ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/OpenMD/branches/development/src/brains/SimInfo.cpp
(Generate patch)

Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 507 by gezelter, Fri Apr 15 22:04:00 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"
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();
137
138 #ifdef IS_MPI    
159        molToProcMap_.resize(nGlobalMols_);
140 #endif
141
160      }
161  
162    SimInfo::~SimInfo() {
# Line 148 | Line 166 | namespace oopse {
166      }
167      molecules_.clear();
168        
151    delete stamps_;
169      delete sman_;
170      delete simParams_;
171      delete forceField_;
# Line 255 | 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 273 | 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 335 | 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 346 | 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 357 | 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  
369    Molecule::RigidBodyIterator rbIter;
370    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 392 | 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 404 | 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 415 | Line 532 | namespace oopse {
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  
426    Molecule::RigidBodyIterator rbIter;
427    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 462 | Line 599 | namespace oopse {
599      //setup fortran force field
600      /** @deprecate */    
601      int isError = 0;
602 <    initFortranFF( &fInfo_.SIM_uses_RF , &isError );
602 >    
603 >    setupCutoff();
604 >    
605 >    setupElectrostaticSummationMethod( isError );
606 >    setupSwitchingFunction();
607 >    setupAccumulateBoxDipole();
608 >
609      if(isError){
610        sprintf( painCave.errMsg,
611                 "ForceField error: There was an error initializing the forceField in fortran.\n" );
612        painCave.isFatal = 1;
613        simError();
614      }
472  
473    
474    setupCutoff();
615  
616      calcNdf();
617      calcNdfRaw();
# Line 506 | 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;
653      int useGayBerne = 0;
654      int useSticky = 0;
655 +    int useStickyPower = 0;
656      int useShape = 0;
657      int useFLARB = 0; //it is not in AtomType yet
658      int useDirectionalAtom = 0;    
659      int useElectrostatics = 0;
660      //usePBC and useRF are from simParams
661 <    int usePBC = simParams_->getPBC();
662 <    int useRF = simParams_->getUseRF();
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();
702        useGayBerne |= (*i)->isGayBerne();
703        useSticky |= (*i)->isSticky();
704 +      useStickyPower |= (*i)->isStickyPower();
705        useShape |= (*i)->isShape();
706      }
707  
708 <    if (useSticky || useDipole || useGayBerne || useShape) {
708 >    if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
709        useDirectionalAtom = 1;
710      }
711  
# Line 564 | Line 737 | namespace oopse {
737      temp = useSticky;
738      MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
739  
740 +    temp = useStickyPower;
741 +    MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
742 +    
743      temp = useGayBerne;
744      MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
745  
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  
# Line 578 | Line 757 | namespace oopse {
757  
758      temp = useRF;
759      MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
760 <    
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 588 | Line 779 | namespace oopse {
779      fInfo_.SIM_uses_Charges = useCharge;
780      fInfo_.SIM_uses_Dipoles = useDipole;
781      fInfo_.SIM_uses_Sticky = useSticky;
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      fInfo_.SIM_uses_RF = useRF;
789 <
790 <    if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) {
791 <
792 <      if (simParams_->haveDielectric()) {
600 <        fInfo_.dielect = simParams_->getDielectric();
601 <      } else {
602 <        sprintf(painCave.errMsg,
603 <                "SimSetup Error: No Dielectric constant was set.\n"
604 <                "\tYou are trying to use Reaction Field without"
605 <                "\tsetting a dielectric constant!\n");
606 <        painCave.isFatal = 1;
607 <        simError();
608 <      }
609 <        
610 <    } else {
611 <      fInfo_.dielect = 0.0;
612 <    }
613 <
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 627 | 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 644 | 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 673 | 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  
697 #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 746 | 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
764 <    atomTypes = getUniqueAtomTypes();
765 <
766 <    //query the max cutoff radius among these atom types
767 <    for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
768 <      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
965 <    //pick the max cutoff radius among the processors
966 < #endif
963 >    if (!myPolicy.empty()){
964 >      toUpper(myPolicy);
965 >      if (myPolicy == "MIX") {
966 >        cp = MIX_CUTOFF_POLICY;
967 >      } else {
968 >        if (myPolicy == "MAX") {
969 >          cp = MAX_CUTOFF_POLICY;
970 >        } else {
971 >          if (myPolicy == "TRADITIONAL") {            
972 >            cp = TRADITIONAL_CUTOFF_POLICY;
973 >          } else {
974 >            // throw error        
975 >            sprintf( painCave.errMsg,
976 >                     "SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
977 >            painCave.isFatal = 1;
978 >            simError();
979 >          }    
980 >        }          
981 >      }
982 >    }          
983 >    notifyFortranCutoffPolicy(&cp);
984  
985 <    return maxCutoffRadius;
986 <  }
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 <  void SimInfo::getCutoff(double& rcut, double& rsw) {
1021 <    
1022 <    if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
1020 >      if (simParams_->haveElectrostaticSummationMethod()) {
1021 >        std::string myMethod = simParams_->getElectrostaticSummationMethod();
1022 >        toUpper(myMethod);
1023          
1024 <      if (!simParams_->haveRcut()){
1025 <        sprintf(painCave.errMsg,
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;
1040 >        painCave.isFatal = 0;
1041          simError();
1042 <        rcut = 15.0;
1043 <      } else{
1044 <        rcut = simParams_->getRcut();
1045 <      }
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 <      if (!simParams_->haveRsw()){
796 <        sprintf(painCave.errMsg,
797 <                "SimCreator Warning: No value was set for switchingRadius.\n"
798 <                "\tOOPSE will use a default value of\n"
799 <                "\t0.95 * cutoffRadius for the switchingRadius\n");
800 <        painCave.isFatal = 0;
801 <        simError();
802 <        rsw = 0.95 * rcut;
803 <      } else{
804 <        rsw = simParams_->getRsw();
805 <      }
1079 >        notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1080  
807    } else {
808      // if charge, dipole or reaction field is not used and the cutofff radius is not specified in
809      //meta-data file, the maximum cutoff radius calculated from forcefiled will be used
810        
811      if (simParams_->haveRcut()) {
812        rcut = simParams_->getRcut();
1081        } else {
1082 <        //set cutoff radius to the maximum cutoff radius based on atom types in the whole system
1083 <        rcut = calcMaxCutoffRadius();
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 +    }
1089 +  }
1090  
1091 <      if (simParams_->haveRsw()) {
1092 <        rsw  = simParams_->getRsw();
1091 >  void SimInfo::setupElectrostaticSummationMethod( int isError ) {    
1092 >    
1093 >    int errorOut;
1094 >    int esm =  NONE;
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 <        rsw = rcut;
1107 >        if (myMethod == "SWITCHING_FUNCTION") {
1108 >          esm = SWITCHING_FUNCTION;
1109 >        } else {
1110 >          if (myMethod == "SHIFTED_POTENTIAL") {
1111 >            esm = SHIFTED_POTENTIAL;
1112 >          } else {
1113 >            if (myMethod == "SHIFTED_FORCE") {            
1114 >              esm = SHIFTED_FORCE;
1115 >            } else {
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      
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::setupCutoff() {
1192 <    getCutoff(rcut_, rsw_);    
829 <    double rnblist = rcut_ + 1; // skin of neighbor list
1191 >  void SimInfo::setupSwitchingFunction() {    
1192 >    int ft = CUBIC;
1193  
1194 <    //Pass these cutoff radius etc. to fortran. This function should be called once and only once
1195 <    notifyFortranCutoffs(&rcut_, &rsw_, &rnblist);
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 888 | 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 914 | 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 939 | Line 1332 | namespace oopse {
1332  
1333      return o;
1334    }
1335 +  
1336 +  
1337 +   /*
1338 +   Returns center of mass and center of mass velocity in one function call.
1339 +   */
1340 +  
1341 +   void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1342 +      SimInfo::MoleculeIterator i;
1343 +      Molecule* mol;
1344 +      
1345 +    
1346 +      RealType totalMass = 0.0;
1347 +    
1348  
1349 +      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
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 +      RealType tmpMass = totalMass;
1358 +      Vector3d tmpCom(com);  
1359 +      Vector3d tmpComVel(comVel);
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;
1366 +      comVel /= totalMass;
1367 +   }        
1368 +  
1369 +   /*
1370 +   Return intertia tensor for entire system and angular momentum Vector.
1371 +
1372 +
1373 +       [  Ixx -Ixy  -Ixz ]
1374 +  J =| -Iyx  Iyy  -Iyz |
1375 +       [ -Izx -Iyz   Izz ]
1376 +    */
1377 +
1378 +   void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1379 +      
1380 +
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 +      
1390 +      getComAll(com, comVel);
1391 +      
1392 +      SimInfo::MoleculeIterator i;
1393 +      Molecule* mol;
1394 +      
1395 +      Vector3d thisq(0.0);
1396 +      Vector3d thisv(0.0);
1397 +
1398 +      RealType thisMass = 0.0;
1399 +    
1400 +      
1401 +      
1402 +  
1403 +      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1404 +        
1405 +         thisq = mol->getCom()-com;
1406 +         thisv = mol->getComVel()-comVel;
1407 +         thisMass = mol->getMass();
1408 +         // Compute moment of intertia coefficients.
1409 +         xx += thisq[0]*thisq[0]*thisMass;
1410 +         yy += thisq[1]*thisq[1]*thisMass;
1411 +         zz += thisq[2]*thisq[2]*thisMass;
1412 +        
1413 +         // compute products of intertia
1414 +         xy += thisq[0]*thisq[1]*thisMass;
1415 +         xz += thisq[0]*thisq[2]*thisMass;
1416 +         yz += thisq[1]*thisq[2]*thisMass;
1417 +            
1418 +         angularMomentum += cross( thisq, thisv ) * thisMass;
1419 +            
1420 +      }  
1421 +      
1422 +      
1423 +      inertiaTensor(0,0) = yy + zz;
1424 +      inertiaTensor(0,1) = -xy;
1425 +      inertiaTensor(0,2) = -xz;
1426 +      inertiaTensor(1,0) = -xy;
1427 +      inertiaTensor(1,1) = xx + zz;
1428 +      inertiaTensor(1,2) = -yz;
1429 +      inertiaTensor(2,0) = -xz;
1430 +      inertiaTensor(2,1) = -yz;
1431 +      inertiaTensor(2,2) = xx + yy;
1432 +      
1433 + #ifdef IS_MPI
1434 +      Mat3x3d tmpI(inertiaTensor);
1435 +      Vector3d tmpAngMom;
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;
1441 +   }
1442 +
1443 +   //Returns the angular momentum of the system
1444 +   Vector3d SimInfo::getAngularMomentum(){
1445 +      
1446 +      Vector3d com(0.0);
1447 +      Vector3d comVel(0.0);
1448 +      Vector3d angularMomentum(0.0);
1449 +      
1450 +      getComAll(com,comVel);
1451 +      
1452 +      SimInfo::MoleculeIterator i;
1453 +      Molecule* mol;
1454 +      
1455 +      Vector3d thisr(0.0);
1456 +      Vector3d thisp(0.0);
1457 +      
1458 +      RealType thisMass;
1459 +      
1460 +      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {        
1461 +        thisMass = mol->getMass();
1462 +        thisr = mol->getCom()-com;
1463 +        thisp = (mol->getComVel()-comVel)*thisMass;
1464 +        
1465 +        angularMomentum += cross( thisr, thisp );
1466 +        
1467 +      }  
1468 +      
1469 + #ifdef IS_MPI
1470 +      Vector3d tmpAngMom;
1471 +      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1472 + #endif
1473 +      
1474 +      return angularMomentum;
1475 +   }
1476 +  
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  

Diff Legend

Removed lines
+ Added lines
< Changed lines
> Changed lines