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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 853 by chrisfen, Thu Jan 12 16:47:25 2006 UTC vs.
Revision 1287 by gezelter, Wed Sep 10 18:11:32 2008 UTC

# Line 53 | Line 53
53   #include "brains/SimInfo.hpp"
54   #include "math/Vector3.hpp"
55   #include "primitives/Molecule.hpp"
56 + #include "primitives/StuntDouble.hpp"
57   #include "UseTheForce/fCutoffPolicy.h"
58   #include "UseTheForce/DarkSide/fElectrostaticSummationMethod.h"
59   #include "UseTheForce/DarkSide/fElectrostaticScreeningMethod.h"
60   #include "UseTheForce/DarkSide/fSwitchingFunctionType.h"
61   #include "UseTheForce/doForces_interface.h"
62 + #include "UseTheForce/DarkSide/neighborLists_interface.h"
63   #include "UseTheForce/DarkSide/electrostatic_interface.h"
64   #include "UseTheForce/DarkSide/switcheroo_interface.h"
65   #include "utils/MemoryUtils.hpp"
# Line 66 | Line 68
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"
# Line 84 | Line 87 | namespace oopse {
87    
88    SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
89      forceField_(ff), simParams_(simParams),
90 <    ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
90 >    ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
91      nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
92      nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
93 <    nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nRigidBodies_(0),
94 <    nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
95 <    sman_(NULL), fortranInitialized_(false) {
93 >    nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
94 >    nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
95 >    nConstraints_(0), sman_(NULL), fortranInitialized_(false),
96 >    calcBoxDipole_(false), useAtomicVirial_(true) {
97  
98 +
99        MoleculeStamp* molStamp;
100        int nMolWithSameStamp;
101        int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
# Line 98 | Line 103 | namespace oopse {
103        CutoffGroupStamp* cgStamp;    
104        RigidBodyStamp* rbStamp;
105        int nRigidAtoms = 0;
106 +
107        std::vector<Component*> components = simParams->getComponents();
108        
109        for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
# Line 152 | Line 158 | namespace oopse {
158                                                  + nGlobalRigidBodies_;
159    
160        nGlobalMols_ = molStampIds_.size();
155 –
156 – #ifdef IS_MPI    
161        molToProcMap_.resize(nGlobalMols_);
158 – #endif
159 –
162      }
163  
164    SimInfo::~SimInfo() {
# Line 194 | Line 196 | namespace oopse {
196        nBonds_ += mol->getNBonds();
197        nBends_ += mol->getNBends();
198        nTorsions_ += mol->getNTorsions();
199 +      nInversions_ += mol->getNInversions();
200        nRigidBodies_ += mol->getNRigidBodies();
201        nIntegrableObjects_ += mol->getNIntegrableObjects();
202        nCutoffGroups_ += mol->getNCutoffGroups();
203        nConstraints_ += mol->getNConstraintPairs();
204  
205 <      addExcludePairs(mol);
206 <        
205 >      addInteractionPairs(mol);
206 >  
207        return true;
208      } else {
209        return false;
# Line 219 | Line 222 | namespace oopse {
222        nBonds_ -= mol->getNBonds();
223        nBends_ -= mol->getNBends();
224        nTorsions_ -= mol->getNTorsions();
225 +      nInversions_ -= mol->getNInversions();
226        nRigidBodies_ -= mol->getNRigidBodies();
227        nIntegrableObjects_ -= mol->getNIntegrableObjects();
228        nCutoffGroups_ -= mol->getNCutoffGroups();
229        nConstraints_ -= mol->getNConstraintPairs();
230  
231 <      removeExcludePairs(mol);
231 >      removeInteractionPairs(mol);
232        molecules_.erase(mol->getGlobalIndex());
233  
234        delete mol;
# Line 290 | Line 294 | namespace oopse {
294  
295    }
296  
297 +  int SimInfo::getFdf() {
298 + #ifdef IS_MPI
299 +    MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
300 + #else
301 +    fdf_ = fdf_local;
302 + #endif
303 +    return fdf_;
304 +  }
305 +    
306    void SimInfo::calcNdfRaw() {
307      int ndfRaw_local;
308  
# Line 341 | Line 354 | namespace oopse {
354  
355    }
356  
357 <  void SimInfo::addExcludePairs(Molecule* mol) {
357 >  void SimInfo::addInteractionPairs(Molecule* mol) {
358 >    ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
359      std::vector<Bond*>::iterator bondIter;
360      std::vector<Bend*>::iterator bendIter;
361      std::vector<Torsion*>::iterator torsionIter;
362 +    std::vector<Inversion*>::iterator inversionIter;
363      Bond* bond;
364      Bend* bend;
365      Torsion* torsion;
366 +    Inversion* inversion;
367      int a;
368      int b;
369      int c;
370      int d;
371  
372 <    std::map<int, std::set<int> > atomGroups;
372 >    // atomGroups can be used to add special interaction maps between
373 >    // groups of atoms that are in two separate rigid bodies.
374 >    // However, most site-site interactions between two rigid bodies
375 >    // are probably not special, just the ones between the physically
376 >    // bonded atoms.  Interactions *within* a single rigid body should
377 >    // always be excluded.  These are done at the bottom of this
378 >    // function.
379  
380 +    std::map<int, std::set<int> > atomGroups;
381      Molecule::RigidBodyIterator rbIter;
382      RigidBody* rb;
383      Molecule::IntegrableObjectIterator ii;
384      StuntDouble* integrableObject;
385      
386 <    for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
387 <           integrableObject = mol->nextIntegrableObject(ii)) {
388 <
386 >    for (integrableObject = mol->beginIntegrableObject(ii);
387 >         integrableObject != NULL;
388 >         integrableObject = mol->nextIntegrableObject(ii)) {
389 >      
390        if (integrableObject->isRigidBody()) {
391 <          rb = static_cast<RigidBody*>(integrableObject);
392 <          std::vector<Atom*> atoms = rb->getAtoms();
393 <          std::set<int> rigidAtoms;
394 <          for (int i = 0; i < atoms.size(); ++i) {
395 <            rigidAtoms.insert(atoms[i]->getGlobalIndex());
396 <          }
397 <          for (int i = 0; i < atoms.size(); ++i) {
398 <            atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
399 <          }      
391 >        rb = static_cast<RigidBody*>(integrableObject);
392 >        std::vector<Atom*> atoms = rb->getAtoms();
393 >        std::set<int> rigidAtoms;
394 >        for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
395 >          rigidAtoms.insert(atoms[i]->getGlobalIndex());
396 >        }
397 >        for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
398 >          atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
399 >        }      
400        } else {
401          std::set<int> oneAtomSet;
402          oneAtomSet.insert(integrableObject->getGlobalIndex());
403          atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));        
404        }
405      }  
406 +          
407 +    for (bond= mol->beginBond(bondIter); bond != NULL;
408 +         bond = mol->nextBond(bondIter)) {
409  
383 –    
384 –    
385 –    for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
410        a = bond->getAtomA()->getGlobalIndex();
411 <      b = bond->getAtomB()->getGlobalIndex();        
412 <      exclude_.addPair(a, b);
411 >      b = bond->getAtomB()->getGlobalIndex();  
412 >    
413 >      if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
414 >        oneTwoInteractions_.addPair(a, b);
415 >      } else {
416 >        excludedInteractions_.addPair(a, b);
417 >      }
418      }
419  
420 <    for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
420 >    for (bend= mol->beginBend(bendIter); bend != NULL;
421 >         bend = mol->nextBend(bendIter)) {
422 >
423        a = bend->getAtomA()->getGlobalIndex();
424        b = bend->getAtomB()->getGlobalIndex();        
425        c = bend->getAtomC()->getGlobalIndex();
395 –      std::set<int> rigidSetA = getRigidSet(a, atomGroups);
396 –      std::set<int> rigidSetB = getRigidSet(b, atomGroups);
397 –      std::set<int> rigidSetC = getRigidSet(c, atomGroups);
398 –
399 –      exclude_.addPairs(rigidSetA, rigidSetB);
400 –      exclude_.addPairs(rigidSetA, rigidSetC);
401 –      exclude_.addPairs(rigidSetB, rigidSetC);
426        
427 <      //exclude_.addPair(a, b);
428 <      //exclude_.addPair(a, c);
429 <      //exclude_.addPair(b, c);        
427 >      if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
428 >        oneTwoInteractions_.addPair(a, b);      
429 >        oneTwoInteractions_.addPair(b, c);
430 >      } else {
431 >        excludedInteractions_.addPair(a, b);
432 >        excludedInteractions_.addPair(b, c);
433 >      }
434 >
435 >      if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
436 >        oneThreeInteractions_.addPair(a, c);      
437 >      } else {
438 >        excludedInteractions_.addPair(a, c);
439 >      }
440      }
441  
442 <    for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
442 >    for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
443 >         torsion = mol->nextTorsion(torsionIter)) {
444 >
445        a = torsion->getAtomA()->getGlobalIndex();
446        b = torsion->getAtomB()->getGlobalIndex();        
447        c = torsion->getAtomC()->getGlobalIndex();        
448 <      d = torsion->getAtomD()->getGlobalIndex();        
449 <      std::set<int> rigidSetA = getRigidSet(a, atomGroups);
450 <      std::set<int> rigidSetB = getRigidSet(b, atomGroups);
451 <      std::set<int> rigidSetC = getRigidSet(c, atomGroups);
452 <      std::set<int> rigidSetD = getRigidSet(d, atomGroups);
448 >      d = torsion->getAtomD()->getGlobalIndex();      
449 >  
450 >      if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
451 >        oneTwoInteractions_.addPair(a, b);      
452 >        oneTwoInteractions_.addPair(b, c);
453 >        oneTwoInteractions_.addPair(c, d);
454 >      } else {
455 >        excludedInteractions_.addPair(a, b);
456 >        excludedInteractions_.addPair(b, c);
457 >        excludedInteractions_.addPair(c, d);
458 >      }
459  
460 <      exclude_.addPairs(rigidSetA, rigidSetB);
461 <      exclude_.addPairs(rigidSetA, rigidSetC);
462 <      exclude_.addPairs(rigidSetA, rigidSetD);
463 <      exclude_.addPairs(rigidSetB, rigidSetC);
464 <      exclude_.addPairs(rigidSetB, rigidSetD);
465 <      exclude_.addPairs(rigidSetC, rigidSetD);
460 >      if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
461 >        oneThreeInteractions_.addPair(a, c);      
462 >        oneThreeInteractions_.addPair(b, d);      
463 >      } else {
464 >        excludedInteractions_.addPair(a, c);
465 >        excludedInteractions_.addPair(b, d);
466 >      }
467  
468 <      /*
469 <      exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
470 <      exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
471 <      exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
472 <      exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
430 <      exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
431 <      exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
432 <        
433 <      
434 <      exclude_.addPair(a, b);
435 <      exclude_.addPair(a, c);
436 <      exclude_.addPair(a, d);
437 <      exclude_.addPair(b, c);
438 <      exclude_.addPair(b, d);
439 <      exclude_.addPair(c, d);        
440 <      */
468 >      if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
469 >        oneFourInteractions_.addPair(a, d);      
470 >      } else {
471 >        excludedInteractions_.addPair(a, d);
472 >      }
473      }
474  
475 <    for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
475 >    for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
476 >         inversion = mol->nextInversion(inversionIter)) {
477 >
478 >      a = inversion->getAtomA()->getGlobalIndex();
479 >      b = inversion->getAtomB()->getGlobalIndex();        
480 >      c = inversion->getAtomC()->getGlobalIndex();        
481 >      d = inversion->getAtomD()->getGlobalIndex();        
482 >
483 >      if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
484 >        oneTwoInteractions_.addPair(a, b);      
485 >        oneTwoInteractions_.addPair(a, c);
486 >        oneTwoInteractions_.addPair(a, d);
487 >      } else {
488 >        excludedInteractions_.addPair(a, b);
489 >        excludedInteractions_.addPair(a, c);
490 >        excludedInteractions_.addPair(a, d);
491 >      }
492 >
493 >      if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
494 >        oneThreeInteractions_.addPair(b, c);    
495 >        oneThreeInteractions_.addPair(b, d);    
496 >        oneThreeInteractions_.addPair(c, d);      
497 >      } else {
498 >        excludedInteractions_.addPair(b, c);
499 >        excludedInteractions_.addPair(b, d);
500 >        excludedInteractions_.addPair(c, d);
501 >      }
502 >    }
503 >
504 >    for (rb = mol->beginRigidBody(rbIter); rb != NULL;
505 >         rb = mol->nextRigidBody(rbIter)) {
506        std::vector<Atom*> atoms = rb->getAtoms();
507 <      for (int i = 0; i < atoms.size() -1 ; ++i) {
508 <        for (int j = i + 1; j < atoms.size(); ++j) {
507 >      for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
508 >        for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
509            a = atoms[i]->getGlobalIndex();
510            b = atoms[j]->getGlobalIndex();
511 <          exclude_.addPair(a, b);
511 >          excludedInteractions_.addPair(a, b);
512          }
513        }
514      }        
515  
516    }
517  
518 <  void SimInfo::removeExcludePairs(Molecule* mol) {
518 >  void SimInfo::removeInteractionPairs(Molecule* mol) {
519 >    ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
520      std::vector<Bond*>::iterator bondIter;
521      std::vector<Bend*>::iterator bendIter;
522      std::vector<Torsion*>::iterator torsionIter;
523 +    std::vector<Inversion*>::iterator inversionIter;
524      Bond* bond;
525      Bend* bend;
526      Torsion* torsion;
527 +    Inversion* inversion;
528      int a;
529      int b;
530      int c;
531      int d;
532  
533      std::map<int, std::set<int> > atomGroups;
469 –
534      Molecule::RigidBodyIterator rbIter;
535      RigidBody* rb;
536      Molecule::IntegrableObjectIterator ii;
537      StuntDouble* integrableObject;
538      
539 <    for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
540 <           integrableObject = mol->nextIntegrableObject(ii)) {
541 <
539 >    for (integrableObject = mol->beginIntegrableObject(ii);
540 >         integrableObject != NULL;
541 >         integrableObject = mol->nextIntegrableObject(ii)) {
542 >      
543        if (integrableObject->isRigidBody()) {
544 <          rb = static_cast<RigidBody*>(integrableObject);
545 <          std::vector<Atom*> atoms = rb->getAtoms();
546 <          std::set<int> rigidAtoms;
547 <          for (int i = 0; i < atoms.size(); ++i) {
548 <            rigidAtoms.insert(atoms[i]->getGlobalIndex());
549 <          }
550 <          for (int i = 0; i < atoms.size(); ++i) {
551 <            atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
552 <          }      
544 >        rb = static_cast<RigidBody*>(integrableObject);
545 >        std::vector<Atom*> atoms = rb->getAtoms();
546 >        std::set<int> rigidAtoms;
547 >        for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
548 >          rigidAtoms.insert(atoms[i]->getGlobalIndex());
549 >        }
550 >        for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
551 >          atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
552 >        }      
553        } else {
554          std::set<int> oneAtomSet;
555          oneAtomSet.insert(integrableObject->getGlobalIndex());
# Line 492 | Line 557 | namespace oopse {
557        }
558      }  
559  
560 <    
561 <    for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
560 >    for (bond= mol->beginBond(bondIter); bond != NULL;
561 >         bond = mol->nextBond(bondIter)) {
562 >      
563        a = bond->getAtomA()->getGlobalIndex();
564 <      b = bond->getAtomB()->getGlobalIndex();        
565 <      exclude_.removePair(a, b);
564 >      b = bond->getAtomB()->getGlobalIndex();  
565 >    
566 >      if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
567 >        oneTwoInteractions_.removePair(a, b);
568 >      } else {
569 >        excludedInteractions_.removePair(a, b);
570 >      }
571      }
572  
573 <    for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
573 >    for (bend= mol->beginBend(bendIter); bend != NULL;
574 >         bend = mol->nextBend(bendIter)) {
575 >
576        a = bend->getAtomA()->getGlobalIndex();
577        b = bend->getAtomB()->getGlobalIndex();        
578        c = bend->getAtomC()->getGlobalIndex();
506 –
507 –      std::set<int> rigidSetA = getRigidSet(a, atomGroups);
508 –      std::set<int> rigidSetB = getRigidSet(b, atomGroups);
509 –      std::set<int> rigidSetC = getRigidSet(c, atomGroups);
510 –
511 –      exclude_.removePairs(rigidSetA, rigidSetB);
512 –      exclude_.removePairs(rigidSetA, rigidSetC);
513 –      exclude_.removePairs(rigidSetB, rigidSetC);
579        
580 <      //exclude_.removePair(a, b);
581 <      //exclude_.removePair(a, c);
582 <      //exclude_.removePair(b, c);        
580 >      if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
581 >        oneTwoInteractions_.removePair(a, b);      
582 >        oneTwoInteractions_.removePair(b, c);
583 >      } else {
584 >        excludedInteractions_.removePair(a, b);
585 >        excludedInteractions_.removePair(b, c);
586 >      }
587 >
588 >      if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
589 >        oneThreeInteractions_.removePair(a, c);      
590 >      } else {
591 >        excludedInteractions_.removePair(a, c);
592 >      }
593      }
594  
595 <    for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
595 >    for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
596 >         torsion = mol->nextTorsion(torsionIter)) {
597 >
598        a = torsion->getAtomA()->getGlobalIndex();
599        b = torsion->getAtomB()->getGlobalIndex();        
600        c = torsion->getAtomC()->getGlobalIndex();        
601 <      d = torsion->getAtomD()->getGlobalIndex();        
601 >      d = torsion->getAtomD()->getGlobalIndex();      
602 >  
603 >      if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
604 >        oneTwoInteractions_.removePair(a, b);      
605 >        oneTwoInteractions_.removePair(b, c);
606 >        oneTwoInteractions_.removePair(c, d);
607 >      } else {
608 >        excludedInteractions_.removePair(a, b);
609 >        excludedInteractions_.removePair(b, c);
610 >        excludedInteractions_.removePair(c, d);
611 >      }
612  
613 <      std::set<int> rigidSetA = getRigidSet(a, atomGroups);
614 <      std::set<int> rigidSetB = getRigidSet(b, atomGroups);
615 <      std::set<int> rigidSetC = getRigidSet(c, atomGroups);
616 <      std::set<int> rigidSetD = getRigidSet(d, atomGroups);
613 >      if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
614 >        oneThreeInteractions_.removePair(a, c);      
615 >        oneThreeInteractions_.removePair(b, d);      
616 >      } else {
617 >        excludedInteractions_.removePair(a, c);
618 >        excludedInteractions_.removePair(b, d);
619 >      }
620  
621 <      exclude_.removePairs(rigidSetA, rigidSetB);
622 <      exclude_.removePairs(rigidSetA, rigidSetC);
623 <      exclude_.removePairs(rigidSetA, rigidSetD);
624 <      exclude_.removePairs(rigidSetB, rigidSetC);
625 <      exclude_.removePairs(rigidSetB, rigidSetD);
626 <      exclude_.removePairs(rigidSetC, rigidSetD);
621 >      if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
622 >        oneFourInteractions_.removePair(a, d);      
623 >      } else {
624 >        excludedInteractions_.removePair(a, d);
625 >      }
626 >    }
627  
628 <      /*
629 <      exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
540 <      exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
541 <      exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
542 <      exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
543 <      exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
544 <      exclude_.removePairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
628 >    for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
629 >         inversion = mol->nextInversion(inversionIter)) {
630  
631 <      
632 <      exclude_.removePair(a, b);
633 <      exclude_.removePair(a, c);
634 <      exclude_.removePair(a, d);
635 <      exclude_.removePair(b, c);
636 <      exclude_.removePair(b, d);
637 <      exclude_.removePair(c, d);        
638 <      */
631 >      a = inversion->getAtomA()->getGlobalIndex();
632 >      b = inversion->getAtomB()->getGlobalIndex();        
633 >      c = inversion->getAtomC()->getGlobalIndex();        
634 >      d = inversion->getAtomD()->getGlobalIndex();        
635 >
636 >      if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
637 >        oneTwoInteractions_.removePair(a, b);      
638 >        oneTwoInteractions_.removePair(a, c);
639 >        oneTwoInteractions_.removePair(a, d);
640 >      } else {
641 >        excludedInteractions_.removePair(a, b);
642 >        excludedInteractions_.removePair(a, c);
643 >        excludedInteractions_.removePair(a, d);
644 >      }
645 >
646 >      if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
647 >        oneThreeInteractions_.removePair(b, c);    
648 >        oneThreeInteractions_.removePair(b, d);    
649 >        oneThreeInteractions_.removePair(c, d);      
650 >      } else {
651 >        excludedInteractions_.removePair(b, c);
652 >        excludedInteractions_.removePair(b, d);
653 >        excludedInteractions_.removePair(c, d);
654 >      }
655      }
656  
657 <    for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
657 >    for (rb = mol->beginRigidBody(rbIter); rb != NULL;
658 >         rb = mol->nextRigidBody(rbIter)) {
659        std::vector<Atom*> atoms = rb->getAtoms();
660 <      for (int i = 0; i < atoms.size() -1 ; ++i) {
661 <        for (int j = i + 1; j < atoms.size(); ++j) {
660 >      for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
661 >        for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
662            a = atoms[i]->getGlobalIndex();
663            b = atoms[j]->getGlobalIndex();
664 <          exclude_.removePair(a, b);
664 >          excludedInteractions_.removePair(a, b);
665          }
666        }
667      }        
668 <
668 >    
669    }
670 <
671 <
670 >  
671 >  
672    void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
673      int curStampId;
674 <
674 >    
675      //index from 0
676      curStampId = moleculeStamps_.size();
677  
# Line 591 | Line 693 | namespace oopse {
693      /** @deprecate */    
694      int isError = 0;
695      
696 +    setupCutoff();
697 +    
698      setupElectrostaticSummationMethod( isError );
699      setupSwitchingFunction();
700 +    setupAccumulateBoxDipole();
701  
702      if(isError){
703        sprintf( painCave.errMsg,
# Line 600 | Line 705 | namespace oopse {
705        painCave.isFatal = 1;
706        simError();
707      }
603 –  
604 –    
605 –    setupCutoff();
708  
709      calcNdf();
710      calcNdfRaw();
# Line 652 | Line 754 | namespace oopse {
754      int usePBC = simParams_->getUsePeriodicBoundaryConditions();
755      int useRF;
756      int useSF;
757 +    int useSP;
758 +    int useBoxDipole;
759 +
760      std::string myMethod;
761  
762      // set the useRF logical
763      useRF = 0;
764      useSF = 0;
765 +    useSP = 0;
766  
767  
768      if (simParams_->haveElectrostaticSummationMethod()) {
769        std::string myMethod = simParams_->getElectrostaticSummationMethod();
770        toUpper(myMethod);
771 <      if (myMethod == "REACTION_FIELD") {
772 <        useRF=1;
773 <      } else {
774 <        if (myMethod == "SHIFTED_FORCE") {
775 <          useSF = 1;
776 <        }
771 >      if (myMethod == "REACTION_FIELD"){
772 >        useRF = 1;
773 >      } else if (myMethod == "SHIFTED_FORCE"){
774 >        useSF = 1;
775 >      } else if (myMethod == "SHIFTED_POTENTIAL"){
776 >        useSP = 1;
777        }
778      }
779 +    
780 +    if (simParams_->haveAccumulateBoxDipole())
781 +      if (simParams_->getAccumulateBoxDipole())
782 +        useBoxDipole = 1;
783  
784 +    useAtomicVirial_ = simParams_->getUseAtomicVirial();
785 +
786      //loop over all of the atom types
787      for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
788        useLennardJones |= (*i)->isLennardJones();
# Line 740 | Line 852 | namespace oopse {
852      MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
853  
854      temp = useSF;
855 <    MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
855 >    MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);  
856  
857 +    temp = useSP;
858 +    MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
859 +
860 +    temp = useBoxDipole;
861 +    MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
862 +
863 +    temp = useAtomicVirial_;
864 +    MPI_Allreduce(&temp, &useAtomicVirial_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
865 +
866   #endif
867  
868      fInfo_.SIM_uses_PBC = usePBC;    
# Line 759 | Line 880 | namespace oopse {
880      fInfo_.SIM_uses_FLARB = useFLARB;
881      fInfo_.SIM_uses_RF = useRF;
882      fInfo_.SIM_uses_SF = useSF;
883 <
884 <    if( myMethod == "REACTION_FIELD") {
885 <      
765 <      if (simParams_->haveDielectric()) {
766 <        fInfo_.dielect = simParams_->getDielectric();
767 <      } else {
768 <        sprintf(painCave.errMsg,
769 <                "SimSetup Error: No Dielectric constant was set.\n"
770 <                "\tYou are trying to use Reaction Field without"
771 <                "\tsetting a dielectric constant!\n");
772 <        painCave.isFatal = 1;
773 <        simError();
774 <      }      
775 <    }
776 <
883 >    fInfo_.SIM_uses_SP = useSP;
884 >    fInfo_.SIM_uses_BoxDipole = useBoxDipole;
885 >    fInfo_.SIM_uses_AtomicVirial = useAtomicVirial_;
886    }
887  
888    void SimInfo::setupFortranSim() {
889      int isError;
890 <    int nExclude;
890 >    int nExclude, nOneTwo, nOneThree, nOneFour;
891      std::vector<int> fortranGlobalGroupMembership;
892      
784 –    nExclude = exclude_.getSize();
893      isError = 0;
894  
895      //globalGroupMembership_ is filled by SimCreator    
# Line 790 | Line 898 | namespace oopse {
898      }
899  
900      //calculate mass ratio of cutoff group
901 <    std::vector<double> mfact;
901 >    std::vector<RealType> mfact;
902      SimInfo::MoleculeIterator mi;
903      Molecule* mol;
904      Molecule::CutoffGroupIterator ci;
905      CutoffGroup* cg;
906      Molecule::AtomIterator ai;
907      Atom* atom;
908 <    double totalMass;
908 >    RealType totalMass;
909  
910      //to avoid memory reallocation, reserve enough space for mfact
911      mfact.reserve(getNCutoffGroups());
# Line 813 | Line 921 | namespace oopse {
921            else
922              mfact.push_back( 1.0 );
923          }
816 –
924        }      
925      }
926  
# Line 837 | Line 944 | namespace oopse {
944      }
945      
946      //setup fortran simulation
840 –    int nGlobalExcludes = 0;
841 –    int* globalExcludes = NULL;
842 –    int* excludeList = exclude_.getExcludeList();
843 –    setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
844 –                   &nGlobalExcludes, globalExcludes, &molMembershipArray[0],
845 –                   &mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
947  
948 <    if( isError ){
948 >    nExclude = excludedInteractions_.getSize();
949 >    nOneTwo = oneTwoInteractions_.getSize();
950 >    nOneThree = oneThreeInteractions_.getSize();
951 >    nOneFour = oneFourInteractions_.getSize();
952  
953 +    std::cerr << "exculdes:\n";
954 +    std::cerr << excludedInteractions_;
955 +    std::cerr << "\noneTwo:\n";
956 +    std::cerr << oneTwoInteractions_;
957 +    std::cerr << "\noneThree:\n";
958 +    std::cerr << oneThreeInteractions_;
959 +    std::cerr << "\noneFour:\n";
960 +    std::cerr << oneFourInteractions_;
961 +
962 +    int* excludeList = excludedInteractions_.getPairList();
963 +    int* oneTwoList = oneTwoInteractions_.getPairList();
964 +    int* oneThreeList = oneThreeInteractions_.getPairList();
965 +    int* oneFourList = oneFourInteractions_.getPairList();
966 +
967 +    setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
968 +                   &nExclude, excludeList,
969 +                   &nOneTwo, oneTwoList,
970 +                   &nOneThree, oneThreeList,
971 +                   &nOneFour, oneFourList,
972 +                   &molMembershipArray[0], &mfact[0], &nCutoffGroups_,
973 +                   &fortranGlobalGroupMembership[0], &isError);
974 +    
975 +    if( isError ){
976 +      
977        sprintf( painCave.errMsg,
978                 "There was an error setting the simulation information in fortran.\n" );
979        painCave.isFatal = 1;
980        painCave.severity = OOPSE_ERROR;
981        simError();
982      }
983 <
984 < #ifdef IS_MPI
983 >    
984 >    
985      sprintf( checkPointMsg,
986               "succesfully sent the simulation information to fortran.\n");
987 <    MPIcheckPoint();
988 < #endif // is_mpi
987 >    
988 >    errorCheckPoint();
989 >    
990 >    // Setup number of neighbors in neighbor list if present
991 >    if (simParams_->haveNeighborListNeighbors()) {
992 >      int nlistNeighbors = simParams_->getNeighborListNeighbors();
993 >      setNeighbors(&nlistNeighbors);
994 >    }
995 >  
996 >
997    }
998  
999  
864 – #ifdef IS_MPI
1000    void SimInfo::setupFortranParallel() {
1001 <    
1001 > #ifdef IS_MPI    
1002      //SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
1003      std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
1004      std::vector<int> localToGlobalCutoffGroupIndex;
# Line 913 | Line 1048 | namespace oopse {
1048      }
1049  
1050      sprintf(checkPointMsg, " mpiRefresh successful.\n");
1051 <    MPIcheckPoint();
1051 >    errorCheckPoint();
1052  
1053 <
1053 > #endif
1054    }
1055  
921 – #endif
922 –
1056    void SimInfo::setupCutoff() {          
1057      
1058      ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
# Line 927 | Line 1060 | namespace oopse {
1060      // Check the cutoff policy
1061      int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
1062  
1063 +    // Set LJ shifting bools to false
1064 +    ljsp_ = false;
1065 +    ljsf_ = false;
1066 +
1067      std::string myPolicy;
1068      if (forceFieldOptions_.haveCutoffPolicy()){
1069        myPolicy = forceFieldOptions_.getCutoffPolicy();
# Line 957 | Line 1094 | namespace oopse {
1094      notifyFortranCutoffPolicy(&cp);
1095  
1096      // Check the Skin Thickness for neighborlists
1097 <    double skin;
1097 >    RealType skin;
1098      if (simParams_->haveSkinThickness()) {
1099        skin = simParams_->getSkinThickness();
1100        notifyFortranSkinThickness(&skin);
# Line 969 | Line 1106 | namespace oopse {
1106        if (simParams_->haveSwitchingRadius()) {
1107          rsw_  = simParams_->getSwitchingRadius();
1108        } else {
1109 <        rsw_ = rcut_;
1109 >        if (fInfo_.SIM_uses_Charges |
1110 >            fInfo_.SIM_uses_Dipoles |
1111 >            fInfo_.SIM_uses_RF) {
1112 >          
1113 >          rsw_ = 0.85 * rcut_;
1114 >          sprintf(painCave.errMsg,
1115 >                  "SimCreator Warning: No value was set for the switchingRadius.\n"
1116 >                  "\tOOPSE will use a default value of 85 percent of the cutoffRadius.\n"
1117 >                  "\tswitchingRadius = %f. for this simulation\n", rsw_);
1118 >        painCave.isFatal = 0;
1119 >        simError();
1120 >        } else {
1121 >          rsw_ = rcut_;
1122 >          sprintf(painCave.errMsg,
1123 >                  "SimCreator Warning: No value was set for the switchingRadius.\n"
1124 >                  "\tOOPSE will use the same value as the cutoffRadius.\n"
1125 >                  "\tswitchingRadius = %f. for this simulation\n", rsw_);
1126 >          painCave.isFatal = 0;
1127 >          simError();
1128 >        }
1129        }
1130 <      notifyFortranCutoffs(&rcut_, &rsw_);
1130 >
1131 >      if (simParams_->haveElectrostaticSummationMethod()) {
1132 >        std::string myMethod = simParams_->getElectrostaticSummationMethod();
1133 >        toUpper(myMethod);
1134 >        
1135 >        if (myMethod == "SHIFTED_POTENTIAL") {
1136 >          ljsp_ = true;
1137 >        } else if (myMethod == "SHIFTED_FORCE") {
1138 >          ljsf_ = true;
1139 >        }
1140 >      }
1141 >      notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1142        
1143      } else {
1144        
# Line 988 | Line 1155 | namespace oopse {
1155          if (simParams_->haveElectrostaticSummationMethod()) {
1156            std::string myMethod = simParams_->getElectrostaticSummationMethod();
1157            toUpper(myMethod);
1158 <          if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1158 >      
1159 >      // For the time being, we're tethering the LJ shifted behavior to the
1160 >      // electrostaticSummationMethod keyword options
1161 >          if (myMethod == "SHIFTED_POTENTIAL") {
1162 >            ljsp_ = true;
1163 >          } else if (myMethod == "SHIFTED_FORCE") {
1164 >            ljsf_ = true;
1165 >          }
1166 >          if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1167              if (simParams_->haveSwitchingRadius()){
1168                sprintf(painCave.errMsg,
1169                        "SimInfo Warning: A value was set for the switchingRadius\n"
# Line 1011 | Line 1186 | namespace oopse {
1186            simError();
1187            rsw_ = 0.85 * rcut_;
1188          }
1189 <        notifyFortranCutoffs(&rcut_, &rsw_);
1189 >
1190 >        notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1191 >
1192        } else {
1193          // We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1194          // We'll punt and let fortran figure out the cutoffs later.
# Line 1027 | Line 1204 | namespace oopse {
1204      int errorOut;
1205      int esm =  NONE;
1206      int sm = UNDAMPED;
1207 <    double alphaVal;
1208 <    double dielectric;
1209 <
1207 >    RealType alphaVal;
1208 >    RealType dielectric;
1209 >    
1210      errorOut = isError;
1034 –    alphaVal = simParams_->getDampingAlpha();
1035 –    dielectric = simParams_->getDielectric();
1211  
1212      if (simParams_->haveElectrostaticSummationMethod()) {
1213        std::string myMethod = simParams_->getElectrostaticSummationMethod();
# Line 1049 | Line 1224 | namespace oopse {
1224              if (myMethod == "SHIFTED_FORCE") {            
1225                esm = SHIFTED_FORCE;
1226              } else {
1227 <              if (myMethod == "REACTION_FIELD") {            
1227 >              if (myMethod == "REACTION_FIELD") {
1228                  esm = REACTION_FIELD;
1229 +                dielectric = simParams_->getDielectric();
1230 +                if (!simParams_->haveDielectric()) {
1231 +                  // throw warning
1232 +                  sprintf( painCave.errMsg,
1233 +                           "SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
1234 +                           "\tA default value of %f will be used for the dielectric.\n", dielectric);
1235 +                  painCave.isFatal = 0;
1236 +                  simError();
1237 +                }
1238                } else {
1239                  // throw error        
1240                  sprintf( painCave.errMsg,
# Line 1077 | Line 1261 | namespace oopse {
1261          if (myScreen == "DAMPED") {
1262            sm = DAMPED;
1263            if (!simParams_->haveDampingAlpha()) {
1264 <            //throw error
1264 >            // first set a cutoff dependent alpha value
1265 >            // we assume alpha depends linearly with rcut from 0 to 20.5 ang
1266 >            alphaVal = 0.5125 - rcut_* 0.025;
1267 >            // for values rcut > 20.5, alpha is zero
1268 >            if (alphaVal < 0) alphaVal = 0;
1269 >
1270 >            // throw warning
1271              sprintf( painCave.errMsg,
1272                       "SimInfo warning: dampingAlpha was not specified in the input file.\n"
1273 <                     "\tA default value of %f (1/ang) will be used.\n", alphaVal);
1273 >                     "\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1274              painCave.isFatal = 0;
1275              simError();
1276 +          } else {
1277 +            alphaVal = simParams_->getDampingAlpha();
1278            }
1279 +          
1280          } else {
1281            // throw error        
1282            sprintf( painCave.errMsg,
# Line 1132 | Line 1325 | namespace oopse {
1325  
1326    }
1327  
1328 +  void SimInfo::setupAccumulateBoxDipole() {    
1329 +
1330 +    // we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1331 +    if ( simParams_->haveAccumulateBoxDipole() )
1332 +      if ( simParams_->getAccumulateBoxDipole() ) {
1333 +        setAccumulateBoxDipole();
1334 +        calcBoxDipole_ = true;
1335 +      }
1336 +
1337 +  }
1338 +
1339    void SimInfo::addProperty(GenericData* genData) {
1340      properties_.addProperty(genData);  
1341    }
# Line 1188 | Line 1392 | namespace oopse {
1392      Molecule* mol;
1393  
1394      Vector3d comVel(0.0);
1395 <    double totalMass = 0.0;
1395 >    RealType totalMass = 0.0;
1396      
1397  
1398      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1399 <      double mass = mol->getMass();
1399 >      RealType mass = mol->getMass();
1400        totalMass += mass;
1401        comVel += mass * mol->getComVel();
1402      }  
1403  
1404   #ifdef IS_MPI
1405 <    double tmpMass = totalMass;
1405 >    RealType tmpMass = totalMass;
1406      Vector3d tmpComVel(comVel);    
1407 <    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1408 <    MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1407 >    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1408 >    MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1409   #endif
1410  
1411      comVel /= totalMass;
# Line 1214 | Line 1418 | namespace oopse {
1418      Molecule* mol;
1419  
1420      Vector3d com(0.0);
1421 <    double totalMass = 0.0;
1421 >    RealType totalMass = 0.0;
1422      
1423      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1424 <      double mass = mol->getMass();
1424 >      RealType mass = mol->getMass();
1425        totalMass += mass;
1426        com += mass * mol->getCom();
1427      }  
1428  
1429   #ifdef IS_MPI
1430 <    double tmpMass = totalMass;
1430 >    RealType tmpMass = totalMass;
1431      Vector3d tmpCom(com);    
1432 <    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1433 <    MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1432 >    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1433 >    MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1434   #endif
1435  
1436      com /= totalMass;
# Line 1250 | Line 1454 | namespace oopse {
1454        Molecule* mol;
1455        
1456      
1457 <      double totalMass = 0.0;
1457 >      RealType totalMass = 0.0;
1458      
1459  
1460        for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1461 <         double mass = mol->getMass();
1461 >         RealType mass = mol->getMass();
1462           totalMass += mass;
1463           com += mass * mol->getCom();
1464           comVel += mass * mol->getComVel();          
1465        }  
1466        
1467   #ifdef IS_MPI
1468 <      double tmpMass = totalMass;
1468 >      RealType tmpMass = totalMass;
1469        Vector3d tmpCom(com);  
1470        Vector3d tmpComVel(comVel);
1471 <      MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1472 <      MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1473 <      MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1471 >      MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1472 >      MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1473 >      MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1474   #endif
1475        
1476        com /= totalMass;
# Line 1285 | Line 1489 | namespace oopse {
1489     void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1490        
1491  
1492 <      double xx = 0.0;
1493 <      double yy = 0.0;
1494 <      double zz = 0.0;
1495 <      double xy = 0.0;
1496 <      double xz = 0.0;
1497 <      double yz = 0.0;
1492 >      RealType xx = 0.0;
1493 >      RealType yy = 0.0;
1494 >      RealType zz = 0.0;
1495 >      RealType xy = 0.0;
1496 >      RealType xz = 0.0;
1497 >      RealType yz = 0.0;
1498        Vector3d com(0.0);
1499        Vector3d comVel(0.0);
1500        
# Line 1302 | Line 1506 | namespace oopse {
1506        Vector3d thisq(0.0);
1507        Vector3d thisv(0.0);
1508  
1509 <      double thisMass = 0.0;
1509 >      RealType thisMass = 0.0;
1510      
1511        
1512        
# Line 1340 | Line 1544 | namespace oopse {
1544   #ifdef IS_MPI
1545        Mat3x3d tmpI(inertiaTensor);
1546        Vector3d tmpAngMom;
1547 <      MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1548 <      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1547 >      MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1548 >      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1549   #endif
1550                
1551        return;
# Line 1362 | Line 1566 | namespace oopse {
1566        Vector3d thisr(0.0);
1567        Vector3d thisp(0.0);
1568        
1569 <      double thisMass;
1569 >      RealType thisMass;
1570        
1571        for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {        
1572          thisMass = mol->getMass();
# Line 1375 | Line 1579 | namespace oopse {
1579        
1580   #ifdef IS_MPI
1581        Vector3d tmpAngMom;
1582 <      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1582 >      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1583   #endif
1584        
1585        return angularMomentum;
1586     }
1587    
1588 <  
1588 >  StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1589 >    return IOIndexToIntegrableObject.at(index);
1590 >  }
1591 >  
1592 >  void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1593 >    IOIndexToIntegrableObject= v;
1594 >  }
1595 >
1596 >  /* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1597 >     based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1598 >     where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1599 >     V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1600 >  */
1601 >  void SimInfo::getGyrationalVolume(RealType &volume){
1602 >    Mat3x3d intTensor;
1603 >    RealType det;
1604 >    Vector3d dummyAngMom;
1605 >    RealType sysconstants;
1606 >    RealType geomCnst;
1607 >
1608 >    geomCnst = 3.0/2.0;
1609 >    /* Get the inertial tensor and angular momentum for free*/
1610 >    getInertiaTensor(intTensor,dummyAngMom);
1611 >    
1612 >    det = intTensor.determinant();
1613 >    sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1614 >    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1615 >    return;
1616 >  }
1617 >
1618 >  void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1619 >    Mat3x3d intTensor;
1620 >    Vector3d dummyAngMom;
1621 >    RealType sysconstants;
1622 >    RealType geomCnst;
1623 >
1624 >    geomCnst = 3.0/2.0;
1625 >    /* Get the inertial tensor and angular momentum for free*/
1626 >    getInertiaTensor(intTensor,dummyAngMom);
1627 >    
1628 >    detI = intTensor.determinant();
1629 >    sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1630 >    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1631 >    return;
1632 >  }
1633 > /*
1634 >   void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1635 >      assert( v.size() == nAtoms_ + nRigidBodies_);
1636 >      sdByGlobalIndex_ = v;
1637 >    }
1638 >
1639 >    StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1640 >      //assert(index < nAtoms_ + nRigidBodies_);
1641 >      return sdByGlobalIndex_.at(index);
1642 >    }  
1643 > */  
1644   }//end namespace oopse
1645  

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