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 853 by chrisfen, Thu Jan 12 16:47:25 2006 UTC vs.
Revision 1313 by gezelter, Wed Oct 22 20:01:49 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();        
413 <      std::set<int> rigidSetA = getRigidSet(a, atomGroups);
414 <      std::set<int> rigidSetB = getRigidSet(b, atomGroups);
415 <      std::set<int> rigidSetC = getRigidSet(c, atomGroups);
416 <      std::set<int> rigidSetD = getRigidSet(d, atomGroups);
448 >      d = torsion->getAtomD()->getGlobalIndex();      
449  
450 <      exclude_.addPairs(rigidSetA, rigidSetB);
451 <      exclude_.addPairs(rigidSetA, rigidSetC);
452 <      exclude_.addPairs(rigidSetA, rigidSetD);
453 <      exclude_.addPairs(rigidSetB, rigidSetC);
454 <      exclude_.addPairs(rigidSetB, rigidSetD);
455 <      exclude_.addPairs(rigidSetC, rigidSetD);
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 <      /*
461 <      exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
462 <      exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
463 <      exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
464 <      exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
465 <      exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
466 <      exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
467 <        
468 <      
469 <      exclude_.addPair(a, b);
470 <      exclude_.addPair(a, c);
471 <      exclude_.addPair(a, d);
472 <      exclude_.addPair(b, c);
438 <      exclude_.addPair(b, d);
439 <      exclude_.addPair(c, d);        
440 <      */
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 >      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);
550 <      exclude_.removePair(b, c);
551 <      exclude_.removePair(b, d);
552 <      exclude_.removePair(c, d);        
553 <      */
554 <    }
631 >      a = inversion->getAtomA()->getGlobalIndex();
632 >      b = inversion->getAtomB()->getGlobalIndex();        
633 >      c = inversion->getAtomC()->getGlobalIndex();        
634 >      d = inversion->getAtomD()->getGlobalIndex();        
635  
636 <    for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
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;
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 +    useBoxDipole = 0;
767  
768  
769      if (simParams_->haveElectrostaticSummationMethod()) {
770        std::string myMethod = simParams_->getElectrostaticSummationMethod();
771        toUpper(myMethod);
772 <      if (myMethod == "REACTION_FIELD") {
773 <        useRF=1;
774 <      } else {
775 <        if (myMethod == "SHIFTED_FORCE") {
776 <          useSF = 1;
777 <        }
772 >      if (myMethod == "REACTION_FIELD"){
773 >        useRF = 1;
774 >      } else if (myMethod == "SHIFTED_FORCE"){
775 >        useSF = 1;
776 >      } else if (myMethod == "SHIFTED_POTENTIAL"){
777 >        useSP = 1;
778        }
779      }
780 +    
781 +    if (simParams_->haveAccumulateBoxDipole())
782 +      if (simParams_->getAccumulateBoxDipole())
783 +        useBoxDipole = 1;
784  
785 +    useAtomicVirial_ = simParams_->getUseAtomicVirial();
786 +
787      //loop over all of the atom types
788      for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
789        useLennardJones |= (*i)->isLennardJones();
# Line 740 | Line 853 | namespace oopse {
853      MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
854  
855      temp = useSF;
856 <    MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
856 >    MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);  
857  
858 +    temp = useSP;
859 +    MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
860 +
861 +    temp = useBoxDipole;
862 +    MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
863 +
864 +    temp = useAtomicVirial_;
865 +    MPI_Allreduce(&temp, &useAtomicVirial_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
866 +
867   #endif
868  
869      fInfo_.SIM_uses_PBC = usePBC;    
# Line 759 | Line 881 | namespace oopse {
881      fInfo_.SIM_uses_FLARB = useFLARB;
882      fInfo_.SIM_uses_RF = useRF;
883      fInfo_.SIM_uses_SF = useSF;
884 <
885 <    if( myMethod == "REACTION_FIELD") {
886 <      
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 <
884 >    fInfo_.SIM_uses_SP = useSP;
885 >    fInfo_.SIM_uses_BoxDipole = useBoxDipole;
886 >    fInfo_.SIM_uses_AtomicVirial = useAtomicVirial_;
887    }
888  
889    void SimInfo::setupFortranSim() {
890      int isError;
891 <    int nExclude;
891 >    int nExclude, nOneTwo, nOneThree, nOneFour;
892      std::vector<int> fortranGlobalGroupMembership;
893      
784 –    nExclude = exclude_.getSize();
894      isError = 0;
895  
896      //globalGroupMembership_ is filled by SimCreator    
# Line 790 | Line 899 | namespace oopse {
899      }
900  
901      //calculate mass ratio of cutoff group
902 <    std::vector<double> mfact;
902 >    std::vector<RealType> mfact;
903      SimInfo::MoleculeIterator mi;
904      Molecule* mol;
905      Molecule::CutoffGroupIterator ci;
906      CutoffGroup* cg;
907      Molecule::AtomIterator ai;
908      Atom* atom;
909 <    double totalMass;
909 >    RealType totalMass;
910  
911      //to avoid memory reallocation, reserve enough space for mfact
912      mfact.reserve(getNCutoffGroups());
# Line 813 | Line 922 | namespace oopse {
922            else
923              mfact.push_back( 1.0 );
924          }
816 –
925        }      
926      }
927  
# Line 837 | Line 945 | namespace oopse {
945      }
946      
947      //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);
948  
949 <    if( isError ){
949 >    nExclude = excludedInteractions_.getSize();
950 >    nOneTwo = oneTwoInteractions_.getSize();
951 >    nOneThree = oneThreeInteractions_.getSize();
952 >    nOneFour = oneFourInteractions_.getSize();
953  
954 +    int* excludeList = excludedInteractions_.getPairList();
955 +    int* oneTwoList = oneTwoInteractions_.getPairList();
956 +    int* oneThreeList = oneThreeInteractions_.getPairList();
957 +    int* oneFourList = oneFourInteractions_.getPairList();
958 +
959 +    setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
960 +                   &nExclude, excludeList,
961 +                   &nOneTwo, oneTwoList,
962 +                   &nOneThree, oneThreeList,
963 +                   &nOneFour, oneFourList,
964 +                   &molMembershipArray[0], &mfact[0], &nCutoffGroups_,
965 +                   &fortranGlobalGroupMembership[0], &isError);
966 +    
967 +    if( isError ){
968 +      
969        sprintf( painCave.errMsg,
970                 "There was an error setting the simulation information in fortran.\n" );
971        painCave.isFatal = 1;
972        painCave.severity = OOPSE_ERROR;
973        simError();
974      }
975 <
976 < #ifdef IS_MPI
975 >    
976 >    
977      sprintf( checkPointMsg,
978               "succesfully sent the simulation information to fortran.\n");
979 <    MPIcheckPoint();
980 < #endif // is_mpi
979 >    
980 >    errorCheckPoint();
981 >    
982 >    // Setup number of neighbors in neighbor list if present
983 >    if (simParams_->haveNeighborListNeighbors()) {
984 >      int nlistNeighbors = simParams_->getNeighborListNeighbors();
985 >      setNeighbors(&nlistNeighbors);
986 >    }
987 >  
988 >
989    }
990  
991  
864 – #ifdef IS_MPI
992    void SimInfo::setupFortranParallel() {
993 <    
993 > #ifdef IS_MPI    
994      //SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
995      std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
996      std::vector<int> localToGlobalCutoffGroupIndex;
# Line 913 | Line 1040 | namespace oopse {
1040      }
1041  
1042      sprintf(checkPointMsg, " mpiRefresh successful.\n");
1043 <    MPIcheckPoint();
1043 >    errorCheckPoint();
1044  
1045 <
1045 > #endif
1046    }
1047  
921 – #endif
922 –
1048    void SimInfo::setupCutoff() {          
1049      
1050      ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
# Line 927 | Line 1052 | namespace oopse {
1052      // Check the cutoff policy
1053      int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
1054  
1055 +    // Set LJ shifting bools to false
1056 +    ljsp_ = false;
1057 +    ljsf_ = false;
1058 +
1059      std::string myPolicy;
1060      if (forceFieldOptions_.haveCutoffPolicy()){
1061        myPolicy = forceFieldOptions_.getCutoffPolicy();
# Line 957 | Line 1086 | namespace oopse {
1086      notifyFortranCutoffPolicy(&cp);
1087  
1088      // Check the Skin Thickness for neighborlists
1089 <    double skin;
1089 >    RealType skin;
1090      if (simParams_->haveSkinThickness()) {
1091        skin = simParams_->getSkinThickness();
1092        notifyFortranSkinThickness(&skin);
# Line 969 | Line 1098 | namespace oopse {
1098        if (simParams_->haveSwitchingRadius()) {
1099          rsw_  = simParams_->getSwitchingRadius();
1100        } else {
1101 <        rsw_ = rcut_;
1101 >        if (fInfo_.SIM_uses_Charges |
1102 >            fInfo_.SIM_uses_Dipoles |
1103 >            fInfo_.SIM_uses_RF) {
1104 >          
1105 >          rsw_ = 0.85 * rcut_;
1106 >          sprintf(painCave.errMsg,
1107 >                  "SimCreator Warning: No value was set for the switchingRadius.\n"
1108 >                  "\tOOPSE will use a default value of 85 percent of the cutoffRadius.\n"
1109 >                  "\tswitchingRadius = %f. for this simulation\n", rsw_);
1110 >        painCave.isFatal = 0;
1111 >        simError();
1112 >        } else {
1113 >          rsw_ = rcut_;
1114 >          sprintf(painCave.errMsg,
1115 >                  "SimCreator Warning: No value was set for the switchingRadius.\n"
1116 >                  "\tOOPSE will use the same value as the cutoffRadius.\n"
1117 >                  "\tswitchingRadius = %f. for this simulation\n", rsw_);
1118 >          painCave.isFatal = 0;
1119 >          simError();
1120 >        }
1121        }
1122 <      notifyFortranCutoffs(&rcut_, &rsw_);
1122 >
1123 >      if (simParams_->haveElectrostaticSummationMethod()) {
1124 >        std::string myMethod = simParams_->getElectrostaticSummationMethod();
1125 >        toUpper(myMethod);
1126 >        
1127 >        if (myMethod == "SHIFTED_POTENTIAL") {
1128 >          ljsp_ = true;
1129 >        } else if (myMethod == "SHIFTED_FORCE") {
1130 >          ljsf_ = true;
1131 >        }
1132 >      }
1133 >      notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1134        
1135      } else {
1136        
# Line 988 | Line 1147 | namespace oopse {
1147          if (simParams_->haveElectrostaticSummationMethod()) {
1148            std::string myMethod = simParams_->getElectrostaticSummationMethod();
1149            toUpper(myMethod);
1150 <          if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1150 >      
1151 >      // For the time being, we're tethering the LJ shifted behavior to the
1152 >      // electrostaticSummationMethod keyword options
1153 >          if (myMethod == "SHIFTED_POTENTIAL") {
1154 >            ljsp_ = true;
1155 >          } else if (myMethod == "SHIFTED_FORCE") {
1156 >            ljsf_ = true;
1157 >          }
1158 >          if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1159              if (simParams_->haveSwitchingRadius()){
1160                sprintf(painCave.errMsg,
1161                        "SimInfo Warning: A value was set for the switchingRadius\n"
# Line 1011 | Line 1178 | namespace oopse {
1178            simError();
1179            rsw_ = 0.85 * rcut_;
1180          }
1181 <        notifyFortranCutoffs(&rcut_, &rsw_);
1181 >
1182 >        notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1183 >
1184        } else {
1185          // We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1186          // We'll punt and let fortran figure out the cutoffs later.
# Line 1027 | Line 1196 | namespace oopse {
1196      int errorOut;
1197      int esm =  NONE;
1198      int sm = UNDAMPED;
1199 <    double alphaVal;
1200 <    double dielectric;
1201 <
1199 >    RealType alphaVal;
1200 >    RealType dielectric;
1201 >    
1202      errorOut = isError;
1034 –    alphaVal = simParams_->getDampingAlpha();
1035 –    dielectric = simParams_->getDielectric();
1203  
1204      if (simParams_->haveElectrostaticSummationMethod()) {
1205        std::string myMethod = simParams_->getElectrostaticSummationMethod();
# Line 1049 | Line 1216 | namespace oopse {
1216              if (myMethod == "SHIFTED_FORCE") {            
1217                esm = SHIFTED_FORCE;
1218              } else {
1219 <              if (myMethod == "REACTION_FIELD") {            
1219 >              if (myMethod == "REACTION_FIELD") {
1220                  esm = REACTION_FIELD;
1221 +                dielectric = simParams_->getDielectric();
1222 +                if (!simParams_->haveDielectric()) {
1223 +                  // throw warning
1224 +                  sprintf( painCave.errMsg,
1225 +                           "SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
1226 +                           "\tA default value of %f will be used for the dielectric.\n", dielectric);
1227 +                  painCave.isFatal = 0;
1228 +                  simError();
1229 +                }
1230                } else {
1231                  // throw error        
1232                  sprintf( painCave.errMsg,
# Line 1077 | Line 1253 | namespace oopse {
1253          if (myScreen == "DAMPED") {
1254            sm = DAMPED;
1255            if (!simParams_->haveDampingAlpha()) {
1256 <            //throw error
1256 >            // first set a cutoff dependent alpha value
1257 >            // we assume alpha depends linearly with rcut from 0 to 20.5 ang
1258 >            alphaVal = 0.5125 - rcut_* 0.025;
1259 >            // for values rcut > 20.5, alpha is zero
1260 >            if (alphaVal < 0) alphaVal = 0;
1261 >
1262 >            // throw warning
1263              sprintf( painCave.errMsg,
1264                       "SimInfo warning: dampingAlpha was not specified in the input file.\n"
1265 <                     "\tA default value of %f (1/ang) will be used.\n", alphaVal);
1265 >                     "\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1266              painCave.isFatal = 0;
1267              simError();
1268 +          } else {
1269 +            alphaVal = simParams_->getDampingAlpha();
1270            }
1271 +          
1272          } else {
1273            // throw error        
1274            sprintf( painCave.errMsg,
# Line 1132 | Line 1317 | namespace oopse {
1317  
1318    }
1319  
1320 +  void SimInfo::setupAccumulateBoxDipole() {    
1321 +
1322 +    // we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1323 +    if ( simParams_->haveAccumulateBoxDipole() )
1324 +      if ( simParams_->getAccumulateBoxDipole() ) {
1325 +        setAccumulateBoxDipole();
1326 +        calcBoxDipole_ = true;
1327 +      }
1328 +
1329 +  }
1330 +
1331    void SimInfo::addProperty(GenericData* genData) {
1332      properties_.addProperty(genData);  
1333    }
# Line 1188 | Line 1384 | namespace oopse {
1384      Molecule* mol;
1385  
1386      Vector3d comVel(0.0);
1387 <    double totalMass = 0.0;
1387 >    RealType totalMass = 0.0;
1388      
1389  
1390      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1391 <      double mass = mol->getMass();
1391 >      RealType mass = mol->getMass();
1392        totalMass += mass;
1393        comVel += mass * mol->getComVel();
1394      }  
1395  
1396   #ifdef IS_MPI
1397 <    double tmpMass = totalMass;
1397 >    RealType tmpMass = totalMass;
1398      Vector3d tmpComVel(comVel);    
1399 <    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1400 <    MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1399 >    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1400 >    MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1401   #endif
1402  
1403      comVel /= totalMass;
# Line 1214 | Line 1410 | namespace oopse {
1410      Molecule* mol;
1411  
1412      Vector3d com(0.0);
1413 <    double totalMass = 0.0;
1413 >    RealType totalMass = 0.0;
1414      
1415      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1416 <      double mass = mol->getMass();
1416 >      RealType mass = mol->getMass();
1417        totalMass += mass;
1418        com += mass * mol->getCom();
1419      }  
1420  
1421   #ifdef IS_MPI
1422 <    double tmpMass = totalMass;
1422 >    RealType tmpMass = totalMass;
1423      Vector3d tmpCom(com);    
1424 <    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1425 <    MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1424 >    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1425 >    MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1426   #endif
1427  
1428      com /= totalMass;
# Line 1250 | Line 1446 | namespace oopse {
1446        Molecule* mol;
1447        
1448      
1449 <      double totalMass = 0.0;
1449 >      RealType totalMass = 0.0;
1450      
1451  
1452        for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1453 <         double mass = mol->getMass();
1453 >         RealType mass = mol->getMass();
1454           totalMass += mass;
1455           com += mass * mol->getCom();
1456           comVel += mass * mol->getComVel();          
1457        }  
1458        
1459   #ifdef IS_MPI
1460 <      double tmpMass = totalMass;
1460 >      RealType tmpMass = totalMass;
1461        Vector3d tmpCom(com);  
1462        Vector3d tmpComVel(comVel);
1463 <      MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1464 <      MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1465 <      MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1463 >      MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1464 >      MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1465 >      MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1466   #endif
1467        
1468        com /= totalMass;
# Line 1285 | Line 1481 | namespace oopse {
1481     void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1482        
1483  
1484 <      double xx = 0.0;
1485 <      double yy = 0.0;
1486 <      double zz = 0.0;
1487 <      double xy = 0.0;
1488 <      double xz = 0.0;
1489 <      double yz = 0.0;
1484 >      RealType xx = 0.0;
1485 >      RealType yy = 0.0;
1486 >      RealType zz = 0.0;
1487 >      RealType xy = 0.0;
1488 >      RealType xz = 0.0;
1489 >      RealType yz = 0.0;
1490        Vector3d com(0.0);
1491        Vector3d comVel(0.0);
1492        
# Line 1302 | Line 1498 | namespace oopse {
1498        Vector3d thisq(0.0);
1499        Vector3d thisv(0.0);
1500  
1501 <      double thisMass = 0.0;
1501 >      RealType thisMass = 0.0;
1502      
1503        
1504        
# Line 1340 | Line 1536 | namespace oopse {
1536   #ifdef IS_MPI
1537        Mat3x3d tmpI(inertiaTensor);
1538        Vector3d tmpAngMom;
1539 <      MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1540 <      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1539 >      MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1540 >      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1541   #endif
1542                
1543        return;
# Line 1362 | Line 1558 | namespace oopse {
1558        Vector3d thisr(0.0);
1559        Vector3d thisp(0.0);
1560        
1561 <      double thisMass;
1561 >      RealType thisMass;
1562        
1563        for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {        
1564          thisMass = mol->getMass();
# Line 1375 | Line 1571 | namespace oopse {
1571        
1572   #ifdef IS_MPI
1573        Vector3d tmpAngMom;
1574 <      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1574 >      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1575   #endif
1576        
1577        return angularMomentum;
1578     }
1579    
1580 <  
1580 >  StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1581 >    return IOIndexToIntegrableObject.at(index);
1582 >  }
1583 >  
1584 >  void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1585 >    IOIndexToIntegrableObject= v;
1586 >  }
1587 >
1588 >  /* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1589 >     based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1590 >     where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1591 >     V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1592 >  */
1593 >  void SimInfo::getGyrationalVolume(RealType &volume){
1594 >    Mat3x3d intTensor;
1595 >    RealType det;
1596 >    Vector3d dummyAngMom;
1597 >    RealType sysconstants;
1598 >    RealType geomCnst;
1599 >
1600 >    geomCnst = 3.0/2.0;
1601 >    /* Get the inertial tensor and angular momentum for free*/
1602 >    getInertiaTensor(intTensor,dummyAngMom);
1603 >    
1604 >    det = intTensor.determinant();
1605 >    sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1606 >    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1607 >    return;
1608 >  }
1609 >
1610 >  void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1611 >    Mat3x3d intTensor;
1612 >    Vector3d dummyAngMom;
1613 >    RealType sysconstants;
1614 >    RealType geomCnst;
1615 >
1616 >    geomCnst = 3.0/2.0;
1617 >    /* Get the inertial tensor and angular momentum for free*/
1618 >    getInertiaTensor(intTensor,dummyAngMom);
1619 >    
1620 >    detI = intTensor.determinant();
1621 >    sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1622 >    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1623 >    return;
1624 >  }
1625 > /*
1626 >   void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1627 >      assert( v.size() == nAtoms_ + nRigidBodies_);
1628 >      sdByGlobalIndex_ = v;
1629 >    }
1630 >
1631 >    StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1632 >      //assert(index < nAtoms_ + nRigidBodies_);
1633 >      return sdByGlobalIndex_.at(index);
1634 >    }  
1635 > */  
1636   }//end namespace oopse
1637  

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines