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root/group/trunk/OOPSE-2.0/src/brains/SimInfo.cpp
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Comparing trunk/OOPSE-2.0/src/brains/SimInfo.cpp (file contents):
Revision 2307 by chrisfen, Fri Sep 16 21:07:45 2005 UTC vs.
Revision 2508 by gezelter, Mon Dec 12 19:32:50 2005 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"
# Line 66 | Line 70 | namespace oopse {
70   #endif
71  
72   namespace oopse {
73 +  std::set<int> getRigidSet(int index, std::map<int, std::set<int> >& container) {
74 +    std::map<int, std::set<int> >::iterator i = container.find(index);
75 +    std::set<int> result;
76 +    if (i != container.end()) {
77 +        result = i->second;
78 +    }
79  
80 <  SimInfo::SimInfo(MakeStamps* stamps, std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
81 <                   ForceField* ff, Globals* simParams) :
82 <    stamps_(stamps), forceField_(ff), simParams_(simParams),
80 >    return result;
81 >  }
82 >  
83 >  SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
84 >    forceField_(ff), simParams_(simParams),
85      ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
86      nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
87      nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
# Line 77 | Line 89 | namespace oopse {
89      nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
90      sman_(NULL), fortranInitialized_(false) {
91  
80 –            
81 –      std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
92        MoleculeStamp* molStamp;
93        int nMolWithSameStamp;
94        int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
95 <      int nGroups = 0;          //total cutoff groups defined in meta-data file
95 >      int nGroups = 0;      //total cutoff groups defined in meta-data file
96        CutoffGroupStamp* cgStamp;    
97        RigidBodyStamp* rbStamp;
98        int nRigidAtoms = 0;
99 <    
100 <      for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
101 <        molStamp = i->first;
102 <        nMolWithSameStamp = i->second;
99 >      std::vector<Component*> components = simParams->getComponents();
100 >      
101 >      for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
102 >        molStamp = (*i)->getMoleculeStamp();
103 >        nMolWithSameStamp = (*i)->getNMol();
104          
105          addMoleculeStamp(molStamp, nMolWithSameStamp);
106  
107          //calculate atoms in molecules
108          nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;  
109  
99 –
110          //calculate atoms in cutoff groups
111          int nAtomsInGroups = 0;
112          int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
113          
114          for (int j=0; j < nCutoffGroupsInStamp; j++) {
115 <          cgStamp = molStamp->getCutoffGroup(j);
115 >          cgStamp = molStamp->getCutoffGroupStamp(j);
116            nAtomsInGroups += cgStamp->getNMembers();
117          }
118  
119          nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
120 +
121          nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;            
122  
123          //calculate atoms in rigid bodies
# Line 114 | Line 125 | namespace oopse {
125          int nRigidBodiesInStamp = molStamp->getNRigidBodies();
126          
127          for (int j=0; j < nRigidBodiesInStamp; j++) {
128 <          rbStamp = molStamp->getRigidBody(j);
128 >          rbStamp = molStamp->getRigidBodyStamp(j);
129            nAtomsInRigidBodies += rbStamp->getNMembers();
130          }
131  
# Line 123 | Line 134 | namespace oopse {
134          
135        }
136  
137 <      //every free atom (atom does not belong to cutoff groups) is a cutoff group
138 <      //therefore the total number of cutoff groups in the system is equal to
139 <      //the total number of atoms minus number of atoms belong to cutoff group defined in meta-data
140 <      //file plus the number of cutoff groups defined in meta-data file
137 >      //every free atom (atom does not belong to cutoff groups) is a cutoff
138 >      //group therefore the total number of cutoff groups in the system is
139 >      //equal to the total number of atoms minus number of atoms belong to
140 >      //cutoff group defined in meta-data file plus the number of cutoff
141 >      //groups defined in meta-data file
142        nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
143  
144 <      //every free atom (atom does not belong to rigid bodies) is an integrable object
145 <      //therefore the total number of  integrable objects in the system is equal to
146 <      //the total number of atoms minus number of atoms belong to  rigid body defined in meta-data
147 <      //file plus the number of  rigid bodies defined in meta-data file
148 <      nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_;
149 <
144 >      //every free atom (atom does not belong to rigid bodies) is an
145 >      //integrable object therefore the total number of integrable objects
146 >      //in the system is equal to the total number of atoms minus number of
147 >      //atoms belong to rigid body defined in meta-data file plus the number
148 >      //of rigid bodies defined in meta-data file
149 >      nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
150 >                                                + nGlobalRigidBodies_;
151 >  
152        nGlobalMols_ = molStampIds_.size();
153  
154   #ifdef IS_MPI    
# Line 150 | Line 164 | namespace oopse {
164      }
165      molecules_.clear();
166        
153 –    delete stamps_;
167      delete sman_;
168      delete simParams_;
169      delete forceField_;
# Line 257 | Line 270 | namespace oopse {
270            }
271          }
272              
273 <      }//end for (integrableObject)
274 <    }// end for (mol)
273 >      }
274 >    }
275      
276      // n_constraints is local, so subtract them on each processor
277      ndf_local -= nConstraints_;
# Line 337 | Line 350 | namespace oopse {
350      int b;
351      int c;
352      int d;
353 +
354 +    std::map<int, std::set<int> > atomGroups;
355 +
356 +    Molecule::RigidBodyIterator rbIter;
357 +    RigidBody* rb;
358 +    Molecule::IntegrableObjectIterator ii;
359 +    StuntDouble* integrableObject;
360      
361 +    for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
362 +           integrableObject = mol->nextIntegrableObject(ii)) {
363 +
364 +      if (integrableObject->isRigidBody()) {
365 +          rb = static_cast<RigidBody*>(integrableObject);
366 +          std::vector<Atom*> atoms = rb->getAtoms();
367 +          std::set<int> rigidAtoms;
368 +          for (int i = 0; i < atoms.size(); ++i) {
369 +            rigidAtoms.insert(atoms[i]->getGlobalIndex());
370 +          }
371 +          for (int i = 0; i < atoms.size(); ++i) {
372 +            atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
373 +          }      
374 +      } else {
375 +        std::set<int> oneAtomSet;
376 +        oneAtomSet.insert(integrableObject->getGlobalIndex());
377 +        atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));        
378 +      }
379 +    }  
380 +
381 +    
382 +    
383      for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
384        a = bond->getAtomA()->getGlobalIndex();
385        b = bond->getAtomB()->getGlobalIndex();        
# Line 348 | Line 390 | namespace oopse {
390        a = bend->getAtomA()->getGlobalIndex();
391        b = bend->getAtomB()->getGlobalIndex();        
392        c = bend->getAtomC()->getGlobalIndex();
393 +      std::set<int> rigidSetA = getRigidSet(a, atomGroups);
394 +      std::set<int> rigidSetB = getRigidSet(b, atomGroups);
395 +      std::set<int> rigidSetC = getRigidSet(c, atomGroups);
396  
397 <      exclude_.addPair(a, b);
398 <      exclude_.addPair(a, c);
399 <      exclude_.addPair(b, c);        
397 >      exclude_.addPairs(rigidSetA, rigidSetB);
398 >      exclude_.addPairs(rigidSetA, rigidSetC);
399 >      exclude_.addPairs(rigidSetB, rigidSetC);
400 >      
401 >      //exclude_.addPair(a, b);
402 >      //exclude_.addPair(a, c);
403 >      //exclude_.addPair(b, c);        
404      }
405  
406      for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
# Line 359 | Line 408 | namespace oopse {
408        b = torsion->getAtomB()->getGlobalIndex();        
409        c = torsion->getAtomC()->getGlobalIndex();        
410        d = torsion->getAtomD()->getGlobalIndex();        
411 +      std::set<int> rigidSetA = getRigidSet(a, atomGroups);
412 +      std::set<int> rigidSetB = getRigidSet(b, atomGroups);
413 +      std::set<int> rigidSetC = getRigidSet(c, atomGroups);
414 +      std::set<int> rigidSetD = getRigidSet(d, atomGroups);
415  
416 +      exclude_.addPairs(rigidSetA, rigidSetB);
417 +      exclude_.addPairs(rigidSetA, rigidSetC);
418 +      exclude_.addPairs(rigidSetA, rigidSetD);
419 +      exclude_.addPairs(rigidSetB, rigidSetC);
420 +      exclude_.addPairs(rigidSetB, rigidSetD);
421 +      exclude_.addPairs(rigidSetC, rigidSetD);
422 +
423 +      /*
424 +      exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
425 +      exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
426 +      exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
427 +      exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
428 +      exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
429 +      exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
430 +        
431 +      
432        exclude_.addPair(a, b);
433        exclude_.addPair(a, c);
434        exclude_.addPair(a, d);
435        exclude_.addPair(b, c);
436        exclude_.addPair(b, d);
437        exclude_.addPair(c, d);        
438 +      */
439      }
440  
371 –    Molecule::RigidBodyIterator rbIter;
372 –    RigidBody* rb;
441      for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
442        std::vector<Atom*> atoms = rb->getAtoms();
443        for (int i = 0; i < atoms.size() -1 ; ++i) {
# Line 394 | Line 462 | namespace oopse {
462      int b;
463      int c;
464      int d;
465 +
466 +    std::map<int, std::set<int> > atomGroups;
467 +
468 +    Molecule::RigidBodyIterator rbIter;
469 +    RigidBody* rb;
470 +    Molecule::IntegrableObjectIterator ii;
471 +    StuntDouble* integrableObject;
472      
473 +    for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
474 +           integrableObject = mol->nextIntegrableObject(ii)) {
475 +
476 +      if (integrableObject->isRigidBody()) {
477 +          rb = static_cast<RigidBody*>(integrableObject);
478 +          std::vector<Atom*> atoms = rb->getAtoms();
479 +          std::set<int> rigidAtoms;
480 +          for (int i = 0; i < atoms.size(); ++i) {
481 +            rigidAtoms.insert(atoms[i]->getGlobalIndex());
482 +          }
483 +          for (int i = 0; i < atoms.size(); ++i) {
484 +            atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
485 +          }      
486 +      } else {
487 +        std::set<int> oneAtomSet;
488 +        oneAtomSet.insert(integrableObject->getGlobalIndex());
489 +        atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));        
490 +      }
491 +    }  
492 +
493 +    
494      for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
495        a = bond->getAtomA()->getGlobalIndex();
496        b = bond->getAtomB()->getGlobalIndex();        
# Line 406 | Line 502 | namespace oopse {
502        b = bend->getAtomB()->getGlobalIndex();        
503        c = bend->getAtomC()->getGlobalIndex();
504  
505 <      exclude_.removePair(a, b);
506 <      exclude_.removePair(a, c);
507 <      exclude_.removePair(b, c);        
505 >      std::set<int> rigidSetA = getRigidSet(a, atomGroups);
506 >      std::set<int> rigidSetB = getRigidSet(b, atomGroups);
507 >      std::set<int> rigidSetC = getRigidSet(c, atomGroups);
508 >
509 >      exclude_.removePairs(rigidSetA, rigidSetB);
510 >      exclude_.removePairs(rigidSetA, rigidSetC);
511 >      exclude_.removePairs(rigidSetB, rigidSetC);
512 >      
513 >      //exclude_.removePair(a, b);
514 >      //exclude_.removePair(a, c);
515 >      //exclude_.removePair(b, c);        
516      }
517  
518      for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
# Line 417 | Line 521 | namespace oopse {
521        c = torsion->getAtomC()->getGlobalIndex();        
522        d = torsion->getAtomD()->getGlobalIndex();        
523  
524 +      std::set<int> rigidSetA = getRigidSet(a, atomGroups);
525 +      std::set<int> rigidSetB = getRigidSet(b, atomGroups);
526 +      std::set<int> rigidSetC = getRigidSet(c, atomGroups);
527 +      std::set<int> rigidSetD = getRigidSet(d, atomGroups);
528 +
529 +      exclude_.removePairs(rigidSetA, rigidSetB);
530 +      exclude_.removePairs(rigidSetA, rigidSetC);
531 +      exclude_.removePairs(rigidSetA, rigidSetD);
532 +      exclude_.removePairs(rigidSetB, rigidSetC);
533 +      exclude_.removePairs(rigidSetB, rigidSetD);
534 +      exclude_.removePairs(rigidSetC, rigidSetD);
535 +
536 +      /*
537 +      exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
538 +      exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
539 +      exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
540 +      exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
541 +      exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
542 +      exclude_.removePairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
543 +
544 +      
545        exclude_.removePair(a, b);
546        exclude_.removePair(a, c);
547        exclude_.removePair(a, d);
548        exclude_.removePair(b, c);
549        exclude_.removePair(b, d);
550        exclude_.removePair(c, d);        
551 +      */
552      }
553  
428 –    Molecule::RigidBodyIterator rbIter;
429 –    RigidBody* rb;
554      for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
555        std::vector<Atom*> atoms = rb->getAtoms();
556        for (int i = 0; i < atoms.size() -1 ; ++i) {
# Line 466 | Line 590 | namespace oopse {
590      int isError = 0;
591      
592      setupElectrostaticSummationMethod( isError );
593 +    setupSwitchingFunction();
594  
595      if(isError){
596        sprintf( painCave.errMsg,
# Line 510 | Line 635 | namespace oopse {
635      int useLennardJones = 0;
636      int useElectrostatic = 0;
637      int useEAM = 0;
638 +    int useSC = 0;
639      int useCharge = 0;
640      int useDirectional = 0;
641      int useDipole = 0;
# Line 521 | Line 647 | namespace oopse {
647      int useDirectionalAtom = 0;    
648      int useElectrostatics = 0;
649      //usePBC and useRF are from simParams
650 <    int usePBC = simParams_->getPBC();
650 >    int usePBC = simParams_->getUsePeriodicBoundaryConditions();
651 >    int useRF;
652 >    int useSF;
653 >    std::string myMethod;
654  
655 +    // set the useRF logical
656 +    useRF = 0;
657 +    useSF = 0;
658 +
659 +
660 +    if (simParams_->haveElectrostaticSummationMethod()) {
661 +      std::string myMethod = simParams_->getElectrostaticSummationMethod();
662 +      toUpper(myMethod);
663 +      if (myMethod == "REACTION_FIELD") {
664 +        useRF=1;
665 +      } else {
666 +        if (myMethod == "SHIFTED_FORCE") {
667 +          useSF = 1;
668 +        }
669 +      }
670 +    }
671 +
672      //loop over all of the atom types
673      for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
674        useLennardJones |= (*i)->isLennardJones();
675        useElectrostatic |= (*i)->isElectrostatic();
676        useEAM |= (*i)->isEAM();
677 +      useSC |= (*i)->isSC();
678        useCharge |= (*i)->isCharge();
679        useDirectional |= (*i)->isDirectional();
680        useDipole |= (*i)->isDipole();
# Line 578 | Line 725 | namespace oopse {
725      temp = useEAM;
726      MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
727  
728 +    temp = useSC;
729 +    MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
730 +    
731      temp = useShape;
732      MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);  
733  
734      temp = useFLARB;
735      MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
736  
737 +    temp = useRF;
738 +    MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
739 +
740 +    temp = useSF;
741 +    MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
742 +
743   #endif
744  
745      fInfo_.SIM_uses_PBC = usePBC;    
# Line 596 | Line 752 | namespace oopse {
752      fInfo_.SIM_uses_StickyPower = useStickyPower;
753      fInfo_.SIM_uses_GayBerne = useGayBerne;
754      fInfo_.SIM_uses_EAM = useEAM;
755 +    fInfo_.SIM_uses_SC = useSC;
756      fInfo_.SIM_uses_Shapes = useShape;
757      fInfo_.SIM_uses_FLARB = useFLARB;
758 +    fInfo_.SIM_uses_RF = useRF;
759 +    fInfo_.SIM_uses_SF = useSF;
760  
761 <    if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) {
762 <
761 >    if( myMethod == "REACTION_FIELD") {
762 >      
763        if (simParams_->haveDielectric()) {
764          fInfo_.dielect = simParams_->getDielectric();
765        } else {
# Line 610 | Line 769 | namespace oopse {
769                  "\tsetting a dielectric constant!\n");
770          painCave.isFatal = 1;
771          simError();
772 <      }
614 <        
615 <    } else {
616 <      fInfo_.dielect = 0.0;
772 >      }      
773      }
774  
775    }
# Line 649 | Line 805 | namespace oopse {
805  
806          totalMass = cg->getMass();
807          for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
808 <          mfact.push_back(atom->getMass()/totalMass);
808 >          // Check for massless groups - set mfact to 1 if true
809 >          if (totalMass != 0)
810 >            mfact.push_back(atom->getMass()/totalMass);
811 >          else
812 >            mfact.push_back( 1.0 );
813          }
814  
815        }      
# Line 758 | Line 918 | namespace oopse {
918  
919   #endif
920  
921 <  double SimInfo::calcMaxCutoffRadius() {
762 <
763 <
764 <    std::set<AtomType*> atomTypes;
765 <    std::set<AtomType*>::iterator i;
766 <    std::vector<double> cutoffRadius;
767 <
768 <    //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));
774 <    }
775 <
776 <    double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
777 < #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) {
921 >  void SimInfo::setupCutoff() {          
922      
923 <    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 <    
923 >    // Check the cutoff policy
924      int cp =  TRADITIONAL_CUTOFF_POLICY;
925      if (simParams_->haveCutoffPolicy()) {
926        std::string myPolicy = simParams_->getCutoffPolicy();
927 +      toUpper(myPolicy);
928        if (myPolicy == "MIX") {
929          cp = MIX_CUTOFF_POLICY;
930        } else {
# Line 854 | Line 941 | namespace oopse {
941              simError();
942            }    
943          }          
944 +      }
945 +    }          
946 +    notifyFortranCutoffPolicy(&cp);
947 +
948 +    // Check the Skin Thickness for neighborlists
949 +    double skin;
950 +    if (simParams_->haveSkinThickness()) {
951 +      skin = simParams_->getSkinThickness();
952 +      notifyFortranSkinThickness(&skin);
953 +    }            
954 +        
955 +    // Check if the cutoff was set explicitly:
956 +    if (simParams_->haveCutoffRadius()) {
957 +      rcut_ = simParams_->getCutoffRadius();
958 +      if (simParams_->haveSwitchingRadius()) {
959 +        rsw_  = simParams_->getSwitchingRadius();
960 +      } else {
961 +        rsw_ = rcut_;
962 +      }
963 +      notifyFortranCutoffs(&rcut_, &rsw_);
964 +      
965 +    } else {
966 +      
967 +      // For electrostatic atoms, we'll assume a large safe value:
968 +      if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
969 +        sprintf(painCave.errMsg,
970 +                "SimCreator Warning: No value was set for the cutoffRadius.\n"
971 +                "\tOOPSE will use a default value of 15.0 angstroms"
972 +                "\tfor the cutoffRadius.\n");
973 +        painCave.isFatal = 0;
974 +        simError();
975 +        rcut_ = 15.0;
976 +      
977 +        if (simParams_->haveElectrostaticSummationMethod()) {
978 +          std::string myMethod = simParams_->getElectrostaticSummationMethod();
979 +          toUpper(myMethod);
980 +          if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
981 +            if (simParams_->haveSwitchingRadius()){
982 +              sprintf(painCave.errMsg,
983 +                      "SimInfo Warning: A value was set for the switchingRadius\n"
984 +                      "\teven though the electrostaticSummationMethod was\n"
985 +                      "\tset to %s\n", myMethod.c_str());
986 +              painCave.isFatal = 1;
987 +              simError();            
988 +            }
989 +          }
990 +        }
991 +      
992 +        if (simParams_->haveSwitchingRadius()){
993 +          rsw_ = simParams_->getSwitchingRadius();
994 +        } else {        
995 +          sprintf(painCave.errMsg,
996 +                  "SimCreator Warning: No value was set for switchingRadius.\n"
997 +                  "\tOOPSE will use a default value of\n"
998 +                  "\t0.85 * cutoffRadius for the switchingRadius\n");
999 +          painCave.isFatal = 0;
1000 +          simError();
1001 +          rsw_ = 0.85 * rcut_;
1002 +        }
1003 +        notifyFortranCutoffs(&rcut_, &rsw_);
1004 +      } else {
1005 +        // We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1006 +        // We'll punt and let fortran figure out the cutoffs later.
1007 +        
1008 +        notifyFortranYouAreOnYourOwn();
1009 +
1010        }
1011      }
859 –    notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp);
1012    }
1013  
1014    void SimInfo::setupElectrostaticSummationMethod( int isError ) {    
1015      
1016      int errorOut;
1017      int esm =  NONE;
1018 +    int sm = UNDAMPED;
1019      double alphaVal;
1020 +    double dielectric;
1021  
1022      errorOut = isError;
1023 +    alphaVal = simParams_->getDampingAlpha();
1024 +    dielectric = simParams_->getDielectric();
1025  
1026      if (simParams_->haveElectrostaticSummationMethod()) {
1027        std::string myMethod = simParams_->getElectrostaticSummationMethod();
1028 +      toUpper(myMethod);
1029        if (myMethod == "NONE") {
1030          esm = NONE;
1031        } else {
1032 <        if (myMethod == "UNDAMPED_WOLF") {
1033 <          esm = UNDAMPED_WOLF;
1032 >        if (myMethod == "SWITCHING_FUNCTION") {
1033 >          esm = SWITCHING_FUNCTION;
1034          } else {
1035 <          if (myMethod == "DAMPED_WOLF") {            
1036 <            esm = DAMPED_WOLF;
1037 <            if (!simParams_->haveDampingAlpha()) {
1038 <              //throw error
1039 <              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;
1035 >          if (myMethod == "SHIFTED_POTENTIAL") {
1036 >            esm = SHIFTED_POTENTIAL;
1037 >          } else {
1038 >            if (myMethod == "SHIFTED_FORCE") {            
1039 >              esm = SHIFTED_FORCE;
1040              } else {
1041 <              // throw error        
1042 <              sprintf( painCave.errMsg,
1043 <                       "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() );
1044 <              painCave.isFatal = 1;
1045 <              simError();
1046 <            }    
1047 <          }          
1041 >              if (myMethod == "REACTION_FIELD") {            
1042 >                esm = REACTION_FIELD;
1043 >              } else {
1044 >                // throw error        
1045 >                sprintf( painCave.errMsg,
1046 >                         "SimInfo error: Unknown electrostaticSummationMethod.\n"
1047 >                         "\t(Input file specified %s .)\n"
1048 >                         "\telectrostaticSummationMethod must be one of: \"none\",\n"
1049 >                         "\t\"shifted_potential\", \"shifted_force\", or \n"
1050 >                         "\t\"reaction_field\".\n", myMethod.c_str() );
1051 >                painCave.isFatal = 1;
1052 >                simError();
1053 >              }    
1054 >            }          
1055 >          }
1056          }
1057        }
1058      }
1059 <    initFortranFF( &esm, &alphaVal, &errorOut );
1059 >    
1060 >    if (simParams_->haveElectrostaticScreeningMethod()) {
1061 >      std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1062 >      toUpper(myScreen);
1063 >      if (myScreen == "UNDAMPED") {
1064 >        sm = UNDAMPED;
1065 >      } else {
1066 >        if (myScreen == "DAMPED") {
1067 >          sm = DAMPED;
1068 >          if (!simParams_->haveDampingAlpha()) {
1069 >            //throw error
1070 >            sprintf( painCave.errMsg,
1071 >                     "SimInfo warning: dampingAlpha was not specified in the input file.\n"
1072 >                     "\tA default value of %f (1/ang) will be used.\n", alphaVal);
1073 >            painCave.isFatal = 0;
1074 >            simError();
1075 >          }
1076 >        } else {
1077 >          // throw error        
1078 >          sprintf( painCave.errMsg,
1079 >                   "SimInfo error: Unknown electrostaticScreeningMethod.\n"
1080 >                   "\t(Input file specified %s .)\n"
1081 >                   "\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1082 >                   "or \"damped\".\n", myScreen.c_str() );
1083 >          painCave.isFatal = 1;
1084 >          simError();
1085 >        }
1086 >      }
1087 >    }
1088 >    
1089 >    // let's pass some summation method variables to fortran
1090 >    setElectrostaticSumMethod( &esm );
1091 >    setFortranElectrostaticMethod( &esm );
1092 >    setScreeningMethod( &sm );
1093 >    setDampingAlpha( &alphaVal );
1094 >    setReactionFieldDielectric( &dielectric );
1095 >    initFortranFF( &errorOut );
1096    }
1097  
1098 +  void SimInfo::setupSwitchingFunction() {    
1099 +    int ft = CUBIC;
1100 +
1101 +    if (simParams_->haveSwitchingFunctionType()) {
1102 +      std::string funcType = simParams_->getSwitchingFunctionType();
1103 +      toUpper(funcType);
1104 +      if (funcType == "CUBIC") {
1105 +        ft = CUBIC;
1106 +      } else {
1107 +        if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1108 +          ft = FIFTH_ORDER_POLY;
1109 +        } else {
1110 +          // throw error        
1111 +          sprintf( painCave.errMsg,
1112 +                   "SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1113 +          painCave.isFatal = 1;
1114 +          simError();
1115 +        }          
1116 +      }
1117 +    }
1118 +
1119 +    // send switching function notification to switcheroo
1120 +    setFunctionType(&ft);
1121 +
1122 +  }
1123 +
1124    void SimInfo::addProperty(GenericData* genData) {
1125      properties_.addProperty(genData);  
1126    }

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