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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 598 by chrisfen, Thu Sep 15 00:14:35 2005 UTC vs.
Revision 878 by chrisfen, Wed Feb 1 20:54:46 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/fCoulombicCorrection.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),
82 >    return result;
83 >  }
84 >  
85 >  SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
86 >    forceField_(ff), simParams_(simParams),
87      ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
88      nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
89      nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
# Line 77 | Line 91 | namespace oopse {
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 337 | Line 352 | namespace oopse {
352      int b;
353      int c;
354      int d;
355 +
356 +    std::map<int, std::set<int> > atomGroups;
357 +
358 +    Molecule::RigidBodyIterator rbIter;
359 +    RigidBody* rb;
360 +    Molecule::IntegrableObjectIterator ii;
361 +    StuntDouble* integrableObject;
362      
363 +    for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
364 +           integrableObject = mol->nextIntegrableObject(ii)) {
365 +
366 +      if (integrableObject->isRigidBody()) {
367 +          rb = static_cast<RigidBody*>(integrableObject);
368 +          std::vector<Atom*> atoms = rb->getAtoms();
369 +          std::set<int> rigidAtoms;
370 +          for (int i = 0; i < atoms.size(); ++i) {
371 +            rigidAtoms.insert(atoms[i]->getGlobalIndex());
372 +          }
373 +          for (int i = 0; i < atoms.size(); ++i) {
374 +            atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
375 +          }      
376 +      } else {
377 +        std::set<int> oneAtomSet;
378 +        oneAtomSet.insert(integrableObject->getGlobalIndex());
379 +        atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));        
380 +      }
381 +    }  
382 +
383 +    
384 +    
385      for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
386        a = bond->getAtomA()->getGlobalIndex();
387        b = bond->getAtomB()->getGlobalIndex();        
# Line 348 | Line 392 | namespace oopse {
392        a = bend->getAtomA()->getGlobalIndex();
393        b = bend->getAtomB()->getGlobalIndex();        
394        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_.addPair(a, b);
400 <      exclude_.addPair(a, c);
401 <      exclude_.addPair(b, c);        
399 >      exclude_.addPairs(rigidSetA, rigidSetB);
400 >      exclude_.addPairs(rigidSetA, rigidSetC);
401 >      exclude_.addPairs(rigidSetB, rigidSetC);
402 >      
403 >      //exclude_.addPair(a, b);
404 >      //exclude_.addPair(a, c);
405 >      //exclude_.addPair(b, c);        
406      }
407  
408      for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
# Line 359 | Line 410 | namespace oopse {
410        b = torsion->getAtomB()->getGlobalIndex();        
411        c = torsion->getAtomC()->getGlobalIndex();        
412        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);
417  
418 +      exclude_.addPairs(rigidSetA, rigidSetB);
419 +      exclude_.addPairs(rigidSetA, rigidSetC);
420 +      exclude_.addPairs(rigidSetA, rigidSetD);
421 +      exclude_.addPairs(rigidSetB, rigidSetC);
422 +      exclude_.addPairs(rigidSetB, rigidSetD);
423 +      exclude_.addPairs(rigidSetC, rigidSetD);
424 +
425 +      /*
426 +      exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
427 +      exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
428 +      exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
429 +      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 +      */
441      }
442  
371 –    Molecule::RigidBodyIterator rbIter;
372 –    RigidBody* rb;
443      for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
444        std::vector<Atom*> atoms = rb->getAtoms();
445        for (int i = 0; i < atoms.size() -1 ; ++i) {
# Line 394 | Line 464 | namespace oopse {
464      int b;
465      int c;
466      int d;
467 +
468 +    std::map<int, std::set<int> > atomGroups;
469 +
470 +    Molecule::RigidBodyIterator rbIter;
471 +    RigidBody* rb;
472 +    Molecule::IntegrableObjectIterator ii;
473 +    StuntDouble* integrableObject;
474      
475 +    for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
476 +           integrableObject = mol->nextIntegrableObject(ii)) {
477 +
478 +      if (integrableObject->isRigidBody()) {
479 +          rb = static_cast<RigidBody*>(integrableObject);
480 +          std::vector<Atom*> atoms = rb->getAtoms();
481 +          std::set<int> rigidAtoms;
482 +          for (int i = 0; i < atoms.size(); ++i) {
483 +            rigidAtoms.insert(atoms[i]->getGlobalIndex());
484 +          }
485 +          for (int i = 0; i < atoms.size(); ++i) {
486 +            atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
487 +          }      
488 +      } else {
489 +        std::set<int> oneAtomSet;
490 +        oneAtomSet.insert(integrableObject->getGlobalIndex());
491 +        atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));        
492 +      }
493 +    }  
494 +
495 +    
496      for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
497        a = bond->getAtomA()->getGlobalIndex();
498        b = bond->getAtomB()->getGlobalIndex();        
# Line 406 | Line 504 | namespace oopse {
504        b = bend->getAtomB()->getGlobalIndex();        
505        c = bend->getAtomC()->getGlobalIndex();
506  
507 <      exclude_.removePair(a, b);
508 <      exclude_.removePair(a, c);
509 <      exclude_.removePair(b, c);        
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);
514 >      
515 >      //exclude_.removePair(a, b);
516 >      //exclude_.removePair(a, c);
517 >      //exclude_.removePair(b, c);        
518      }
519  
520      for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
# Line 417 | Line 523 | namespace oopse {
523        c = torsion->getAtomC()->getGlobalIndex();        
524        d = torsion->getAtomD()->getGlobalIndex();        
525  
526 +      std::set<int> rigidSetA = getRigidSet(a, atomGroups);
527 +      std::set<int> rigidSetB = getRigidSet(b, atomGroups);
528 +      std::set<int> rigidSetC = getRigidSet(c, atomGroups);
529 +      std::set<int> rigidSetD = getRigidSet(d, atomGroups);
530 +
531 +      exclude_.removePairs(rigidSetA, rigidSetB);
532 +      exclude_.removePairs(rigidSetA, rigidSetC);
533 +      exclude_.removePairs(rigidSetA, rigidSetD);
534 +      exclude_.removePairs(rigidSetB, rigidSetC);
535 +      exclude_.removePairs(rigidSetB, rigidSetD);
536 +      exclude_.removePairs(rigidSetC, rigidSetD);
537 +
538 +      /*
539 +      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());
545 +
546 +      
547        exclude_.removePair(a, b);
548        exclude_.removePair(a, c);
549        exclude_.removePair(a, d);
550        exclude_.removePair(b, c);
551        exclude_.removePair(b, d);
552        exclude_.removePair(c, d);        
553 +      */
554      }
555  
428 –    Molecule::RigidBodyIterator rbIter;
429 –    RigidBody* rb;
556      for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
557        std::vector<Atom*> atoms = rb->getAtoms();
558        for (int i = 0; i < atoms.size() -1 ; ++i) {
# Line 465 | Line 591 | namespace oopse {
591      /** @deprecate */    
592      int isError = 0;
593      
594 <    setupCoulombicCorrection( isError );
594 >    setupElectrostaticSummationMethod( isError );
595 >    setupSwitchingFunction();
596  
597      if(isError){
598        sprintf( painCave.errMsg,
# Line 510 | Line 637 | namespace oopse {
637      int useLennardJones = 0;
638      int useElectrostatic = 0;
639      int useEAM = 0;
640 +    int useSC = 0;
641      int useCharge = 0;
642      int useDirectional = 0;
643      int useDipole = 0;
# Line 521 | Line 649 | namespace oopse {
649      int useDirectionalAtom = 0;    
650      int useElectrostatics = 0;
651      //usePBC and useRF are from simParams
652 <    int usePBC = simParams_->getPBC();
653 <    int useRF = simParams_->getUseRF();
652 >    int usePBC = simParams_->getUsePeriodicBoundaryConditions();
653 >    int useRF;
654 >    int useSF;
655 >    std::string myMethod;
656  
657 +    // set the useRF logical
658 +    useRF = 0;
659 +    useSF = 0;
660 +
661 +
662 +    if (simParams_->haveElectrostaticSummationMethod()) {
663 +      std::string myMethod = simParams_->getElectrostaticSummationMethod();
664 +      toUpper(myMethod);
665 +      if (myMethod == "REACTION_FIELD") {
666 +        useRF=1;
667 +      } else {
668 +        if (myMethod == "SHIFTED_FORCE") {
669 +          useSF = 1;
670 +        }
671 +      }
672 +    }
673 +
674      //loop over all of the atom types
675      for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
676        useLennardJones |= (*i)->isLennardJones();
677        useElectrostatic |= (*i)->isElectrostatic();
678        useEAM |= (*i)->isEAM();
679 +      useSC |= (*i)->isSC();
680        useCharge |= (*i)->isCharge();
681        useDirectional |= (*i)->isDirectional();
682        useDipole |= (*i)->isDipole();
# Line 579 | Line 727 | namespace oopse {
727      temp = useEAM;
728      MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
729  
730 +    temp = useSC;
731 +    MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
732 +    
733      temp = useShape;
734      MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);  
735  
# Line 588 | Line 739 | namespace oopse {
739      temp = useRF;
740      MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
741  
742 <    temp = useUW;
743 <    MPI_Allreduce(&temp, &useUW, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);  
742 >    temp = useSF;
743 >    MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
744  
594 –    temp = useDW;
595 –    MPI_Allreduce(&temp, &useDW, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);  
596 –    
745   #endif
746  
747      fInfo_.SIM_uses_PBC = usePBC;    
# Line 606 | Line 754 | namespace oopse {
754      fInfo_.SIM_uses_StickyPower = useStickyPower;
755      fInfo_.SIM_uses_GayBerne = useGayBerne;
756      fInfo_.SIM_uses_EAM = useEAM;
757 +    fInfo_.SIM_uses_SC = useSC;
758      fInfo_.SIM_uses_Shapes = useShape;
759      fInfo_.SIM_uses_FLARB = useFLARB;
760      fInfo_.SIM_uses_RF = useRF;
761 +    fInfo_.SIM_uses_SF = useSF;
762  
763 <    if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) {
764 <
763 >    if( myMethod == "REACTION_FIELD") {
764 >      
765        if (simParams_->haveDielectric()) {
766          fInfo_.dielect = simParams_->getDielectric();
767        } else {
# Line 621 | Line 771 | namespace oopse {
771                  "\tsetting a dielectric constant!\n");
772          painCave.isFatal = 1;
773          simError();
774 <      }
625 <        
626 <    } else {
627 <      fInfo_.dielect = 0.0;
774 >      }      
775      }
776  
777    }
# Line 660 | Line 807 | namespace oopse {
807  
808          totalMass = cg->getMass();
809          for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
810 <          mfact.push_back(atom->getMass()/totalMass);
810 >          // Check for massless groups - set mfact to 1 if true
811 >          if (totalMass != 0)
812 >            mfact.push_back(atom->getMass()/totalMass);
813 >          else
814 >            mfact.push_back( 1.0 );
815          }
816  
817        }      
# Line 769 | Line 920 | namespace oopse {
920  
921   #endif
922  
923 <  double SimInfo::calcMaxCutoffRadius() {
923 >  void SimInfo::setupCutoff() {          
924 >    
925 >    ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
926  
927 +    // Check the cutoff policy
928 +    int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
929  
930 <    std::set<AtomType*> atomTypes;
931 <    std::set<AtomType*>::iterator i;
932 <    std::vector<double> cutoffRadius;
933 <
934 <    //get the unique atom types
780 <    atomTypes = getUniqueAtomTypes();
781 <
782 <    //query the max cutoff radius among these atom types
783 <    for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
784 <      cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
930 >    std::string myPolicy;
931 >    if (forceFieldOptions_.haveCutoffPolicy()){
932 >      myPolicy = forceFieldOptions_.getCutoffPolicy();
933 >    }else if (simParams_->haveCutoffPolicy()) {
934 >      myPolicy = simParams_->getCutoffPolicy();
935      }
786 –
787 –    double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
788 – #ifdef IS_MPI
789 –    //pick the max cutoff radius among the processors
790 – #endif
936  
937 <    return maxCutoffRadius;
938 <  }
794 <
795 <  void SimInfo::getCutoff(double& rcut, double& rsw) {
796 <    
797 <    if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
798 <        
799 <      if (!simParams_->haveRcut()){
800 <        sprintf(painCave.errMsg,
801 <                "SimCreator Warning: No value was set for the cutoffRadius.\n"
802 <                "\tOOPSE will use a default value of 15.0 angstroms"
803 <                "\tfor the cutoffRadius.\n");
804 <        painCave.isFatal = 0;
805 <        simError();
806 <        rcut = 15.0;
807 <      } else{
808 <        rcut = simParams_->getRcut();
809 <      }
810 <
811 <      if (!simParams_->haveRsw()){
812 <        sprintf(painCave.errMsg,
813 <                "SimCreator Warning: No value was set for switchingRadius.\n"
814 <                "\tOOPSE will use a default value of\n"
815 <                "\t0.95 * cutoffRadius for the switchingRadius\n");
816 <        painCave.isFatal = 0;
817 <        simError();
818 <        rsw = 0.95 * rcut;
819 <      } else{
820 <        rsw = simParams_->getRsw();
821 <      }
822 <
823 <    } else {
824 <      // if charge, dipole or reaction field is not used and the cutofff radius is not specified in
825 <      //meta-data file, the maximum cutoff radius calculated from forcefiled will be used
826 <        
827 <      if (simParams_->haveRcut()) {
828 <        rcut = simParams_->getRcut();
829 <      } else {
830 <        //set cutoff radius to the maximum cutoff radius based on atom types in the whole system
831 <        rcut = calcMaxCutoffRadius();
832 <      }
833 <
834 <      if (simParams_->haveRsw()) {
835 <        rsw  = simParams_->getRsw();
836 <      } else {
837 <        rsw = rcut;
838 <      }
839 <    
840 <    }
841 <  }
842 <
843 <  void SimInfo::setupCutoff() {    
844 <    getCutoff(rcut_, rsw_);    
845 <    double rnblist = rcut_ + 1; // skin of neighbor list
846 <
847 <    //Pass these cutoff radius etc. to fortran. This function should be called once and only once
848 <    
849 <    int cp =  TRADITIONAL_CUTOFF_POLICY;
850 <    if (simParams_->haveCutoffPolicy()) {
851 <      std::string myPolicy = simParams_->getCutoffPolicy();
937 >    if (!myPolicy.empty()){
938 >      toUpper(myPolicy);
939        if (myPolicy == "MIX") {
940          cp = MIX_CUTOFF_POLICY;
941        } else {
# Line 866 | Line 953 | namespace oopse {
953            }    
954          }          
955        }
956 +    }          
957 +    notifyFortranCutoffPolicy(&cp);
958 +
959 +    // Check the Skin Thickness for neighborlists
960 +    double skin;
961 +    if (simParams_->haveSkinThickness()) {
962 +      skin = simParams_->getSkinThickness();
963 +      notifyFortranSkinThickness(&skin);
964 +    }            
965 +        
966 +    // Check if the cutoff was set explicitly:
967 +    if (simParams_->haveCutoffRadius()) {
968 +      rcut_ = simParams_->getCutoffRadius();
969 +      if (simParams_->haveSwitchingRadius()) {
970 +        rsw_  = simParams_->getSwitchingRadius();
971 +      } else {
972 +        if (fInfo_.SIM_uses_Charges |
973 +            fInfo_.SIM_uses_Dipoles |
974 +            fInfo_.SIM_uses_RF) {
975 +          
976 +          rsw_ = 0.85 * rcut_;
977 +          sprintf(painCave.errMsg,
978 +                  "SimCreator Warning: No value was set for the switchingRadius.\n"
979 +                  "\tOOPSE will use a default value of 85\% of the cutoffRadius"
980 +                  "\tswitchingRadius = %f. for this simulation\n", rsw_);
981 +        painCave.isFatal = 0;
982 +        simError();
983 +        } else {
984 +          rsw_ = rcut_;
985 +          sprintf(painCave.errMsg,
986 +                  "SimCreator Warning: No value was set for the switchingRadius.\n"
987 +                  "\tOOPSE will use the same value as the cutoffRadius.\n"
988 +                  "\tswitchingRadius = %f. for this simulation\n", rsw_);
989 +          painCave.isFatal = 0;
990 +          simError();
991 +        }
992 +          
993 +      notifyFortranCutoffs(&rcut_, &rsw_);
994 +      
995 +    } else {
996 +      
997 +      // For electrostatic atoms, we'll assume a large safe value:
998 +      if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
999 +        sprintf(painCave.errMsg,
1000 +                "SimCreator Warning: No value was set for the cutoffRadius.\n"
1001 +                "\tOOPSE will use a default value of 15.0 angstroms"
1002 +                "\tfor the cutoffRadius.\n");
1003 +        painCave.isFatal = 0;
1004 +        simError();
1005 +        rcut_ = 15.0;
1006 +      
1007 +        if (simParams_->haveElectrostaticSummationMethod()) {
1008 +          std::string myMethod = simParams_->getElectrostaticSummationMethod();
1009 +          toUpper(myMethod);
1010 +          if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1011 +            if (simParams_->haveSwitchingRadius()){
1012 +              sprintf(painCave.errMsg,
1013 +                      "SimInfo Warning: A value was set for the switchingRadius\n"
1014 +                      "\teven though the electrostaticSummationMethod was\n"
1015 +                      "\tset to %s\n", myMethod.c_str());
1016 +              painCave.isFatal = 1;
1017 +              simError();            
1018 +            }
1019 +          }
1020 +        }
1021 +      
1022 +        if (simParams_->haveSwitchingRadius()){
1023 +          rsw_ = simParams_->getSwitchingRadius();
1024 +        } else {        
1025 +          sprintf(painCave.errMsg,
1026 +                  "SimCreator Warning: No value was set for switchingRadius.\n"
1027 +                  "\tOOPSE will use a default value of\n"
1028 +                  "\t0.85 * cutoffRadius for the switchingRadius\n");
1029 +          painCave.isFatal = 0;
1030 +          simError();
1031 +          rsw_ = 0.85 * rcut_;
1032 +        }
1033 +        notifyFortranCutoffs(&rcut_, &rsw_);
1034 +      } else {
1035 +        // We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1036 +        // We'll punt and let fortran figure out the cutoffs later.
1037 +        
1038 +        notifyFortranYouAreOnYourOwn();
1039 +
1040 +      }
1041      }
870 –    notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp);
1042    }
1043  
1044 <  void SimInfo::setupCoulombicCorrection( int isError ) {    
1044 >  void SimInfo::setupElectrostaticSummationMethod( int isError ) {    
1045      
1046      int errorOut;
1047 <    int cc =  NONE;
1047 >    int esm =  NONE;
1048 >    int sm = UNDAMPED;
1049      double alphaVal;
1050 +    double dielectric;
1051  
1052      errorOut = isError;
1053 +    alphaVal = simParams_->getDampingAlpha();
1054 +    dielectric = simParams_->getDielectric();
1055  
1056 <    if (simParams_->haveCoulombicCorrection()) {
1057 <      std::string myCorrection = simParams_->getCoulombicCorrection();
1058 <      if (myCorrection == "NONE") {
1059 <        cc = NONE;
1056 >    if (simParams_->haveElectrostaticSummationMethod()) {
1057 >      std::string myMethod = simParams_->getElectrostaticSummationMethod();
1058 >      toUpper(myMethod);
1059 >      if (myMethod == "NONE") {
1060 >        esm = NONE;
1061        } else {
1062 <        if (myCorrection == "UNDAMPED_WOLF") {
1063 <          cc = UNDAMPED_WOLF;
1062 >        if (myMethod == "SWITCHING_FUNCTION") {
1063 >          esm = SWITCHING_FUNCTION;
1064          } else {
1065 <          if (myCorrection == "WOLF") {            
1066 <            cc = WOLF;
1067 <            if (!simParams_->haveDampingAlpha()) {
1068 <              //throw error
1069 <              sprintf( painCave.errMsg,
894 <                       "SimInfo warning: dampingAlpha was not specified in the input file. A default value of %f (1/ang) will be used for the Wolf Coulombic Correction.", simParams_->getDampingAlpha());
895 <              painCave.isFatal = 0;
896 <              simError();
897 <            }
898 <            alphaVal = simParams_->getDampingAlpha();
899 <          } else {
900 <            if (myCorrection == "REACTION_FIELD") {
901 <              cc = REACTION_FIELD;
1065 >          if (myMethod == "SHIFTED_POTENTIAL") {
1066 >            esm = SHIFTED_POTENTIAL;
1067 >          } else {
1068 >            if (myMethod == "SHIFTED_FORCE") {            
1069 >              esm = SHIFTED_FORCE;
1070              } else {
1071 <              // throw error        
1072 <              sprintf( painCave.errMsg,
1073 <                       "SimInfo error: Unknown coulombicCorrection. (Input file specified %s .)\n\tcoulombicCorrection must be one of: \"none\", \"undamped_wolf\", \"wolf\", or \"reaction_field\".", myCorrection.c_str() );
1074 <              painCave.isFatal = 1;
1075 <              simError();
1076 <            }    
1077 <          }          
1071 >              if (myMethod == "REACTION_FIELD") {            
1072 >                esm = REACTION_FIELD;
1073 >              } else {
1074 >                // throw error        
1075 >                sprintf( painCave.errMsg,
1076 >                         "SimInfo error: Unknown electrostaticSummationMethod.\n"
1077 >                         "\t(Input file specified %s .)\n"
1078 >                         "\telectrostaticSummationMethod must be one of: \"none\",\n"
1079 >                         "\t\"shifted_potential\", \"shifted_force\", or \n"
1080 >                         "\t\"reaction_field\".\n", myMethod.c_str() );
1081 >                painCave.isFatal = 1;
1082 >                simError();
1083 >              }    
1084 >            }          
1085 >          }
1086          }
1087        }
1088      }
1089 <    initFortranFF( &fInfo_.SIM_uses_RF, &cc, &alphaVal, &errorOut );
1089 >    
1090 >    if (simParams_->haveElectrostaticScreeningMethod()) {
1091 >      std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1092 >      toUpper(myScreen);
1093 >      if (myScreen == "UNDAMPED") {
1094 >        sm = UNDAMPED;
1095 >      } else {
1096 >        if (myScreen == "DAMPED") {
1097 >          sm = DAMPED;
1098 >          if (!simParams_->haveDampingAlpha()) {
1099 >            //throw error
1100 >            sprintf( painCave.errMsg,
1101 >                     "SimInfo warning: dampingAlpha was not specified in the input file.\n"
1102 >                     "\tA default value of %f (1/ang) will be used.\n", alphaVal);
1103 >            painCave.isFatal = 0;
1104 >            simError();
1105 >          }
1106 >        } else {
1107 >          // throw error        
1108 >          sprintf( painCave.errMsg,
1109 >                   "SimInfo error: Unknown electrostaticScreeningMethod.\n"
1110 >                   "\t(Input file specified %s .)\n"
1111 >                   "\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1112 >                   "or \"damped\".\n", myScreen.c_str() );
1113 >          painCave.isFatal = 1;
1114 >          simError();
1115 >        }
1116 >      }
1117 >    }
1118 >    
1119 >    // let's pass some summation method variables to fortran
1120 >    setElectrostaticSummationMethod( &esm );
1121 >    setFortranElectrostaticMethod( &esm );
1122 >    setScreeningMethod( &sm );
1123 >    setDampingAlpha( &alphaVal );
1124 >    setReactionFieldDielectric( &dielectric );
1125 >    initFortranFF( &errorOut );
1126 >  }
1127 >
1128 >  void SimInfo::setupSwitchingFunction() {    
1129 >    int ft = CUBIC;
1130 >
1131 >    if (simParams_->haveSwitchingFunctionType()) {
1132 >      std::string funcType = simParams_->getSwitchingFunctionType();
1133 >      toUpper(funcType);
1134 >      if (funcType == "CUBIC") {
1135 >        ft = CUBIC;
1136 >      } else {
1137 >        if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1138 >          ft = FIFTH_ORDER_POLY;
1139 >        } else {
1140 >          // throw error        
1141 >          sprintf( painCave.errMsg,
1142 >                   "SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1143 >          painCave.isFatal = 1;
1144 >          simError();
1145 >        }          
1146 >      }
1147 >    }
1148 >
1149 >    // send switching function notification to switcheroo
1150 >    setFunctionType(&ft);
1151 >
1152    }
1153  
1154    void SimInfo::addProperty(GenericData* genData) {

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