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Comparing trunk/OOPSE-2.0/src/brains/SimInfo.cpp (file contents):
Revision 2303 by chrisfen, Fri Sep 16 19:00:12 2005 UTC vs.
Revision 2463 by gezelter, Mon Nov 21 22:59:21 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"
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 +    return result;
81 +  }
82 +  
83    SimInfo::SimInfo(MakeStamps* stamps, std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
84                     ForceField* ff, Globals* simParams) :
85      stamps_(stamps), forceField_(ff), simParams_(simParams),
# Line 82 | Line 95 | namespace oopse {
95        MoleculeStamp* molStamp;
96        int nMolWithSameStamp;
97        int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
98 <      int nGroups = 0;          //total cutoff groups defined in meta-data file
98 >      int nGroups = 0;      //total cutoff groups defined in meta-data file
99        CutoffGroupStamp* cgStamp;    
100        RigidBodyStamp* rbStamp;
101        int nRigidAtoms = 0;
# Line 107 | Line 120 | namespace oopse {
120          }
121  
122          nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
123 +
124          nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;            
125  
126          //calculate atoms in rigid bodies
# Line 123 | Line 137 | namespace oopse {
137          
138        }
139  
140 <      //every free atom (atom does not belong to cutoff groups) is a cutoff group
141 <      //therefore the total number of cutoff groups in the system is equal to
142 <      //the total number of atoms minus number of atoms belong to cutoff group defined in meta-data
143 <      //file plus the number of cutoff groups defined in meta-data file
140 >      //every free atom (atom does not belong to cutoff groups) is a cutoff
141 >      //group therefore the total number of cutoff groups in the system is
142 >      //equal to the total number of atoms minus number of atoms belong to
143 >      //cutoff group defined in meta-data file plus the number of cutoff
144 >      //groups defined in meta-data file
145        nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
146  
147 <      //every free atom (atom does not belong to rigid bodies) is an integrable object
148 <      //therefore the total number of  integrable objects in the system is equal to
149 <      //the total number of atoms minus number of atoms belong to  rigid body defined in meta-data
150 <      //file plus the number of  rigid bodies defined in meta-data file
151 <      nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_;
152 <
147 >      //every free atom (atom does not belong to rigid bodies) is an
148 >      //integrable object therefore the total number of integrable objects
149 >      //in the system is equal to the total number of atoms minus number of
150 >      //atoms belong to rigid body defined in meta-data file plus the number
151 >      //of rigid bodies defined in meta-data file
152 >      nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
153 >                                                + nGlobalRigidBodies_;
154 >  
155        nGlobalMols_ = molStampIds_.size();
156  
157   #ifdef IS_MPI    
# Line 337 | Line 354 | namespace oopse {
354      int b;
355      int c;
356      int d;
357 +
358 +    std::map<int, std::set<int> > atomGroups;
359 +
360 +    Molecule::RigidBodyIterator rbIter;
361 +    RigidBody* rb;
362 +    Molecule::IntegrableObjectIterator ii;
363 +    StuntDouble* integrableObject;
364      
365 +    for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
366 +           integrableObject = mol->nextIntegrableObject(ii)) {
367 +
368 +      if (integrableObject->isRigidBody()) {
369 +          rb = static_cast<RigidBody*>(integrableObject);
370 +          std::vector<Atom*> atoms = rb->getAtoms();
371 +          std::set<int> rigidAtoms;
372 +          for (int i = 0; i < atoms.size(); ++i) {
373 +            rigidAtoms.insert(atoms[i]->getGlobalIndex());
374 +          }
375 +          for (int i = 0; i < atoms.size(); ++i) {
376 +            atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
377 +          }      
378 +      } else {
379 +        std::set<int> oneAtomSet;
380 +        oneAtomSet.insert(integrableObject->getGlobalIndex());
381 +        atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));        
382 +      }
383 +    }  
384 +
385 +    
386 +    
387      for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
388        a = bond->getAtomA()->getGlobalIndex();
389        b = bond->getAtomB()->getGlobalIndex();        
# Line 348 | Line 394 | namespace oopse {
394        a = bend->getAtomA()->getGlobalIndex();
395        b = bend->getAtomB()->getGlobalIndex();        
396        c = bend->getAtomC()->getGlobalIndex();
397 +      std::set<int> rigidSetA = getRigidSet(a, atomGroups);
398 +      std::set<int> rigidSetB = getRigidSet(b, atomGroups);
399 +      std::set<int> rigidSetC = getRigidSet(c, atomGroups);
400  
401 <      exclude_.addPair(a, b);
402 <      exclude_.addPair(a, c);
403 <      exclude_.addPair(b, c);        
401 >      exclude_.addPairs(rigidSetA, rigidSetB);
402 >      exclude_.addPairs(rigidSetA, rigidSetC);
403 >      exclude_.addPairs(rigidSetB, rigidSetC);
404 >      
405 >      //exclude_.addPair(a, b);
406 >      //exclude_.addPair(a, c);
407 >      //exclude_.addPair(b, c);        
408      }
409  
410      for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
# Line 359 | Line 412 | namespace oopse {
412        b = torsion->getAtomB()->getGlobalIndex();        
413        c = torsion->getAtomC()->getGlobalIndex();        
414        d = torsion->getAtomD()->getGlobalIndex();        
415 +      std::set<int> rigidSetA = getRigidSet(a, atomGroups);
416 +      std::set<int> rigidSetB = getRigidSet(b, atomGroups);
417 +      std::set<int> rigidSetC = getRigidSet(c, atomGroups);
418 +      std::set<int> rigidSetD = getRigidSet(d, atomGroups);
419  
420 +      exclude_.addPairs(rigidSetA, rigidSetB);
421 +      exclude_.addPairs(rigidSetA, rigidSetC);
422 +      exclude_.addPairs(rigidSetA, rigidSetD);
423 +      exclude_.addPairs(rigidSetB, rigidSetC);
424 +      exclude_.addPairs(rigidSetB, rigidSetD);
425 +      exclude_.addPairs(rigidSetC, rigidSetD);
426 +
427 +      /*
428 +      exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
429 +      exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
430 +      exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
431 +      exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
432 +      exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
433 +      exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
434 +        
435 +      
436        exclude_.addPair(a, b);
437        exclude_.addPair(a, c);
438        exclude_.addPair(a, d);
439        exclude_.addPair(b, c);
440        exclude_.addPair(b, d);
441        exclude_.addPair(c, d);        
442 +      */
443      }
444  
371 –    Molecule::RigidBodyIterator rbIter;
372 –    RigidBody* rb;
445      for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
446        std::vector<Atom*> atoms = rb->getAtoms();
447        for (int i = 0; i < atoms.size() -1 ; ++i) {
# Line 394 | Line 466 | namespace oopse {
466      int b;
467      int c;
468      int d;
469 +
470 +    std::map<int, std::set<int> > atomGroups;
471 +
472 +    Molecule::RigidBodyIterator rbIter;
473 +    RigidBody* rb;
474 +    Molecule::IntegrableObjectIterator ii;
475 +    StuntDouble* integrableObject;
476 +    
477 +    for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
478 +           integrableObject = mol->nextIntegrableObject(ii)) {
479 +
480 +      if (integrableObject->isRigidBody()) {
481 +          rb = static_cast<RigidBody*>(integrableObject);
482 +          std::vector<Atom*> atoms = rb->getAtoms();
483 +          std::set<int> rigidAtoms;
484 +          for (int i = 0; i < atoms.size(); ++i) {
485 +            rigidAtoms.insert(atoms[i]->getGlobalIndex());
486 +          }
487 +          for (int i = 0; i < atoms.size(); ++i) {
488 +            atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
489 +          }      
490 +      } else {
491 +        std::set<int> oneAtomSet;
492 +        oneAtomSet.insert(integrableObject->getGlobalIndex());
493 +        atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));        
494 +      }
495 +    }  
496 +
497      
498      for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
499        a = bond->getAtomA()->getGlobalIndex();
# Line 406 | Line 506 | namespace oopse {
506        b = bend->getAtomB()->getGlobalIndex();        
507        c = bend->getAtomC()->getGlobalIndex();
508  
509 <      exclude_.removePair(a, b);
510 <      exclude_.removePair(a, c);
511 <      exclude_.removePair(b, c);        
509 >      std::set<int> rigidSetA = getRigidSet(a, atomGroups);
510 >      std::set<int> rigidSetB = getRigidSet(b, atomGroups);
511 >      std::set<int> rigidSetC = getRigidSet(c, atomGroups);
512 >
513 >      exclude_.removePairs(rigidSetA, rigidSetB);
514 >      exclude_.removePairs(rigidSetA, rigidSetC);
515 >      exclude_.removePairs(rigidSetB, rigidSetC);
516 >      
517 >      //exclude_.removePair(a, b);
518 >      //exclude_.removePair(a, c);
519 >      //exclude_.removePair(b, c);        
520      }
521  
522      for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
# Line 417 | Line 525 | namespace oopse {
525        c = torsion->getAtomC()->getGlobalIndex();        
526        d = torsion->getAtomD()->getGlobalIndex();        
527  
528 +      std::set<int> rigidSetA = getRigidSet(a, atomGroups);
529 +      std::set<int> rigidSetB = getRigidSet(b, atomGroups);
530 +      std::set<int> rigidSetC = getRigidSet(c, atomGroups);
531 +      std::set<int> rigidSetD = getRigidSet(d, atomGroups);
532 +
533 +      exclude_.removePairs(rigidSetA, rigidSetB);
534 +      exclude_.removePairs(rigidSetA, rigidSetC);
535 +      exclude_.removePairs(rigidSetA, rigidSetD);
536 +      exclude_.removePairs(rigidSetB, rigidSetC);
537 +      exclude_.removePairs(rigidSetB, rigidSetD);
538 +      exclude_.removePairs(rigidSetC, rigidSetD);
539 +
540 +      /*
541 +      exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
542 +      exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
543 +      exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
544 +      exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
545 +      exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
546 +      exclude_.removePairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
547 +
548 +      
549        exclude_.removePair(a, b);
550        exclude_.removePair(a, c);
551        exclude_.removePair(a, d);
552        exclude_.removePair(b, c);
553        exclude_.removePair(b, d);
554        exclude_.removePair(c, d);        
555 +      */
556      }
557  
428 –    Molecule::RigidBodyIterator rbIter;
429 –    RigidBody* rb;
558      for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
559        std::vector<Atom*> atoms = rb->getAtoms();
560        for (int i = 0; i < atoms.size() -1 ; ++i) {
# Line 466 | Line 594 | namespace oopse {
594      int isError = 0;
595      
596      setupElectrostaticSummationMethod( isError );
597 +    setupSwitchingFunction();
598  
599      if(isError){
600        sprintf( painCave.errMsg,
# Line 510 | Line 639 | namespace oopse {
639      int useLennardJones = 0;
640      int useElectrostatic = 0;
641      int useEAM = 0;
642 +    int useSC = 0;
643      int useCharge = 0;
644      int useDirectional = 0;
645      int useDipole = 0;
# Line 521 | Line 651 | namespace oopse {
651      int useDirectionalAtom = 0;    
652      int useElectrostatics = 0;
653      //usePBC and useRF are from simParams
654 <    int usePBC = simParams_->getPBC();
654 >    int usePBC = simParams_->getUsePeriodicBoundaryConditions();
655 >    int useRF;
656 >    int useSF;
657 >    std::string myMethod;
658 >
659 >    // set the useRF logical
660 >    useRF = 0;
661 >    useSF = 0;
662 >
663  
664 +    if (simParams_->haveElectrostaticSummationMethod()) {
665 +      std::string myMethod = simParams_->getElectrostaticSummationMethod();
666 +      toUpper(myMethod);
667 +      if (myMethod == "REACTION_FIELD") {
668 +        useRF=1;
669 +      } else {
670 +        if (myMethod == "SHIFTED_FORCE") {
671 +          useSF = 1;
672 +        }
673 +      }
674 +    }
675 +
676      //loop over all of the atom types
677      for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
678        useLennardJones |= (*i)->isLennardJones();
679        useElectrostatic |= (*i)->isElectrostatic();
680        useEAM |= (*i)->isEAM();
681 +      useSC |= (*i)->isSC();
682        useCharge |= (*i)->isCharge();
683        useDirectional |= (*i)->isDirectional();
684        useDipole |= (*i)->isDipole();
# Line 578 | Line 729 | namespace oopse {
729      temp = useEAM;
730      MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
731  
732 +    temp = useSC;
733 +    MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
734 +    
735      temp = useShape;
736      MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);  
737  
738      temp = useFLARB;
739      MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
740  
741 +    temp = useRF;
742 +    MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
743 +
744 +    temp = useSF;
745 +    MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
746 +
747   #endif
748  
749      fInfo_.SIM_uses_PBC = usePBC;    
# Line 596 | Line 756 | namespace oopse {
756      fInfo_.SIM_uses_StickyPower = useStickyPower;
757      fInfo_.SIM_uses_GayBerne = useGayBerne;
758      fInfo_.SIM_uses_EAM = useEAM;
759 +    fInfo_.SIM_uses_SC = useSC;
760      fInfo_.SIM_uses_Shapes = useShape;
761      fInfo_.SIM_uses_FLARB = useFLARB;
762 +    fInfo_.SIM_uses_RF = useRF;
763 +    fInfo_.SIM_uses_SF = useSF;
764  
765 <    if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) {
766 <
765 >    if( myMethod == "REACTION_FIELD") {
766 >      
767        if (simParams_->haveDielectric()) {
768          fInfo_.dielect = simParams_->getDielectric();
769        } else {
# Line 610 | Line 773 | namespace oopse {
773                  "\tsetting a dielectric constant!\n");
774          painCave.isFatal = 1;
775          simError();
776 <      }
614 <        
615 <    } else {
616 <      fInfo_.dielect = 0.0;
776 >      }      
777      }
778  
779    }
# Line 649 | Line 809 | namespace oopse {
809  
810          totalMass = cg->getMass();
811          for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
812 <          mfact.push_back(atom->getMass()/totalMass);
812 >          // Check for massless groups - set mfact to 1 if true
813 >          if (totalMass != 0)
814 >            mfact.push_back(atom->getMass()/totalMass);
815 >          else
816 >            mfact.push_back( 1.0 );
817          }
818  
819        }      
# Line 758 | Line 922 | namespace oopse {
922  
923   #endif
924  
925 <  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) {
925 >  void SimInfo::setupCutoff() {          
926      
927 <    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 <    
927 >    // Check the cutoff policy
928      int cp =  TRADITIONAL_CUTOFF_POLICY;
929      if (simParams_->haveCutoffPolicy()) {
930        std::string myPolicy = simParams_->getCutoffPolicy();
931 +      toUpper(myPolicy);
932        if (myPolicy == "MIX") {
933          cp = MIX_CUTOFF_POLICY;
934        } else {
# Line 854 | Line 945 | namespace oopse {
945              simError();
946            }    
947          }          
948 +      }
949 +    }          
950 +    notifyFortranCutoffPolicy(&cp);
951 +
952 +    // Check the Skin Thickness for neighborlists
953 +    double skin;
954 +    if (simParams_->haveSkinThickness()) {
955 +      skin = simParams_->getSkinThickness();
956 +      notifyFortranSkinThickness(&skin);
957 +    }            
958 +        
959 +    // Check if the cutoff was set explicitly:
960 +    if (simParams_->haveCutoffRadius()) {
961 +      rcut_ = simParams_->getCutoffRadius();
962 +      if (simParams_->haveSwitchingRadius()) {
963 +        rsw_  = simParams_->getSwitchingRadius();
964 +      } else {
965 +        rsw_ = rcut_;
966 +      }
967 +      notifyFortranCutoffs(&rcut_, &rsw_);
968 +      
969 +    } else {
970 +      
971 +      // For electrostatic atoms, we'll assume a large safe value:
972 +      if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
973 +        sprintf(painCave.errMsg,
974 +                "SimCreator Warning: No value was set for the cutoffRadius.\n"
975 +                "\tOOPSE will use a default value of 15.0 angstroms"
976 +                "\tfor the cutoffRadius.\n");
977 +        painCave.isFatal = 0;
978 +        simError();
979 +        rcut_ = 15.0;
980 +      
981 +        if (simParams_->haveElectrostaticSummationMethod()) {
982 +          std::string myMethod = simParams_->getElectrostaticSummationMethod();
983 +          toUpper(myMethod);
984 +          if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
985 +            if (simParams_->haveSwitchingRadius()){
986 +              sprintf(painCave.errMsg,
987 +                      "SimInfo Warning: A value was set for the switchingRadius\n"
988 +                      "\teven though the electrostaticSummationMethod was\n"
989 +                      "\tset to %s\n", myMethod.c_str());
990 +              painCave.isFatal = 1;
991 +              simError();            
992 +            }
993 +          }
994 +        }
995 +      
996 +        if (simParams_->haveSwitchingRadius()){
997 +          rsw_ = simParams_->getSwitchingRadius();
998 +        } else {        
999 +          sprintf(painCave.errMsg,
1000 +                  "SimCreator Warning: No value was set for switchingRadius.\n"
1001 +                  "\tOOPSE will use a default value of\n"
1002 +                  "\t0.85 * cutoffRadius for the switchingRadius\n");
1003 +          painCave.isFatal = 0;
1004 +          simError();
1005 +          rsw_ = 0.85 * rcut_;
1006 +        }
1007 +        notifyFortranCutoffs(&rcut_, &rsw_);
1008 +      } else {
1009 +        // We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1010 +        // We'll punt and let fortran figure out the cutoffs later.
1011 +        
1012 +        notifyFortranYouAreOnYourOwn();
1013 +
1014        }
1015      }
859 –    notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp);
1016    }
1017  
1018    void SimInfo::setupElectrostaticSummationMethod( int isError ) {    
1019      
1020      int errorOut;
1021      int esm =  NONE;
1022 +    int sm = UNDAMPED;
1023      double alphaVal;
1024 +    double dielectric;
1025  
1026      errorOut = isError;
1027 +    alphaVal = simParams_->getDampingAlpha();
1028 +    dielectric = simParams_->getDielectric();
1029  
1030      if (simParams_->haveElectrostaticSummationMethod()) {
1031        std::string myMethod = simParams_->getElectrostaticSummationMethod();
1032 +      toUpper(myMethod);
1033        if (myMethod == "NONE") {
1034          esm = NONE;
1035        } else {
1036 <        if (myMethod == "UNDAMPED_WOLF") {
1037 <          esm = UNDAMPED_WOLF;
1036 >        if (myMethod == "SWITCHING_FUNCTION") {
1037 >          esm = SWITCHING_FUNCTION;
1038          } else {
1039 <          if (myMethod == "DAMPED_WOLF") {            
1040 <            esm = DAMPED_WOLF;
1041 <            if (!simParams_->haveDampingAlpha()) {
1042 <              //throw error
1043 <              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;
1039 >          if (myMethod == "SHIFTED_POTENTIAL") {
1040 >            esm = SHIFTED_POTENTIAL;
1041 >          } else {
1042 >            if (myMethod == "SHIFTED_FORCE") {            
1043 >              esm = SHIFTED_FORCE;
1044              } else {
1045 <              // throw error        
1046 <              sprintf( painCave.errMsg,
1047 <                       "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() );
1048 <              painCave.isFatal = 1;
1049 <              simError();
1050 <            }    
1051 <          }          
1045 >              if (myMethod == "REACTION_FIELD") {            
1046 >                esm = REACTION_FIELD;
1047 >              } else {
1048 >                // throw error        
1049 >                sprintf( painCave.errMsg,
1050 >                         "SimInfo error: Unknown electrostaticSummationMethod.\n"
1051 >                         "\t(Input file specified %s .)\n"
1052 >                         "\telectrostaticSummationMethod must be one of: \"none\",\n"
1053 >                         "\t\"shifted_potential\", \"shifted_force\", or \n"
1054 >                         "\t\"reaction_field\".\n", myMethod.c_str() );
1055 >                painCave.isFatal = 1;
1056 >                simError();
1057 >              }    
1058 >            }          
1059 >          }
1060          }
1061        }
1062      }
1063 <    initFortranFF( &fInfo_.SIM_uses_RF, &esm, &alphaVal, &errorOut );
1063 >    
1064 >    if (simParams_->haveElectrostaticScreeningMethod()) {
1065 >      std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1066 >      toUpper(myScreen);
1067 >      if (myScreen == "UNDAMPED") {
1068 >        sm = UNDAMPED;
1069 >      } else {
1070 >        if (myScreen == "DAMPED") {
1071 >          sm = DAMPED;
1072 >          if (!simParams_->haveDampingAlpha()) {
1073 >            //throw error
1074 >            sprintf( painCave.errMsg,
1075 >                     "SimInfo warning: dampingAlpha was not specified in the input file.\n"
1076 >                     "\tA default value of %f (1/ang) will be used.\n", alphaVal);
1077 >            painCave.isFatal = 0;
1078 >            simError();
1079 >          }
1080 >        } else {
1081 >          // throw error        
1082 >          sprintf( painCave.errMsg,
1083 >                   "SimInfo error: Unknown electrostaticScreeningMethod.\n"
1084 >                   "\t(Input file specified %s .)\n"
1085 >                   "\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1086 >                   "or \"damped\".\n", myScreen.c_str() );
1087 >          painCave.isFatal = 1;
1088 >          simError();
1089 >        }
1090 >      }
1091 >    }
1092 >    
1093 >    // let's pass some summation method variables to fortran
1094 >    setElectrostaticSummationMethod( &esm );
1095 >    notifyFortranElectrostaticMethod( &esm );
1096 >    setScreeningMethod( &sm );
1097 >    setDampingAlpha( &alphaVal );
1098 >    setReactionFieldDielectric( &dielectric );
1099 >    initFortranFF( &errorOut );
1100 >  }
1101 >
1102 >  void SimInfo::setupSwitchingFunction() {    
1103 >    int ft = CUBIC;
1104 >
1105 >    if (simParams_->haveSwitchingFunctionType()) {
1106 >      std::string funcType = simParams_->getSwitchingFunctionType();
1107 >      toUpper(funcType);
1108 >      if (funcType == "CUBIC") {
1109 >        ft = CUBIC;
1110 >      } else {
1111 >        if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1112 >          ft = FIFTH_ORDER_POLY;
1113 >        } else {
1114 >          // throw error        
1115 >          sprintf( painCave.errMsg,
1116 >                   "SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1117 >          painCave.isFatal = 1;
1118 >          simError();
1119 >        }          
1120 >      }
1121 >    }
1122 >
1123 >    // send switching function notification to switcheroo
1124 >    setFunctionType(&ft);
1125 >
1126    }
1127  
1128    void SimInfo::addProperty(GenericData* genData) {

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