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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 604 by chrisfen, Fri Sep 16 19:00:12 2005 UTC vs.
Revision 1241 by gezelter, Fri Apr 25 15:14:47 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"
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  
80 –            
81 –      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  
99 –
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 114 | 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 123 | 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();
139 –
140 – #ifdef IS_MPI    
159        molToProcMap_.resize(nGlobalMols_);
142 – #endif
143 –
160      }
161  
162    SimInfo::~SimInfo() {
# Line 150 | Line 166 | namespace oopse {
166      }
167      molecules_.clear();
168        
153 –    delete stamps_;
169      delete sman_;
170      delete simParams_;
171      delete forceField_;
# Line 257 | Line 272 | namespace oopse {
272            }
273          }
274              
275 <      }//end for (integrableObject)
276 <    }// end for (mol)
275 >      }
276 >    }
277      
278      // n_constraints is local, so subtract them on each processor
279      ndf_local -= nConstraints_;
# Line 275 | Line 290 | namespace oopse {
290  
291    }
292  
293 +  int SimInfo::getFdf() {
294 + #ifdef IS_MPI
295 +    MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
296 + #else
297 +    fdf_ = fdf_local;
298 + #endif
299 +    return fdf_;
300 +  }
301 +    
302    void SimInfo::calcNdfRaw() {
303      int ndfRaw_local;
304  
# Line 337 | Line 361 | namespace oopse {
361      int b;
362      int c;
363      int d;
364 +
365 +    std::map<int, std::set<int> > atomGroups;
366 +
367 +    Molecule::RigidBodyIterator rbIter;
368 +    RigidBody* rb;
369 +    Molecule::IntegrableObjectIterator ii;
370 +    StuntDouble* integrableObject;
371      
372 +    for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
373 +           integrableObject = mol->nextIntegrableObject(ii)) {
374 +
375 +      if (integrableObject->isRigidBody()) {
376 +          rb = static_cast<RigidBody*>(integrableObject);
377 +          std::vector<Atom*> atoms = rb->getAtoms();
378 +          std::set<int> rigidAtoms;
379 +          for (int i = 0; i < atoms.size(); ++i) {
380 +            rigidAtoms.insert(atoms[i]->getGlobalIndex());
381 +          }
382 +          for (int i = 0; i < atoms.size(); ++i) {
383 +            atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
384 +          }      
385 +      } else {
386 +        std::set<int> oneAtomSet;
387 +        oneAtomSet.insert(integrableObject->getGlobalIndex());
388 +        atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));        
389 +      }
390 +    }  
391 +
392 +    
393 +    
394      for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
395        a = bond->getAtomA()->getGlobalIndex();
396        b = bond->getAtomB()->getGlobalIndex();        
# Line 348 | Line 401 | namespace oopse {
401        a = bend->getAtomA()->getGlobalIndex();
402        b = bend->getAtomB()->getGlobalIndex();        
403        c = bend->getAtomC()->getGlobalIndex();
404 +      std::set<int> rigidSetA = getRigidSet(a, atomGroups);
405 +      std::set<int> rigidSetB = getRigidSet(b, atomGroups);
406 +      std::set<int> rigidSetC = getRigidSet(c, atomGroups);
407  
408 <      exclude_.addPair(a, b);
409 <      exclude_.addPair(a, c);
410 <      exclude_.addPair(b, c);        
408 >      exclude_.addPairs(rigidSetA, rigidSetB);
409 >      exclude_.addPairs(rigidSetA, rigidSetC);
410 >      exclude_.addPairs(rigidSetB, rigidSetC);
411 >      
412 >      //exclude_.addPair(a, b);
413 >      //exclude_.addPair(a, c);
414 >      //exclude_.addPair(b, c);        
415      }
416  
417      for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
# Line 359 | Line 419 | namespace oopse {
419        b = torsion->getAtomB()->getGlobalIndex();        
420        c = torsion->getAtomC()->getGlobalIndex();        
421        d = torsion->getAtomD()->getGlobalIndex();        
422 +      std::set<int> rigidSetA = getRigidSet(a, atomGroups);
423 +      std::set<int> rigidSetB = getRigidSet(b, atomGroups);
424 +      std::set<int> rigidSetC = getRigidSet(c, atomGroups);
425 +      std::set<int> rigidSetD = getRigidSet(d, atomGroups);
426  
427 +      exclude_.addPairs(rigidSetA, rigidSetB);
428 +      exclude_.addPairs(rigidSetA, rigidSetC);
429 +      exclude_.addPairs(rigidSetA, rigidSetD);
430 +      exclude_.addPairs(rigidSetB, rigidSetC);
431 +      exclude_.addPairs(rigidSetB, rigidSetD);
432 +      exclude_.addPairs(rigidSetC, rigidSetD);
433 +
434 +      /*
435 +      exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
436 +      exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
437 +      exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
438 +      exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
439 +      exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
440 +      exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
441 +        
442 +      
443        exclude_.addPair(a, b);
444        exclude_.addPair(a, c);
445        exclude_.addPair(a, d);
446        exclude_.addPair(b, c);
447        exclude_.addPair(b, d);
448        exclude_.addPair(c, d);        
449 +      */
450      }
451  
371 –    Molecule::RigidBodyIterator rbIter;
372 –    RigidBody* rb;
452      for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
453        std::vector<Atom*> atoms = rb->getAtoms();
454        for (int i = 0; i < atoms.size() -1 ; ++i) {
# Line 394 | Line 473 | namespace oopse {
473      int b;
474      int c;
475      int d;
476 +
477 +    std::map<int, std::set<int> > atomGroups;
478 +
479 +    Molecule::RigidBodyIterator rbIter;
480 +    RigidBody* rb;
481 +    Molecule::IntegrableObjectIterator ii;
482 +    StuntDouble* integrableObject;
483      
484 +    for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
485 +           integrableObject = mol->nextIntegrableObject(ii)) {
486 +
487 +      if (integrableObject->isRigidBody()) {
488 +          rb = static_cast<RigidBody*>(integrableObject);
489 +          std::vector<Atom*> atoms = rb->getAtoms();
490 +          std::set<int> rigidAtoms;
491 +          for (int i = 0; i < atoms.size(); ++i) {
492 +            rigidAtoms.insert(atoms[i]->getGlobalIndex());
493 +          }
494 +          for (int i = 0; i < atoms.size(); ++i) {
495 +            atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
496 +          }      
497 +      } else {
498 +        std::set<int> oneAtomSet;
499 +        oneAtomSet.insert(integrableObject->getGlobalIndex());
500 +        atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));        
501 +      }
502 +    }  
503 +
504 +    
505      for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
506        a = bond->getAtomA()->getGlobalIndex();
507        b = bond->getAtomB()->getGlobalIndex();        
# Line 406 | Line 513 | namespace oopse {
513        b = bend->getAtomB()->getGlobalIndex();        
514        c = bend->getAtomC()->getGlobalIndex();
515  
516 <      exclude_.removePair(a, b);
517 <      exclude_.removePair(a, c);
518 <      exclude_.removePair(b, c);        
516 >      std::set<int> rigidSetA = getRigidSet(a, atomGroups);
517 >      std::set<int> rigidSetB = getRigidSet(b, atomGroups);
518 >      std::set<int> rigidSetC = getRigidSet(c, atomGroups);
519 >
520 >      exclude_.removePairs(rigidSetA, rigidSetB);
521 >      exclude_.removePairs(rigidSetA, rigidSetC);
522 >      exclude_.removePairs(rigidSetB, rigidSetC);
523 >      
524 >      //exclude_.removePair(a, b);
525 >      //exclude_.removePair(a, c);
526 >      //exclude_.removePair(b, c);        
527      }
528  
529      for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
# Line 416 | Line 531 | namespace oopse {
531        b = torsion->getAtomB()->getGlobalIndex();        
532        c = torsion->getAtomC()->getGlobalIndex();        
533        d = torsion->getAtomD()->getGlobalIndex();        
534 +
535 +      std::set<int> rigidSetA = getRigidSet(a, atomGroups);
536 +      std::set<int> rigidSetB = getRigidSet(b, atomGroups);
537 +      std::set<int> rigidSetC = getRigidSet(c, atomGroups);
538 +      std::set<int> rigidSetD = getRigidSet(d, atomGroups);
539 +
540 +      exclude_.removePairs(rigidSetA, rigidSetB);
541 +      exclude_.removePairs(rigidSetA, rigidSetC);
542 +      exclude_.removePairs(rigidSetA, rigidSetD);
543 +      exclude_.removePairs(rigidSetB, rigidSetC);
544 +      exclude_.removePairs(rigidSetB, rigidSetD);
545 +      exclude_.removePairs(rigidSetC, rigidSetD);
546 +
547 +      /*
548 +      exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
549 +      exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
550 +      exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
551 +      exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
552 +      exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
553 +      exclude_.removePairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
554  
555 +      
556        exclude_.removePair(a, b);
557        exclude_.removePair(a, c);
558        exclude_.removePair(a, d);
559        exclude_.removePair(b, c);
560        exclude_.removePair(b, d);
561        exclude_.removePair(c, d);        
562 +      */
563      }
564  
428 –    Molecule::RigidBodyIterator rbIter;
429 –    RigidBody* rb;
565      for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
566        std::vector<Atom*> atoms = rb->getAtoms();
567        for (int i = 0; i < atoms.size() -1 ; ++i) {
# Line 465 | Line 600 | namespace oopse {
600      /** @deprecate */    
601      int isError = 0;
602      
603 +    setupCutoff();
604 +    
605      setupElectrostaticSummationMethod( isError );
606 +    setupSwitchingFunction();
607 +    setupAccumulateBoxDipole();
608  
609      if(isError){
610        sprintf( painCave.errMsg,
# Line 473 | Line 612 | namespace oopse {
612        painCave.isFatal = 1;
613        simError();
614      }
476 –  
477 –    
478 –    setupCutoff();
615  
616      calcNdf();
617      calcNdfRaw();
# Line 510 | Line 646 | namespace oopse {
646      int useLennardJones = 0;
647      int useElectrostatic = 0;
648      int useEAM = 0;
649 +    int useSC = 0;
650      int useCharge = 0;
651      int useDirectional = 0;
652      int useDipole = 0;
# Line 521 | Line 658 | namespace oopse {
658      int useDirectionalAtom = 0;    
659      int useElectrostatics = 0;
660      //usePBC and useRF are from simParams
661 <    int usePBC = simParams_->getPBC();
661 >    int usePBC = simParams_->getUsePeriodicBoundaryConditions();
662 >    int useRF;
663 >    int useSF;
664 >    int useSP;
665 >    int useBoxDipole;
666  
667 +    std::string myMethod;
668 +
669 +    // set the useRF logical
670 +    useRF = 0;
671 +    useSF = 0;
672 +    useSP = 0;
673 +
674 +
675 +    if (simParams_->haveElectrostaticSummationMethod()) {
676 +      std::string myMethod = simParams_->getElectrostaticSummationMethod();
677 +      toUpper(myMethod);
678 +      if (myMethod == "REACTION_FIELD"){
679 +        useRF = 1;
680 +      } else if (myMethod == "SHIFTED_FORCE"){
681 +        useSF = 1;
682 +      } else if (myMethod == "SHIFTED_POTENTIAL"){
683 +        useSP = 1;
684 +      }
685 +    }
686 +    
687 +    if (simParams_->haveAccumulateBoxDipole())
688 +      if (simParams_->getAccumulateBoxDipole())
689 +        useBoxDipole = 1;
690 +
691 +    useAtomicVirial_ = simParams_->getUseAtomicVirial();
692 +
693      //loop over all of the atom types
694      for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
695        useLennardJones |= (*i)->isLennardJones();
696        useElectrostatic |= (*i)->isElectrostatic();
697        useEAM |= (*i)->isEAM();
698 +      useSC |= (*i)->isSC();
699        useCharge |= (*i)->isCharge();
700        useDirectional |= (*i)->isDirectional();
701        useDipole |= (*i)->isDipole();
# Line 578 | Line 746 | namespace oopse {
746      temp = useEAM;
747      MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
748  
749 +    temp = useSC;
750 +    MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
751 +    
752      temp = useShape;
753      MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);  
754  
755      temp = useFLARB;
756      MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
757  
758 +    temp = useRF;
759 +    MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
760 +
761 +    temp = useSF;
762 +    MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);  
763 +
764 +    temp = useSP;
765 +    MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
766 +
767 +    temp = useBoxDipole;
768 +    MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
769 +
770 +    temp = useAtomicVirial_;
771 +    MPI_Allreduce(&temp, &useAtomicVirial_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
772 +
773   #endif
774  
775      fInfo_.SIM_uses_PBC = usePBC;    
# Line 596 | Line 782 | namespace oopse {
782      fInfo_.SIM_uses_StickyPower = useStickyPower;
783      fInfo_.SIM_uses_GayBerne = useGayBerne;
784      fInfo_.SIM_uses_EAM = useEAM;
785 +    fInfo_.SIM_uses_SC = useSC;
786      fInfo_.SIM_uses_Shapes = useShape;
787      fInfo_.SIM_uses_FLARB = useFLARB;
788 <
789 <    if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) {
790 <
791 <      if (simParams_->haveDielectric()) {
792 <        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 <
788 >    fInfo_.SIM_uses_RF = useRF;
789 >    fInfo_.SIM_uses_SF = useSF;
790 >    fInfo_.SIM_uses_SP = useSP;
791 >    fInfo_.SIM_uses_BoxDipole = useBoxDipole;
792 >    fInfo_.SIM_uses_AtomicVirial = useAtomicVirial_;
793    }
794  
795    void SimInfo::setupFortranSim() {
# Line 632 | Line 806 | namespace oopse {
806      }
807  
808      //calculate mass ratio of cutoff group
809 <    std::vector<double> mfact;
809 >    std::vector<RealType> mfact;
810      SimInfo::MoleculeIterator mi;
811      Molecule* mol;
812      Molecule::CutoffGroupIterator ci;
813      CutoffGroup* cg;
814      Molecule::AtomIterator ai;
815      Atom* atom;
816 <    double totalMass;
816 >    RealType totalMass;
817  
818      //to avoid memory reallocation, reserve enough space for mfact
819      mfact.reserve(getNCutoffGroups());
# Line 649 | Line 823 | namespace oopse {
823  
824          totalMass = cg->getMass();
825          for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
826 <          mfact.push_back(atom->getMass()/totalMass);
826 >          // Check for massless groups - set mfact to 1 if true
827 >          if (totalMass != 0)
828 >            mfact.push_back(atom->getMass()/totalMass);
829 >          else
830 >            mfact.push_back( 1.0 );
831          }
832  
833        }      
# Line 678 | Line 856 | namespace oopse {
856      int nGlobalExcludes = 0;
857      int* globalExcludes = NULL;
858      int* excludeList = exclude_.getExcludeList();
859 <    setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
860 <                   &nGlobalExcludes, globalExcludes, &molMembershipArray[0],
861 <                   &mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
862 <
859 >    setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
860 >                   &nExclude, excludeList , &nGlobalExcludes, globalExcludes,
861 >                   &molMembershipArray[0], &mfact[0], &nCutoffGroups_,
862 >                   &fortranGlobalGroupMembership[0], &isError);
863 >    
864      if( isError ){
865 <
865 >      
866        sprintf( painCave.errMsg,
867                 "There was an error setting the simulation information in fortran.\n" );
868        painCave.isFatal = 1;
869        painCave.severity = OOPSE_ERROR;
870        simError();
871      }
872 <
873 < #ifdef IS_MPI
872 >    
873 >    
874      sprintf( checkPointMsg,
875               "succesfully sent the simulation information to fortran.\n");
876 <    MPIcheckPoint();
877 < #endif // is_mpi
876 >    
877 >    errorCheckPoint();
878 >    
879 >    // Setup number of neighbors in neighbor list if present
880 >    if (simParams_->haveNeighborListNeighbors()) {
881 >      int nlistNeighbors = simParams_->getNeighborListNeighbors();
882 >      setNeighbors(&nlistNeighbors);
883 >    }
884 >  
885 >
886    }
887  
888  
702 – #ifdef IS_MPI
889    void SimInfo::setupFortranParallel() {
890 <    
890 > #ifdef IS_MPI    
891      //SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
892      std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
893      std::vector<int> localToGlobalCutoffGroupIndex;
# Line 751 | Line 937 | namespace oopse {
937      }
938  
939      sprintf(checkPointMsg, " mpiRefresh successful.\n");
940 <    MPIcheckPoint();
940 >    errorCheckPoint();
941  
942 <
942 > #endif
943    }
944  
945 < #endif
945 >  void SimInfo::setupCutoff() {          
946 >    
947 >    ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
948  
949 <  double SimInfo::calcMaxCutoffRadius() {
949 >    // Check the cutoff policy
950 >    int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
951  
952 +    // Set LJ shifting bools to false
953 +    ljsp_ = false;
954 +    ljsf_ = false;
955  
956 <    std::set<AtomType*> atomTypes;
957 <    std::set<AtomType*>::iterator i;
958 <    std::vector<double> cutoffRadius;
959 <
960 <    //get the unique atom types
769 <    atomTypes = getUniqueAtomTypes();
770 <
771 <    //query the max cutoff radius among these atom types
772 <    for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
773 <      cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
956 >    std::string myPolicy;
957 >    if (forceFieldOptions_.haveCutoffPolicy()){
958 >      myPolicy = forceFieldOptions_.getCutoffPolicy();
959 >    }else if (simParams_->haveCutoffPolicy()) {
960 >      myPolicy = simParams_->getCutoffPolicy();
961      }
962  
963 <    double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
964 < #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();
963 >    if (!myPolicy.empty()){
964 >      toUpper(myPolicy);
965        if (myPolicy == "MIX") {
966          cp = MIX_CUTOFF_POLICY;
967        } else {
# Line 855 | Line 979 | namespace oopse {
979            }    
980          }          
981        }
982 +    }          
983 +    notifyFortranCutoffPolicy(&cp);
984 +
985 +    // Check the Skin Thickness for neighborlists
986 +    RealType skin;
987 +    if (simParams_->haveSkinThickness()) {
988 +      skin = simParams_->getSkinThickness();
989 +      notifyFortranSkinThickness(&skin);
990 +    }            
991 +        
992 +    // Check if the cutoff was set explicitly:
993 +    if (simParams_->haveCutoffRadius()) {
994 +      rcut_ = simParams_->getCutoffRadius();
995 +      if (simParams_->haveSwitchingRadius()) {
996 +        rsw_  = simParams_->getSwitchingRadius();
997 +      } else {
998 +        if (fInfo_.SIM_uses_Charges |
999 +            fInfo_.SIM_uses_Dipoles |
1000 +            fInfo_.SIM_uses_RF) {
1001 +          
1002 +          rsw_ = 0.85 * rcut_;
1003 +          sprintf(painCave.errMsg,
1004 +                  "SimCreator Warning: No value was set for the switchingRadius.\n"
1005 +                  "\tOOPSE will use a default value of 85 percent of the cutoffRadius.\n"
1006 +                  "\tswitchingRadius = %f. for this simulation\n", rsw_);
1007 +        painCave.isFatal = 0;
1008 +        simError();
1009 +        } else {
1010 +          rsw_ = rcut_;
1011 +          sprintf(painCave.errMsg,
1012 +                  "SimCreator Warning: No value was set for the switchingRadius.\n"
1013 +                  "\tOOPSE will use the same value as the cutoffRadius.\n"
1014 +                  "\tswitchingRadius = %f. for this simulation\n", rsw_);
1015 +          painCave.isFatal = 0;
1016 +          simError();
1017 +        }
1018 +      }
1019 +
1020 +      if (simParams_->haveElectrostaticSummationMethod()) {
1021 +        std::string myMethod = simParams_->getElectrostaticSummationMethod();
1022 +        toUpper(myMethod);
1023 +        
1024 +        if (myMethod == "SHIFTED_POTENTIAL") {
1025 +          ljsp_ = true;
1026 +        } else if (myMethod == "SHIFTED_FORCE") {
1027 +          ljsf_ = true;
1028 +        }
1029 +      }
1030 +      notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1031 +      
1032 +    } else {
1033 +      
1034 +      // For electrostatic atoms, we'll assume a large safe value:
1035 +      if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
1036 +        sprintf(painCave.errMsg,
1037 +                "SimCreator Warning: No value was set for the cutoffRadius.\n"
1038 +                "\tOOPSE will use a default value of 15.0 angstroms"
1039 +                "\tfor the cutoffRadius.\n");
1040 +        painCave.isFatal = 0;
1041 +        simError();
1042 +        rcut_ = 15.0;
1043 +      
1044 +        if (simParams_->haveElectrostaticSummationMethod()) {
1045 +          std::string myMethod = simParams_->getElectrostaticSummationMethod();
1046 +          toUpper(myMethod);
1047 +      
1048 +      // For the time being, we're tethering the LJ shifted behavior to the
1049 +      // electrostaticSummationMethod keyword options
1050 +          if (myMethod == "SHIFTED_POTENTIAL") {
1051 +            ljsp_ = true;
1052 +          } else if (myMethod == "SHIFTED_FORCE") {
1053 +            ljsf_ = true;
1054 +          }
1055 +          if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1056 +            if (simParams_->haveSwitchingRadius()){
1057 +              sprintf(painCave.errMsg,
1058 +                      "SimInfo Warning: A value was set for the switchingRadius\n"
1059 +                      "\teven though the electrostaticSummationMethod was\n"
1060 +                      "\tset to %s\n", myMethod.c_str());
1061 +              painCave.isFatal = 1;
1062 +              simError();            
1063 +            }
1064 +          }
1065 +        }
1066 +      
1067 +        if (simParams_->haveSwitchingRadius()){
1068 +          rsw_ = simParams_->getSwitchingRadius();
1069 +        } else {        
1070 +          sprintf(painCave.errMsg,
1071 +                  "SimCreator Warning: No value was set for switchingRadius.\n"
1072 +                  "\tOOPSE will use a default value of\n"
1073 +                  "\t0.85 * cutoffRadius for the switchingRadius\n");
1074 +          painCave.isFatal = 0;
1075 +          simError();
1076 +          rsw_ = 0.85 * rcut_;
1077 +        }
1078 +
1079 +        notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1080 +
1081 +      } else {
1082 +        // We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1083 +        // We'll punt and let fortran figure out the cutoffs later.
1084 +        
1085 +        notifyFortranYouAreOnYourOwn();
1086 +
1087 +      }
1088      }
859 –    notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp);
1089    }
1090  
1091    void SimInfo::setupElectrostaticSummationMethod( int isError ) {    
1092      
1093      int errorOut;
1094      int esm =  NONE;
1095 <    double alphaVal;
1096 <
1095 >    int sm = UNDAMPED;
1096 >    RealType alphaVal;
1097 >    RealType dielectric;
1098 >    
1099      errorOut = isError;
1100  
1101      if (simParams_->haveElectrostaticSummationMethod()) {
1102        std::string myMethod = simParams_->getElectrostaticSummationMethod();
1103 +      toUpper(myMethod);
1104        if (myMethod == "NONE") {
1105          esm = NONE;
1106        } else {
1107 <        if (myMethod == "UNDAMPED_WOLF") {
1108 <          esm = UNDAMPED_WOLF;
1107 >        if (myMethod == "SWITCHING_FUNCTION") {
1108 >          esm = SWITCHING_FUNCTION;
1109          } else {
1110 <          if (myMethod == "DAMPED_WOLF") {            
1111 <            esm = DAMPED_WOLF;
1112 <            if (!simParams_->haveDampingAlpha()) {
1113 <              //throw error
1114 <              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;
1110 >          if (myMethod == "SHIFTED_POTENTIAL") {
1111 >            esm = SHIFTED_POTENTIAL;
1112 >          } else {
1113 >            if (myMethod == "SHIFTED_FORCE") {            
1114 >              esm = SHIFTED_FORCE;
1115              } else {
1116 <              // throw error        
1117 <              sprintf( painCave.errMsg,
1118 <                       "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() );
1119 <              painCave.isFatal = 1;
1120 <              simError();
1121 <            }    
1122 <          }          
1116 >              if (myMethod == "REACTION_FIELD") {
1117 >                esm = REACTION_FIELD;
1118 >                dielectric = simParams_->getDielectric();
1119 >                if (!simParams_->haveDielectric()) {
1120 >                  // throw warning
1121 >                  sprintf( painCave.errMsg,
1122 >                           "SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
1123 >                           "\tA default value of %f will be used for the dielectric.\n", dielectric);
1124 >                  painCave.isFatal = 0;
1125 >                  simError();
1126 >                }
1127 >              } else {
1128 >                // throw error        
1129 >                sprintf( painCave.errMsg,
1130 >                         "SimInfo error: Unknown electrostaticSummationMethod.\n"
1131 >                         "\t(Input file specified %s .)\n"
1132 >                         "\telectrostaticSummationMethod must be one of: \"none\",\n"
1133 >                         "\t\"shifted_potential\", \"shifted_force\", or \n"
1134 >                         "\t\"reaction_field\".\n", myMethod.c_str() );
1135 >                painCave.isFatal = 1;
1136 >                simError();
1137 >              }    
1138 >            }          
1139 >          }
1140          }
1141        }
1142      }
1143 <    initFortranFF( &fInfo_.SIM_uses_RF, &esm, &alphaVal, &errorOut );
1143 >    
1144 >    if (simParams_->haveElectrostaticScreeningMethod()) {
1145 >      std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1146 >      toUpper(myScreen);
1147 >      if (myScreen == "UNDAMPED") {
1148 >        sm = UNDAMPED;
1149 >      } else {
1150 >        if (myScreen == "DAMPED") {
1151 >          sm = DAMPED;
1152 >          if (!simParams_->haveDampingAlpha()) {
1153 >            // first set a cutoff dependent alpha value
1154 >            // we assume alpha depends linearly with rcut from 0 to 20.5 ang
1155 >            alphaVal = 0.5125 - rcut_* 0.025;
1156 >            // for values rcut > 20.5, alpha is zero
1157 >            if (alphaVal < 0) alphaVal = 0;
1158 >
1159 >            // throw warning
1160 >            sprintf( painCave.errMsg,
1161 >                     "SimInfo warning: dampingAlpha was not specified in the input file.\n"
1162 >                     "\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1163 >            painCave.isFatal = 0;
1164 >            simError();
1165 >          } else {
1166 >            alphaVal = simParams_->getDampingAlpha();
1167 >          }
1168 >          
1169 >        } else {
1170 >          // throw error        
1171 >          sprintf( painCave.errMsg,
1172 >                   "SimInfo error: Unknown electrostaticScreeningMethod.\n"
1173 >                   "\t(Input file specified %s .)\n"
1174 >                   "\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1175 >                   "or \"damped\".\n", myScreen.c_str() );
1176 >          painCave.isFatal = 1;
1177 >          simError();
1178 >        }
1179 >      }
1180 >    }
1181 >    
1182 >    // let's pass some summation method variables to fortran
1183 >    setElectrostaticSummationMethod( &esm );
1184 >    setFortranElectrostaticMethod( &esm );
1185 >    setScreeningMethod( &sm );
1186 >    setDampingAlpha( &alphaVal );
1187 >    setReactionFieldDielectric( &dielectric );
1188 >    initFortranFF( &errorOut );
1189    }
1190  
1191 +  void SimInfo::setupSwitchingFunction() {    
1192 +    int ft = CUBIC;
1193 +
1194 +    if (simParams_->haveSwitchingFunctionType()) {
1195 +      std::string funcType = simParams_->getSwitchingFunctionType();
1196 +      toUpper(funcType);
1197 +      if (funcType == "CUBIC") {
1198 +        ft = CUBIC;
1199 +      } else {
1200 +        if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1201 +          ft = FIFTH_ORDER_POLY;
1202 +        } else {
1203 +          // throw error        
1204 +          sprintf( painCave.errMsg,
1205 +                   "SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1206 +          painCave.isFatal = 1;
1207 +          simError();
1208 +        }          
1209 +      }
1210 +    }
1211 +
1212 +    // send switching function notification to switcheroo
1213 +    setFunctionType(&ft);
1214 +
1215 +  }
1216 +
1217 +  void SimInfo::setupAccumulateBoxDipole() {    
1218 +
1219 +    // we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1220 +    if ( simParams_->haveAccumulateBoxDipole() )
1221 +      if ( simParams_->getAccumulateBoxDipole() ) {
1222 +        setAccumulateBoxDipole();
1223 +        calcBoxDipole_ = true;
1224 +      }
1225 +
1226 +  }
1227 +
1228    void SimInfo::addProperty(GenericData* genData) {
1229      properties_.addProperty(genData);  
1230    }
# Line 958 | Line 1281 | namespace oopse {
1281      Molecule* mol;
1282  
1283      Vector3d comVel(0.0);
1284 <    double totalMass = 0.0;
1284 >    RealType totalMass = 0.0;
1285      
1286  
1287      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1288 <      double mass = mol->getMass();
1288 >      RealType mass = mol->getMass();
1289        totalMass += mass;
1290        comVel += mass * mol->getComVel();
1291      }  
1292  
1293   #ifdef IS_MPI
1294 <    double tmpMass = totalMass;
1294 >    RealType tmpMass = totalMass;
1295      Vector3d tmpComVel(comVel);    
1296 <    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1297 <    MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1296 >    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1297 >    MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1298   #endif
1299  
1300      comVel /= totalMass;
# Line 984 | Line 1307 | namespace oopse {
1307      Molecule* mol;
1308  
1309      Vector3d com(0.0);
1310 <    double totalMass = 0.0;
1310 >    RealType totalMass = 0.0;
1311      
1312      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1313 <      double mass = mol->getMass();
1313 >      RealType mass = mol->getMass();
1314        totalMass += mass;
1315        com += mass * mol->getCom();
1316      }  
1317  
1318   #ifdef IS_MPI
1319 <    double tmpMass = totalMass;
1319 >    RealType tmpMass = totalMass;
1320      Vector3d tmpCom(com);    
1321 <    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1322 <    MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1321 >    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1322 >    MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1323   #endif
1324  
1325      com /= totalMass;
# Line 1020 | Line 1343 | namespace oopse {
1343        Molecule* mol;
1344        
1345      
1346 <      double totalMass = 0.0;
1346 >      RealType totalMass = 0.0;
1347      
1348  
1349        for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1350 <         double mass = mol->getMass();
1350 >         RealType mass = mol->getMass();
1351           totalMass += mass;
1352           com += mass * mol->getCom();
1353           comVel += mass * mol->getComVel();          
1354        }  
1355        
1356   #ifdef IS_MPI
1357 <      double tmpMass = totalMass;
1357 >      RealType tmpMass = totalMass;
1358        Vector3d tmpCom(com);  
1359        Vector3d tmpComVel(comVel);
1360 <      MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1361 <      MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1362 <      MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1360 >      MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1361 >      MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1362 >      MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1363   #endif
1364        
1365        com /= totalMass;
# Line 1055 | Line 1378 | namespace oopse {
1378     void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1379        
1380  
1381 <      double xx = 0.0;
1382 <      double yy = 0.0;
1383 <      double zz = 0.0;
1384 <      double xy = 0.0;
1385 <      double xz = 0.0;
1386 <      double yz = 0.0;
1381 >      RealType xx = 0.0;
1382 >      RealType yy = 0.0;
1383 >      RealType zz = 0.0;
1384 >      RealType xy = 0.0;
1385 >      RealType xz = 0.0;
1386 >      RealType yz = 0.0;
1387        Vector3d com(0.0);
1388        Vector3d comVel(0.0);
1389        
# Line 1072 | Line 1395 | namespace oopse {
1395        Vector3d thisq(0.0);
1396        Vector3d thisv(0.0);
1397  
1398 <      double thisMass = 0.0;
1398 >      RealType thisMass = 0.0;
1399      
1400        
1401        
# Line 1110 | Line 1433 | namespace oopse {
1433   #ifdef IS_MPI
1434        Mat3x3d tmpI(inertiaTensor);
1435        Vector3d tmpAngMom;
1436 <      MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1437 <      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1436 >      MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1437 >      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1438   #endif
1439                
1440        return;
# Line 1132 | Line 1455 | namespace oopse {
1455        Vector3d thisr(0.0);
1456        Vector3d thisp(0.0);
1457        
1458 <      double thisMass;
1458 >      RealType thisMass;
1459        
1460        for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {        
1461          thisMass = mol->getMass();
# Line 1145 | Line 1468 | namespace oopse {
1468        
1469   #ifdef IS_MPI
1470        Vector3d tmpAngMom;
1471 <      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1471 >      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1472   #endif
1473        
1474        return angularMomentum;
1475     }
1476    
1477 <  
1477 >  StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1478 >    return IOIndexToIntegrableObject.at(index);
1479 >  }
1480 >  
1481 >  void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1482 >    IOIndexToIntegrableObject= v;
1483 >  }
1484 >
1485 >  /* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1486 >     based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1487 >     where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1488 >     V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1489 >  */
1490 >  void SimInfo::getGyrationalVolume(RealType &volume){
1491 >    Mat3x3d intTensor;
1492 >    RealType det;
1493 >    Vector3d dummyAngMom;
1494 >    RealType sysconstants;
1495 >    RealType geomCnst;
1496 >
1497 >    geomCnst = 3.0/2.0;
1498 >    /* Get the inertial tensor and angular momentum for free*/
1499 >    getInertiaTensor(intTensor,dummyAngMom);
1500 >    
1501 >    det = intTensor.determinant();
1502 >    sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1503 >    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1504 >    return;
1505 >  }
1506 >
1507 >  void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1508 >    Mat3x3d intTensor;
1509 >    Vector3d dummyAngMom;
1510 >    RealType sysconstants;
1511 >    RealType geomCnst;
1512 >
1513 >    geomCnst = 3.0/2.0;
1514 >    /* Get the inertial tensor and angular momentum for free*/
1515 >    getInertiaTensor(intTensor,dummyAngMom);
1516 >    
1517 >    detI = intTensor.determinant();
1518 >    sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1519 >    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1520 >    return;
1521 >  }
1522 > /*
1523 >   void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1524 >      assert( v.size() == nAtoms_ + nRigidBodies_);
1525 >      sdByGlobalIndex_ = v;
1526 >    }
1527 >
1528 >    StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1529 >      //assert(index < nAtoms_ + nRigidBodies_);
1530 >      return sdByGlobalIndex_.at(index);
1531 >    }  
1532 > */  
1533   }//end namespace oopse
1534  

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