
1294 >      RealType mass = mol->getMass();
1295        totalMass += mass;
1296        comVel += mass * mol->getComVel();
1297      }  
1298  
1299   #ifdef IS_MPI
1300 <    double tmpMass = totalMass;
1300 >    RealType tmpMass = totalMass;
1301      Vector3d tmpComVel(comVel);    
1302 <    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1303 <    MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1302 >    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1303 >    MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1304   #endif
1305  
1306      comVel /= totalMass;
# Line 931 | Line 1313 | namespace oopse {
1313      Molecule* mol;
1314  
1315      Vector3d com(0.0);
1316 <    double totalMass = 0.0;
1316 >    RealType totalMass = 0.0;
1317      
1318      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1319 <      double mass = mol->getMass();
1319 >      RealType mass = mol->getMass();
1320        totalMass += mass;
1321        com += mass * mol->getCom();
1322      }  
1323  
1324   #ifdef IS_MPI
1325 <    double tmpMass = totalMass;
1325 >    RealType tmpMass = totalMass;
1326      Vector3d tmpCom(com);    
1327 <    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1328 <    MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1327 >    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1328 >    MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1329   #endif
1330  
1331      com /= totalMass;
# Line 967 | Line 1349 | namespace oopse {
1349        Molecule* mol;
1350        
1351      
1352 <      double totalMass = 0.0;
1352 >      RealType totalMass = 0.0;
1353      
1354  
1355        for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1356 <         double mass = mol->getMass();
1356 >         RealType mass = mol->getMass();
1357           totalMass += mass;
1358           com += mass * mol->getCom();
1359           comVel += mass * mol->getComVel();          
1360        }  
1361        
1362   #ifdef IS_MPI
1363 <      double tmpMass = totalMass;
1363 >      RealType tmpMass = totalMass;
1364        Vector3d tmpCom(com);  
1365        Vector3d tmpComVel(comVel);
1366 <      MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1367 <      MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1368 <      MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1366 >      MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1367 >      MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1368 >      MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1369   #endif
1370        
1371        com /= totalMass;
# Line 1002 | Line 1384 | namespace oopse {
1384     void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1385        
1386  
1387 <      double xx = 0.0;
1388 <      double yy = 0.0;
1389 <      double zz = 0.0;
1390 <      double xy = 0.0;
1391 <      double xz = 0.0;
1392 <      double yz = 0.0;
1387 >      RealType xx = 0.0;
1388 >      RealType yy = 0.0;
1389 >      RealType zz = 0.0;
1390 >      RealType xy = 0.0;
1391 >      RealType xz = 0.0;
1392 >      RealType yz = 0.0;
1393        Vector3d com(0.0);
1394        Vector3d comVel(0.0);
1395        
# Line 1019 | Line 1401 | namespace oopse {
1401        Vector3d thisq(0.0);
1402        Vector3d thisv(0.0);
1403  
1404 <      double thisMass = 0.0;
1404 >      RealType thisMass = 0.0;
1405      
1406        
1407        
# Line 1057 | Line 1439 | namespace oopse {
1439   #ifdef IS_MPI
1440        Mat3x3d tmpI(inertiaTensor);
1441        Vector3d tmpAngMom;
1442 <      MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1443 <      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1442 >      MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1443 >      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1444   #endif
1445                
1446        return;
# Line 1079 | Line 1461 | namespace oopse {
1461        Vector3d thisr(0.0);
1462        Vector3d thisp(0.0);
1463        
1464 <      double thisMass;
1464 >      RealType thisMass;
1465        
1466        for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {        
1467          thisMass = mol->getMass();
# Line 1092 | Line 1474 | namespace oopse {
1474        
1475   #ifdef IS_MPI
1476        Vector3d tmpAngMom;
1477 <      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1477 >      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1478   #endif
1479        
1480        return angularMomentum;
1481     }
1482    
1483 <  
1483 >  StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1484 >    return IOIndexToIntegrableObject.at(index);
1485 >  }
1486 >  
1487 >  void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1488 >    IOIndexToIntegrableObject= v;
1489 >  }
1490 >
1491 >  /* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1492 >     based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1493 >     where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1494 >     V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1495 >  */
1496 >  void SimInfo::getGyrationalVolume(RealType &volume){
1497 >    Mat3x3d intTensor;
1498 >    RealType det;
1499 >    Vector3d dummyAngMom;
1500 >    RealType sysconstants;
1501 >    RealType geomCnst;
1502 >
1503 >    geomCnst = 3.0/2.0;
1504 >    /* Get the inertial tensor and angular momentum for free*/
1505 >    getInertiaTensor(intTensor,dummyAngMom);
1506 >    
1507 >    det = intTensor.determinant();
1508 >    sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1509 >    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1510 >    return;
1511 >  }
1512 >
1513 >  void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1514 >    Mat3x3d intTensor;
1515 >    Vector3d dummyAngMom;
1516 >    RealType sysconstants;
1517 >    RealType geomCnst;
1518 >
1519 >    geomCnst = 3.0/2.0;
1520 >    /* Get the inertial tensor and angular momentum for free*/
1521 >    getInertiaTensor(intTensor,dummyAngMom);
1522 >    
1523 >    detI = intTensor.determinant();
1524 >    sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1525 >    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1526 >    return;
1527 >  }
1528 > /*
1529 >   void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1530 >      assert( v.size() == nAtoms_ + nRigidBodies_);
1531 >      sdByGlobalIndex_ = v;
1532 >    }
1533 >
1534 >    StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1535 >      //assert(index < nAtoms_ + nRigidBodies_);
1536 >      return sdByGlobalIndex_.at(index);
1537 >    }  
1538 > */  
1539   }//end namespace oopse
1540  

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