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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 608 by chrisfen, Fri Sep 16 21:07:45 2005 UTC vs.
Revision 963 by tim, Wed May 17 21:51:42 2006 UTC

# Line 48 | Line 48
48  
49   #include <algorithm>
50   #include <set>
51 + #include <map>
52  
53   #include "brains/SimInfo.hpp"
54   #include "math/Vector3.hpp"
55   #include "primitives/Molecule.hpp"
56   #include "UseTheForce/fCutoffPolicy.h"
57   #include "UseTheForce/DarkSide/fElectrostaticSummationMethod.h"
58 + #include "UseTheForce/DarkSide/fElectrostaticScreeningMethod.h"
59 + #include "UseTheForce/DarkSide/fSwitchingFunctionType.h"
60   #include "UseTheForce/doForces_interface.h"
61 < #include "UseTheForce/notifyCutoffs_interface.h"
61 > #include "UseTheForce/DarkSide/electrostatic_interface.h"
62 > #include "UseTheForce/DarkSide/switcheroo_interface.h"
63   #include "utils/MemoryUtils.hpp"
64   #include "utils/simError.h"
65   #include "selection/SelectionManager.hpp"
66 + #include "io/ForceFieldOptions.hpp"
67 + #include "UseTheForce/ForceField.hpp"
68  
69   #ifdef IS_MPI
70   #include "UseTheForce/mpiComponentPlan.h"
# Line 66 | Line 72 | namespace oopse {
72   #endif
73  
74   namespace oopse {
75 +  std::set<int> getRigidSet(int index, std::map<int, std::set<int> >& container) {
76 +    std::map<int, std::set<int> >::iterator i = container.find(index);
77 +    std::set<int> result;
78 +    if (i != container.end()) {
79 +        result = i->second;
80 +    }
81  
82 <  SimInfo::SimInfo(MakeStamps* stamps, std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
83 <                   ForceField* ff, Globals* simParams) :
84 <    stamps_(stamps), forceField_(ff), simParams_(simParams),
85 <    ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
82 >    return result;
83 >  }
84 >  
85 >  SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
86 >    forceField_(ff), simParams_(simParams),
87 >    ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
88      nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
89      nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
90      nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nRigidBodies_(0),
91      nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
92      sman_(NULL), fortranInitialized_(false) {
93  
80 –            
81 –      std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
94        MoleculeStamp* molStamp;
95        int nMolWithSameStamp;
96        int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
97 <      int nGroups = 0;          //total cutoff groups defined in meta-data file
97 >      int nGroups = 0;      //total cutoff groups defined in meta-data file
98        CutoffGroupStamp* cgStamp;    
99        RigidBodyStamp* rbStamp;
100        int nRigidAtoms = 0;
101 <    
102 <      for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
103 <        molStamp = i->first;
104 <        nMolWithSameStamp = i->second;
101 >      std::vector<Component*> components = simParams->getComponents();
102 >      
103 >      for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
104 >        molStamp = (*i)->getMoleculeStamp();
105 >        nMolWithSameStamp = (*i)->getNMol();
106          
107          addMoleculeStamp(molStamp, nMolWithSameStamp);
108  
109          //calculate atoms in molecules
110          nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;  
111  
99 –
112          //calculate atoms in cutoff groups
113          int nAtomsInGroups = 0;
114          int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
115          
116          for (int j=0; j < nCutoffGroupsInStamp; j++) {
117 <          cgStamp = molStamp->getCutoffGroup(j);
117 >          cgStamp = molStamp->getCutoffGroupStamp(j);
118            nAtomsInGroups += cgStamp->getNMembers();
119          }
120  
121          nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
122 +
123          nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;            
124  
125          //calculate atoms in rigid bodies
# Line 114 | Line 127 | namespace oopse {
127          int nRigidBodiesInStamp = molStamp->getNRigidBodies();
128          
129          for (int j=0; j < nRigidBodiesInStamp; j++) {
130 <          rbStamp = molStamp->getRigidBody(j);
130 >          rbStamp = molStamp->getRigidBodyStamp(j);
131            nAtomsInRigidBodies += rbStamp->getNMembers();
132          }
133  
# Line 123 | Line 136 | namespace oopse {
136          
137        }
138  
139 <      //every free atom (atom does not belong to cutoff groups) is a cutoff group
140 <      //therefore the total number of cutoff groups in the system is equal to
141 <      //the total number of atoms minus number of atoms belong to cutoff group defined in meta-data
142 <      //file plus the number of cutoff groups defined in meta-data file
139 >      //every free atom (atom does not belong to cutoff groups) is a cutoff
140 >      //group therefore the total number of cutoff groups in the system is
141 >      //equal to the total number of atoms minus number of atoms belong to
142 >      //cutoff group defined in meta-data file plus the number of cutoff
143 >      //groups defined in meta-data file
144        nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
145  
146 <      //every free atom (atom does not belong to rigid bodies) is an integrable object
147 <      //therefore the total number of  integrable objects in the system is equal to
148 <      //the total number of atoms minus number of atoms belong to  rigid body defined in meta-data
149 <      //file plus the number of  rigid bodies defined in meta-data file
150 <      nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_;
151 <
146 >      //every free atom (atom does not belong to rigid bodies) is an
147 >      //integrable object therefore the total number of integrable objects
148 >      //in the system is equal to the total number of atoms minus number of
149 >      //atoms belong to rigid body defined in meta-data file plus the number
150 >      //of rigid bodies defined in meta-data file
151 >      nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
152 >                                                + nGlobalRigidBodies_;
153 >  
154        nGlobalMols_ = molStampIds_.size();
155  
156   #ifdef IS_MPI    
# Line 150 | Line 166 | namespace oopse {
166      }
167      molecules_.clear();
168        
153 –    delete stamps_;
169      delete sman_;
170      delete simParams_;
171      delete forceField_;
# Line 257 | Line 272 | namespace oopse {
272            }
273          }
274              
275 <      }//end for (integrableObject)
276 <    }// end for (mol)
275 >      }
276 >    }
277      
278      // n_constraints is local, so subtract them on each processor
279      ndf_local -= nConstraints_;
# Line 275 | Line 290 | namespace oopse {
290  
291    }
292  
293 +  int SimInfo::getFdf() {
294 + #ifdef IS_MPI
295 +    MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
296 + #else
297 +    fdf_ = fdf_local;
298 + #endif
299 +    return fdf_;
300 +  }
301 +    
302    void SimInfo::calcNdfRaw() {
303      int ndfRaw_local;
304  
# Line 337 | Line 361 | namespace oopse {
361      int b;
362      int c;
363      int d;
364 +
365 +    std::map<int, std::set<int> > atomGroups;
366 +
367 +    Molecule::RigidBodyIterator rbIter;
368 +    RigidBody* rb;
369 +    Molecule::IntegrableObjectIterator ii;
370 +    StuntDouble* integrableObject;
371      
372 +    for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
373 +           integrableObject = mol->nextIntegrableObject(ii)) {
374 +
375 +      if (integrableObject->isRigidBody()) {
376 +          rb = static_cast<RigidBody*>(integrableObject);
377 +          std::vector<Atom*> atoms = rb->getAtoms();
378 +          std::set<int> rigidAtoms;
379 +          for (int i = 0; i < atoms.size(); ++i) {
380 +            rigidAtoms.insert(atoms[i]->getGlobalIndex());
381 +          }
382 +          for (int i = 0; i < atoms.size(); ++i) {
383 +            atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
384 +          }      
385 +      } else {
386 +        std::set<int> oneAtomSet;
387 +        oneAtomSet.insert(integrableObject->getGlobalIndex());
388 +        atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));        
389 +      }
390 +    }  
391 +
392 +    
393 +    
394      for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
395        a = bond->getAtomA()->getGlobalIndex();
396        b = bond->getAtomB()->getGlobalIndex();        
# Line 348 | Line 401 | namespace oopse {
401        a = bend->getAtomA()->getGlobalIndex();
402        b = bend->getAtomB()->getGlobalIndex();        
403        c = bend->getAtomC()->getGlobalIndex();
404 +      std::set<int> rigidSetA = getRigidSet(a, atomGroups);
405 +      std::set<int> rigidSetB = getRigidSet(b, atomGroups);
406 +      std::set<int> rigidSetC = getRigidSet(c, atomGroups);
407  
408 <      exclude_.addPair(a, b);
409 <      exclude_.addPair(a, c);
410 <      exclude_.addPair(b, c);        
408 >      exclude_.addPairs(rigidSetA, rigidSetB);
409 >      exclude_.addPairs(rigidSetA, rigidSetC);
410 >      exclude_.addPairs(rigidSetB, rigidSetC);
411 >      
412 >      //exclude_.addPair(a, b);
413 >      //exclude_.addPair(a, c);
414 >      //exclude_.addPair(b, c);        
415      }
416  
417      for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
# Line 359 | Line 419 | namespace oopse {
419        b = torsion->getAtomB()->getGlobalIndex();        
420        c = torsion->getAtomC()->getGlobalIndex();        
421        d = torsion->getAtomD()->getGlobalIndex();        
422 +      std::set<int> rigidSetA = getRigidSet(a, atomGroups);
423 +      std::set<int> rigidSetB = getRigidSet(b, atomGroups);
424 +      std::set<int> rigidSetC = getRigidSet(c, atomGroups);
425 +      std::set<int> rigidSetD = getRigidSet(d, atomGroups);
426  
427 +      exclude_.addPairs(rigidSetA, rigidSetB);
428 +      exclude_.addPairs(rigidSetA, rigidSetC);
429 +      exclude_.addPairs(rigidSetA, rigidSetD);
430 +      exclude_.addPairs(rigidSetB, rigidSetC);
431 +      exclude_.addPairs(rigidSetB, rigidSetD);
432 +      exclude_.addPairs(rigidSetC, rigidSetD);
433 +
434 +      /*
435 +      exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
436 +      exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
437 +      exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
438 +      exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
439 +      exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
440 +      exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
441 +        
442 +      
443        exclude_.addPair(a, b);
444        exclude_.addPair(a, c);
445        exclude_.addPair(a, d);
446        exclude_.addPair(b, c);
447        exclude_.addPair(b, d);
448        exclude_.addPair(c, d);        
449 +      */
450      }
451  
371 –    Molecule::RigidBodyIterator rbIter;
372 –    RigidBody* rb;
452      for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
453        std::vector<Atom*> atoms = rb->getAtoms();
454        for (int i = 0; i < atoms.size() -1 ; ++i) {
# Line 394 | Line 473 | namespace oopse {
473      int b;
474      int c;
475      int d;
476 +
477 +    std::map<int, std::set<int> > atomGroups;
478 +
479 +    Molecule::RigidBodyIterator rbIter;
480 +    RigidBody* rb;
481 +    Molecule::IntegrableObjectIterator ii;
482 +    StuntDouble* integrableObject;
483 +    
484 +    for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
485 +           integrableObject = mol->nextIntegrableObject(ii)) {
486 +
487 +      if (integrableObject->isRigidBody()) {
488 +          rb = static_cast<RigidBody*>(integrableObject);
489 +          std::vector<Atom*> atoms = rb->getAtoms();
490 +          std::set<int> rigidAtoms;
491 +          for (int i = 0; i < atoms.size(); ++i) {
492 +            rigidAtoms.insert(atoms[i]->getGlobalIndex());
493 +          }
494 +          for (int i = 0; i < atoms.size(); ++i) {
495 +            atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
496 +          }      
497 +      } else {
498 +        std::set<int> oneAtomSet;
499 +        oneAtomSet.insert(integrableObject->getGlobalIndex());
500 +        atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));        
501 +      }
502 +    }  
503 +
504      
505      for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
506        a = bond->getAtomA()->getGlobalIndex();
# Line 406 | Line 513 | namespace oopse {
513        b = bend->getAtomB()->getGlobalIndex();        
514        c = bend->getAtomC()->getGlobalIndex();
515  
516 <      exclude_.removePair(a, b);
517 <      exclude_.removePair(a, c);
518 <      exclude_.removePair(b, c);        
516 >      std::set<int> rigidSetA = getRigidSet(a, atomGroups);
517 >      std::set<int> rigidSetB = getRigidSet(b, atomGroups);
518 >      std::set<int> rigidSetC = getRigidSet(c, atomGroups);
519 >
520 >      exclude_.removePairs(rigidSetA, rigidSetB);
521 >      exclude_.removePairs(rigidSetA, rigidSetC);
522 >      exclude_.removePairs(rigidSetB, rigidSetC);
523 >      
524 >      //exclude_.removePair(a, b);
525 >      //exclude_.removePair(a, c);
526 >      //exclude_.removePair(b, c);        
527      }
528  
529      for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
# Line 417 | Line 532 | namespace oopse {
532        c = torsion->getAtomC()->getGlobalIndex();        
533        d = torsion->getAtomD()->getGlobalIndex();        
534  
535 +      std::set<int> rigidSetA = getRigidSet(a, atomGroups);
536 +      std::set<int> rigidSetB = getRigidSet(b, atomGroups);
537 +      std::set<int> rigidSetC = getRigidSet(c, atomGroups);
538 +      std::set<int> rigidSetD = getRigidSet(d, atomGroups);
539 +
540 +      exclude_.removePairs(rigidSetA, rigidSetB);
541 +      exclude_.removePairs(rigidSetA, rigidSetC);
542 +      exclude_.removePairs(rigidSetA, rigidSetD);
543 +      exclude_.removePairs(rigidSetB, rigidSetC);
544 +      exclude_.removePairs(rigidSetB, rigidSetD);
545 +      exclude_.removePairs(rigidSetC, rigidSetD);
546 +
547 +      /*
548 +      exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
549 +      exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
550 +      exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
551 +      exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
552 +      exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
553 +      exclude_.removePairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
554 +
555 +      
556        exclude_.removePair(a, b);
557        exclude_.removePair(a, c);
558        exclude_.removePair(a, d);
559        exclude_.removePair(b, c);
560        exclude_.removePair(b, d);
561        exclude_.removePair(c, d);        
562 +      */
563      }
564  
428 –    Molecule::RigidBodyIterator rbIter;
429 –    RigidBody* rb;
565      for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
566        std::vector<Atom*> atoms = rb->getAtoms();
567        for (int i = 0; i < atoms.size() -1 ; ++i) {
# Line 466 | Line 601 | namespace oopse {
601      int isError = 0;
602      
603      setupElectrostaticSummationMethod( isError );
604 +    setupSwitchingFunction();
605  
606      if(isError){
607        sprintf( painCave.errMsg,
# Line 510 | Line 646 | namespace oopse {
646      int useLennardJones = 0;
647      int useElectrostatic = 0;
648      int useEAM = 0;
649 +    int useSC = 0;
650      int useCharge = 0;
651      int useDirectional = 0;
652      int useDipole = 0;
# Line 521 | Line 658 | namespace oopse {
658      int useDirectionalAtom = 0;    
659      int useElectrostatics = 0;
660      //usePBC and useRF are from simParams
661 <    int usePBC = simParams_->getPBC();
661 >    int usePBC = simParams_->getUsePeriodicBoundaryConditions();
662 >    int useRF;
663 >    int useSF;
664 >    std::string myMethod;
665  
666 +    // set the useRF logical
667 +    useRF = 0;
668 +    useSF = 0;
669 +
670 +
671 +    if (simParams_->haveElectrostaticSummationMethod()) {
672 +      std::string myMethod = simParams_->getElectrostaticSummationMethod();
673 +      toUpper(myMethod);
674 +      if (myMethod == "REACTION_FIELD") {
675 +        useRF=1;
676 +      } else {
677 +        if (myMethod == "SHIFTED_FORCE") {
678 +          useSF = 1;
679 +        }
680 +      }
681 +    }
682 +
683      //loop over all of the atom types
684      for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
685        useLennardJones |= (*i)->isLennardJones();
686        useElectrostatic |= (*i)->isElectrostatic();
687        useEAM |= (*i)->isEAM();
688 +      useSC |= (*i)->isSC();
689        useCharge |= (*i)->isCharge();
690        useDirectional |= (*i)->isDirectional();
691        useDipole |= (*i)->isDipole();
# Line 578 | Line 736 | namespace oopse {
736      temp = useEAM;
737      MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
738  
739 +    temp = useSC;
740 +    MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
741 +    
742      temp = useShape;
743      MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);  
744  
745      temp = useFLARB;
746      MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
747  
748 +    temp = useRF;
749 +    MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
750 +
751 +    temp = useSF;
752 +    MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
753 +
754   #endif
755  
756      fInfo_.SIM_uses_PBC = usePBC;    
# Line 596 | Line 763 | namespace oopse {
763      fInfo_.SIM_uses_StickyPower = useStickyPower;
764      fInfo_.SIM_uses_GayBerne = useGayBerne;
765      fInfo_.SIM_uses_EAM = useEAM;
766 +    fInfo_.SIM_uses_SC = useSC;
767      fInfo_.SIM_uses_Shapes = useShape;
768      fInfo_.SIM_uses_FLARB = useFLARB;
769 +    fInfo_.SIM_uses_RF = useRF;
770 +    fInfo_.SIM_uses_SF = useSF;
771  
772 <    if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) {
773 <
772 >    if( myMethod == "REACTION_FIELD") {
773 >      
774        if (simParams_->haveDielectric()) {
775          fInfo_.dielect = simParams_->getDielectric();
776        } else {
# Line 610 | Line 780 | namespace oopse {
780                  "\tsetting a dielectric constant!\n");
781          painCave.isFatal = 1;
782          simError();
783 <      }
614 <        
615 <    } else {
616 <      fInfo_.dielect = 0.0;
783 >      }      
784      }
785  
786    }
# Line 632 | Line 799 | namespace oopse {
799      }
800  
801      //calculate mass ratio of cutoff group
802 <    std::vector<double> mfact;
802 >    std::vector<RealType> mfact;
803      SimInfo::MoleculeIterator mi;
804      Molecule* mol;
805      Molecule::CutoffGroupIterator ci;
806      CutoffGroup* cg;
807      Molecule::AtomIterator ai;
808      Atom* atom;
809 <    double totalMass;
809 >    RealType totalMass;
810  
811      //to avoid memory reallocation, reserve enough space for mfact
812      mfact.reserve(getNCutoffGroups());
# Line 649 | Line 816 | namespace oopse {
816  
817          totalMass = cg->getMass();
818          for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
819 <          mfact.push_back(atom->getMass()/totalMass);
819 >          // Check for massless groups - set mfact to 1 if true
820 >          if (totalMass != 0)
821 >            mfact.push_back(atom->getMass()/totalMass);
822 >          else
823 >            mfact.push_back( 1.0 );
824          }
825  
826        }      
# Line 758 | Line 929 | namespace oopse {
929  
930   #endif
931  
932 <  double SimInfo::calcMaxCutoffRadius() {
932 >  void SimInfo::setupCutoff() {          
933 >    
934 >    ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
935  
936 +    // Check the cutoff policy
937 +    int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
938  
939 <    std::set<AtomType*> atomTypes;
940 <    std::set<AtomType*>::iterator i;
941 <    std::vector<double> cutoffRadius;
942 <
943 <    //get the unique atom types
769 <    atomTypes = getUniqueAtomTypes();
770 <
771 <    //query the max cutoff radius among these atom types
772 <    for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
773 <      cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
939 >    std::string myPolicy;
940 >    if (forceFieldOptions_.haveCutoffPolicy()){
941 >      myPolicy = forceFieldOptions_.getCutoffPolicy();
942 >    }else if (simParams_->haveCutoffPolicy()) {
943 >      myPolicy = simParams_->getCutoffPolicy();
944      }
945  
946 <    double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
947 < #ifdef IS_MPI
778 <    //pick the max cutoff radius among the processors
779 < #endif
780 <
781 <    return maxCutoffRadius;
782 <  }
783 <
784 <  void SimInfo::getCutoff(double& rcut, double& rsw) {
785 <    
786 <    if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
787 <        
788 <      if (!simParams_->haveRcut()){
789 <        sprintf(painCave.errMsg,
790 <                "SimCreator Warning: No value was set for the cutoffRadius.\n"
791 <                "\tOOPSE will use a default value of 15.0 angstroms"
792 <                "\tfor the cutoffRadius.\n");
793 <        painCave.isFatal = 0;
794 <        simError();
795 <        rcut = 15.0;
796 <      } else{
797 <        rcut = simParams_->getRcut();
798 <      }
799 <
800 <      if (!simParams_->haveRsw()){
801 <        sprintf(painCave.errMsg,
802 <                "SimCreator Warning: No value was set for switchingRadius.\n"
803 <                "\tOOPSE will use a default value of\n"
804 <                "\t0.95 * cutoffRadius for the switchingRadius\n");
805 <        painCave.isFatal = 0;
806 <        simError();
807 <        rsw = 0.95 * rcut;
808 <      } else{
809 <        rsw = simParams_->getRsw();
810 <      }
811 <
812 <    } else {
813 <      // if charge, dipole or reaction field is not used and the cutofff radius is not specified in
814 <      //meta-data file, the maximum cutoff radius calculated from forcefiled will be used
815 <        
816 <      if (simParams_->haveRcut()) {
817 <        rcut = simParams_->getRcut();
818 <      } else {
819 <        //set cutoff radius to the maximum cutoff radius based on atom types in the whole system
820 <        rcut = calcMaxCutoffRadius();
821 <      }
822 <
823 <      if (simParams_->haveRsw()) {
824 <        rsw  = simParams_->getRsw();
825 <      } else {
826 <        rsw = rcut;
827 <      }
828 <    
829 <    }
830 <  }
831 <
832 <  void SimInfo::setupCutoff() {    
833 <    getCutoff(rcut_, rsw_);    
834 <    double rnblist = rcut_ + 1; // skin of neighbor list
835 <
836 <    //Pass these cutoff radius etc. to fortran. This function should be called once and only once
837 <    
838 <    int cp =  TRADITIONAL_CUTOFF_POLICY;
839 <    if (simParams_->haveCutoffPolicy()) {
840 <      std::string myPolicy = simParams_->getCutoffPolicy();
946 >    if (!myPolicy.empty()){
947 >      toUpper(myPolicy);
948        if (myPolicy == "MIX") {
949          cp = MIX_CUTOFF_POLICY;
950        } else {
# Line 855 | Line 962 | namespace oopse {
962            }    
963          }          
964        }
965 +    }          
966 +    notifyFortranCutoffPolicy(&cp);
967 +
968 +    // Check the Skin Thickness for neighborlists
969 +    RealType skin;
970 +    if (simParams_->haveSkinThickness()) {
971 +      skin = simParams_->getSkinThickness();
972 +      notifyFortranSkinThickness(&skin);
973 +    }            
974 +        
975 +    // Check if the cutoff was set explicitly:
976 +    if (simParams_->haveCutoffRadius()) {
977 +      rcut_ = simParams_->getCutoffRadius();
978 +      if (simParams_->haveSwitchingRadius()) {
979 +        rsw_  = simParams_->getSwitchingRadius();
980 +      } else {
981 +        if (fInfo_.SIM_uses_Charges |
982 +            fInfo_.SIM_uses_Dipoles |
983 +            fInfo_.SIM_uses_RF) {
984 +          
985 +          rsw_ = 0.85 * rcut_;
986 +          sprintf(painCave.errMsg,
987 +                  "SimCreator Warning: No value was set for the switchingRadius.\n"
988 +                  "\tOOPSE will use a default value of 85 percent of the cutoffRadius.\n"
989 +                  "\tswitchingRadius = %f. for this simulation\n", rsw_);
990 +        painCave.isFatal = 0;
991 +        simError();
992 +        } else {
993 +          rsw_ = rcut_;
994 +          sprintf(painCave.errMsg,
995 +                  "SimCreator Warning: No value was set for the switchingRadius.\n"
996 +                  "\tOOPSE will use the same value as the cutoffRadius.\n"
997 +                  "\tswitchingRadius = %f. for this simulation\n", rsw_);
998 +          painCave.isFatal = 0;
999 +          simError();
1000 +        }
1001 +      }
1002 +      
1003 +      notifyFortranCutoffs(&rcut_, &rsw_);
1004 +      
1005 +    } else {
1006 +      
1007 +      // For electrostatic atoms, we'll assume a large safe value:
1008 +      if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
1009 +        sprintf(painCave.errMsg,
1010 +                "SimCreator Warning: No value was set for the cutoffRadius.\n"
1011 +                "\tOOPSE will use a default value of 15.0 angstroms"
1012 +                "\tfor the cutoffRadius.\n");
1013 +        painCave.isFatal = 0;
1014 +        simError();
1015 +        rcut_ = 15.0;
1016 +      
1017 +        if (simParams_->haveElectrostaticSummationMethod()) {
1018 +          std::string myMethod = simParams_->getElectrostaticSummationMethod();
1019 +          toUpper(myMethod);
1020 +          if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1021 +            if (simParams_->haveSwitchingRadius()){
1022 +              sprintf(painCave.errMsg,
1023 +                      "SimInfo Warning: A value was set for the switchingRadius\n"
1024 +                      "\teven though the electrostaticSummationMethod was\n"
1025 +                      "\tset to %s\n", myMethod.c_str());
1026 +              painCave.isFatal = 1;
1027 +              simError();            
1028 +            }
1029 +          }
1030 +        }
1031 +      
1032 +        if (simParams_->haveSwitchingRadius()){
1033 +          rsw_ = simParams_->getSwitchingRadius();
1034 +        } else {        
1035 +          sprintf(painCave.errMsg,
1036 +                  "SimCreator Warning: No value was set for switchingRadius.\n"
1037 +                  "\tOOPSE will use a default value of\n"
1038 +                  "\t0.85 * cutoffRadius for the switchingRadius\n");
1039 +          painCave.isFatal = 0;
1040 +          simError();
1041 +          rsw_ = 0.85 * rcut_;
1042 +        }
1043 +        notifyFortranCutoffs(&rcut_, &rsw_);
1044 +      } else {
1045 +        // We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1046 +        // We'll punt and let fortran figure out the cutoffs later.
1047 +        
1048 +        notifyFortranYouAreOnYourOwn();
1049 +
1050 +      }
1051      }
859 –    notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp);
1052    }
1053  
1054    void SimInfo::setupElectrostaticSummationMethod( int isError ) {    
1055      
1056      int errorOut;
1057      int esm =  NONE;
1058 <    double alphaVal;
1058 >    int sm = UNDAMPED;
1059 >    RealType alphaVal;
1060 >    RealType dielectric;
1061  
1062      errorOut = isError;
1063 +    alphaVal = simParams_->getDampingAlpha();
1064 +    dielectric = simParams_->getDielectric();
1065  
1066      if (simParams_->haveElectrostaticSummationMethod()) {
1067        std::string myMethod = simParams_->getElectrostaticSummationMethod();
1068 +      toUpper(myMethod);
1069        if (myMethod == "NONE") {
1070          esm = NONE;
1071        } else {
1072 <        if (myMethod == "UNDAMPED_WOLF") {
1073 <          esm = UNDAMPED_WOLF;
1074 <        } else {
1075 <          if (myMethod == "DAMPED_WOLF") {            
1076 <            esm = DAMPED_WOLF;
1077 <            if (!simParams_->haveDampingAlpha()) {
1078 <              //throw error
1079 <              sprintf( painCave.errMsg,
883 <                       "SimInfo warning: dampingAlpha was not specified in the input file. A default value of %f (1/ang) will be used for the Damped Wolf Method.", simParams_->getDampingAlpha());
884 <              painCave.isFatal = 0;
885 <              simError();
886 <            }
887 <            alphaVal = simParams_->getDampingAlpha();
888 <          } else {
889 <            if (myMethod == "REACTION_FIELD") {
890 <              esm = REACTION_FIELD;
1072 >        if (myMethod == "SWITCHING_FUNCTION") {
1073 >          esm = SWITCHING_FUNCTION;
1074 >        } else {
1075 >          if (myMethod == "SHIFTED_POTENTIAL") {
1076 >            esm = SHIFTED_POTENTIAL;
1077 >          } else {
1078 >            if (myMethod == "SHIFTED_FORCE") {            
1079 >              esm = SHIFTED_FORCE;
1080              } else {
1081 <              // throw error        
1082 <              sprintf( painCave.errMsg,
1083 <                       "SimInfo error: Unknown electrostaticSummationMethod. (Input file specified %s .)\n\telectrostaticSummationMethod must be one of: \"none\", \"undamped_wolf\", \"damped_wolf\", or \"reaction_field\".", myMethod.c_str() );
1084 <              painCave.isFatal = 1;
1085 <              simError();
1086 <            }    
1087 <          }          
1081 >              if (myMethod == "REACTION_FIELD") {            
1082 >                esm = REACTION_FIELD;
1083 >              } else {
1084 >                // throw error        
1085 >                sprintf( painCave.errMsg,
1086 >                         "SimInfo error: Unknown electrostaticSummationMethod.\n"
1087 >                         "\t(Input file specified %s .)\n"
1088 >                         "\telectrostaticSummationMethod must be one of: \"none\",\n"
1089 >                         "\t\"shifted_potential\", \"shifted_force\", or \n"
1090 >                         "\t\"reaction_field\".\n", myMethod.c_str() );
1091 >                painCave.isFatal = 1;
1092 >                simError();
1093 >              }    
1094 >            }          
1095 >          }
1096          }
1097        }
1098      }
1099 <    initFortranFF( &esm, &alphaVal, &errorOut );
1099 >    
1100 >    if (simParams_->haveElectrostaticScreeningMethod()) {
1101 >      std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1102 >      toUpper(myScreen);
1103 >      if (myScreen == "UNDAMPED") {
1104 >        sm = UNDAMPED;
1105 >      } else {
1106 >        if (myScreen == "DAMPED") {
1107 >          sm = DAMPED;
1108 >          if (!simParams_->haveDampingAlpha()) {
1109 >            //throw error
1110 >            sprintf( painCave.errMsg,
1111 >                     "SimInfo warning: dampingAlpha was not specified in the input file.\n"
1112 >                     "\tA default value of %f (1/ang) will be used.\n", alphaVal);
1113 >            painCave.isFatal = 0;
1114 >            simError();
1115 >          }
1116 >        } else {
1117 >          // throw error        
1118 >          sprintf( painCave.errMsg,
1119 >                   "SimInfo error: Unknown electrostaticScreeningMethod.\n"
1120 >                   "\t(Input file specified %s .)\n"
1121 >                   "\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1122 >                   "or \"damped\".\n", myScreen.c_str() );
1123 >          painCave.isFatal = 1;
1124 >          simError();
1125 >        }
1126 >      }
1127 >    }
1128 >    
1129 >    // let's pass some summation method variables to fortran
1130 >    setElectrostaticSummationMethod( &esm );
1131 >    setFortranElectrostaticMethod( &esm );
1132 >    setScreeningMethod( &sm );
1133 >    setDampingAlpha( &alphaVal );
1134 >    setReactionFieldDielectric( &dielectric );
1135 >    initFortranFF( &errorOut );
1136    }
1137  
1138 +  void SimInfo::setupSwitchingFunction() {    
1139 +    int ft = CUBIC;
1140 +
1141 +    if (simParams_->haveSwitchingFunctionType()) {
1142 +      std::string funcType = simParams_->getSwitchingFunctionType();
1143 +      toUpper(funcType);
1144 +      if (funcType == "CUBIC") {
1145 +        ft = CUBIC;
1146 +      } else {
1147 +        if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1148 +          ft = FIFTH_ORDER_POLY;
1149 +        } else {
1150 +          // throw error        
1151 +          sprintf( painCave.errMsg,
1152 +                   "SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1153 +          painCave.isFatal = 1;
1154 +          simError();
1155 +        }          
1156 +      }
1157 +    }
1158 +
1159 +    // send switching function notification to switcheroo
1160 +    setFunctionType(&ft);
1161 +
1162 +  }
1163 +
1164    void SimInfo::addProperty(GenericData* genData) {
1165      properties_.addProperty(genData);  
1166    }
# Line 958 | Line 1217 | namespace oopse {
1217      Molecule* mol;
1218  
1219      Vector3d comVel(0.0);
1220 <    double totalMass = 0.0;
1220 >    RealType totalMass = 0.0;
1221      
1222  
1223      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1224 <      double mass = mol->getMass();
1224 >      RealType mass = mol->getMass();
1225        totalMass += mass;
1226        comVel += mass * mol->getComVel();
1227      }  
1228  
1229   #ifdef IS_MPI
1230 <    double tmpMass = totalMass;
1230 >    RealType tmpMass = totalMass;
1231      Vector3d tmpComVel(comVel);    
1232 <    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1233 <    MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1232 >    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1233 >    MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1234   #endif
1235  
1236      comVel /= totalMass;
# Line 984 | Line 1243 | namespace oopse {
1243      Molecule* mol;
1244  
1245      Vector3d com(0.0);
1246 <    double totalMass = 0.0;
1246 >    RealType totalMass = 0.0;
1247      
1248      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1249 <      double mass = mol->getMass();
1249 >      RealType mass = mol->getMass();
1250        totalMass += mass;
1251        com += mass * mol->getCom();
1252      }  
1253  
1254   #ifdef IS_MPI
1255 <    double tmpMass = totalMass;
1255 >    RealType tmpMass = totalMass;
1256      Vector3d tmpCom(com);    
1257 <    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1258 <    MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1257 >    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1258 >    MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1259   #endif
1260  
1261      com /= totalMass;
# Line 1020 | Line 1279 | namespace oopse {
1279        Molecule* mol;
1280        
1281      
1282 <      double totalMass = 0.0;
1282 >      RealType totalMass = 0.0;
1283      
1284  
1285        for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1286 <         double mass = mol->getMass();
1286 >         RealType mass = mol->getMass();
1287           totalMass += mass;
1288           com += mass * mol->getCom();
1289           comVel += mass * mol->getComVel();          
1290        }  
1291        
1292   #ifdef IS_MPI
1293 <      double tmpMass = totalMass;
1293 >      RealType tmpMass = totalMass;
1294        Vector3d tmpCom(com);  
1295        Vector3d tmpComVel(comVel);
1296 <      MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1297 <      MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1298 <      MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1296 >      MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1297 >      MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1298 >      MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1299   #endif
1300        
1301        com /= totalMass;
# Line 1055 | Line 1314 | namespace oopse {
1314     void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1315        
1316  
1317 <      double xx = 0.0;
1318 <      double yy = 0.0;
1319 <      double zz = 0.0;
1320 <      double xy = 0.0;
1321 <      double xz = 0.0;
1322 <      double yz = 0.0;
1317 >      RealType xx = 0.0;
1318 >      RealType yy = 0.0;
1319 >      RealType zz = 0.0;
1320 >      RealType xy = 0.0;
1321 >      RealType xz = 0.0;
1322 >      RealType yz = 0.0;
1323        Vector3d com(0.0);
1324        Vector3d comVel(0.0);
1325        
# Line 1072 | Line 1331 | namespace oopse {
1331        Vector3d thisq(0.0);
1332        Vector3d thisv(0.0);
1333  
1334 <      double thisMass = 0.0;
1334 >      RealType thisMass = 0.0;
1335      
1336        
1337        
# Line 1110 | Line 1369 | namespace oopse {
1369   #ifdef IS_MPI
1370        Mat3x3d tmpI(inertiaTensor);
1371        Vector3d tmpAngMom;
1372 <      MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1373 <      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1372 >      MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1373 >      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1374   #endif
1375                
1376        return;
# Line 1132 | Line 1391 | namespace oopse {
1391        Vector3d thisr(0.0);
1392        Vector3d thisp(0.0);
1393        
1394 <      double thisMass;
1394 >      RealType thisMass;
1395        
1396        for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {        
1397          thisMass = mol->getMass();
# Line 1145 | Line 1404 | namespace oopse {
1404        
1405   #ifdef IS_MPI
1406        Vector3d tmpAngMom;
1407 <      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1407 >      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1408   #endif
1409        
1410        return angularMomentum;

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