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Comparing trunk/OOPSE-2.0/src/brains/SimInfo.cpp (file contents):
Revision 2408 by chrisfen, Wed Nov 2 20:36:15 2005 UTC vs.
Revision 2469 by tim, Fri Dec 2 15:38:03 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/fScreeningMethod.h"
58 > #include "UseTheForce/DarkSide/fElectrostaticScreeningMethod.h"
59 > #include "UseTheForce/DarkSide/fSwitchingFunctionType.h"
60   #include "UseTheForce/doForces_interface.h"
61   #include "UseTheForce/DarkSide/electrostatic_interface.h"
62 < #include "UseTheForce/notifyCutoffs_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 68 | 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 79 | Line 89 | namespace oopse {
89      nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
90      sman_(NULL), fortranInitialized_(false) {
91  
82 –            
83 –      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
# Line 88 | Line 96 | namespace oopse {
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  
101 –
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  
# Line 117 | 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 156 | Line 164 | namespace oopse {
164      }
165      molecules_.clear();
166        
159 –    delete stamps_;
167      delete sman_;
168      delete simParams_;
169      delete forceField_;
# Line 263 | 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 343 | 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 354 | 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 365 | 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  
377 –    Molecule::RigidBodyIterator rbIter;
378 –    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 400 | 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 412 | 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 423 | 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  
434 –    Molecule::RigidBodyIterator rbIter;
435 –    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 472 | Line 590 | namespace oopse {
590      int isError = 0;
591      
592      setupElectrostaticSummationMethod( isError );
593 +    setupSwitchingFunction();
594  
595      if(isError){
596        sprintf( painCave.errMsg,
# Line 516 | 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 529 | Line 649 | namespace oopse {
649      //usePBC and useRF are from simParams
650      int usePBC = simParams_->getUsePeriodicBoundaryConditions();
651      int useRF;
652 <    int useDW;
652 >    int useSF;
653      std::string myMethod;
654  
655      // set the useRF logical
656      useRF = 0;
657 <    useDW = 0;
657 >    useSF = 0;
658  
659  
660      if (simParams_->haveElectrostaticSummationMethod()) {
# Line 543 | Line 663 | namespace oopse {
663        if (myMethod == "REACTION_FIELD") {
664          useRF=1;
665        } else {
666 <        if (myMethod == "SHIFTED_POTENTIAL") {
667 <          useDW = 1;
666 >        if (myMethod == "SHIFTED_FORCE") {
667 >          useSF = 1;
668          }
669        }
670      }
# Line 554 | Line 674 | namespace oopse {
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 604 | 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  
# Line 613 | Line 737 | namespace oopse {
737      temp = useRF;
738      MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
739  
740 <    temp = useDW;
741 <    MPI_Allreduce(&temp, &useDW, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
740 >    temp = useSF;
741 >    MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
742  
743   #endif
744  
# Line 628 | 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_DampedWolf = useDW;
759 >    fInfo_.SIM_uses_SF = useSF;
760  
761      if( myMethod == "REACTION_FIELD") {
762        
# Line 790 | Line 915 | namespace oopse {
915  
916  
917    }
793 –
794 – #endif
795 –
796 –  double SimInfo::calcMaxCutoffRadius() {
797 –
798 –
799 –    std::set<AtomType*> atomTypes;
800 –    std::set<AtomType*>::iterator i;
801 –    std::vector<double> cutoffRadius;
802 –
803 –    //get the unique atom types
804 –    atomTypes = getUniqueAtomTypes();
918  
806 –    //query the max cutoff radius among these atom types
807 –    for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
808 –      cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
809 –    }
810 –
811 –    double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
812 – #ifdef IS_MPI
813 –    //pick the max cutoff radius among the processors
919   #endif
920  
921 <    return maxCutoffRadius;
817 <  }
818 <
819 <  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) {
822 <        
823 <      if (!simParams_->haveCutoffRadius()){
824 <        sprintf(painCave.errMsg,
825 <                "SimCreator Warning: No value was set for the cutoffRadius.\n"
826 <                "\tOOPSE will use a default value of 15.0 angstroms"
827 <                "\tfor the cutoffRadius.\n");
828 <        painCave.isFatal = 0;
829 <        simError();
830 <        rcut = 15.0;
831 <      } else{
832 <        rcut = simParams_->getCutoffRadius();
833 <      }
834 <
835 <      if (!simParams_->haveSwitchingRadius()){
836 <        sprintf(painCave.errMsg,
837 <                "SimCreator Warning: No value was set for switchingRadius.\n"
838 <                "\tOOPSE will use a default value of\n"
839 <                "\t0.85 * cutoffRadius for the switchingRadius\n");
840 <        painCave.isFatal = 0;
841 <        simError();
842 <        rsw = 0.85 * rcut;
843 <      } else{
844 <        rsw = simParams_->getSwitchingRadius();
845 <      }
846 <
847 <    } else {
848 <      // if charge, dipole or reaction field is not used and the cutofff radius is not specified in
849 <      //meta-data file, the maximum cutoff radius calculated from forcefiled will be used
850 <        
851 <      if (simParams_->haveCutoffRadius()) {
852 <        rcut = simParams_->getCutoffRadius();
853 <      } else {
854 <        //set cutoff radius to the maximum cutoff radius based on atom types in the whole system
855 <        rcut = calcMaxCutoffRadius();
856 <      }
857 <
858 <      if (simParams_->haveSwitchingRadius()) {
859 <        rsw  = simParams_->getSwitchingRadius();
860 <      } else {
861 <        rsw = rcut;
862 <      }
863 <    
864 <    }
865 <  }
866 <
867 <  void SimInfo::setupCutoff() {    
868 <    getCutoff(rcut_, rsw_);    
869 <    double rnblist = rcut_ + 1; // skin of neighbor list
870 <
871 <    //Pass these cutoff radius etc. to fortran. This function should be called once and only once
872 <    
923 >    // Check the cutoff policy
924      int cp =  TRADITIONAL_CUTOFF_POLICY;
925      if (simParams_->haveCutoffPolicy()) {
926        std::string myPolicy = simParams_->getCutoffPolicy();
# Line 891 | Line 942 | namespace oopse {
942            }    
943          }          
944        }
945 <    }
945 >    }          
946 >    notifyFortranCutoffPolicy(&cp);
947  
948 <
948 >    // Check the Skin Thickness for neighborlists
949 >    double skin;
950      if (simParams_->haveSkinThickness()) {
951 <      double skinThickness = simParams_->getSkinThickness();
952 <    }
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 <    notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp);
1011 <    // also send cutoff notification to electrostatics
903 <    setElectrostaticCutoffRadius(&rcut_, &rsw_);
1010 >      }
1011 >    }
1012    }
1013  
1014    void SimInfo::setupElectrostaticSummationMethod( int isError ) {    
# Line 935 | Line 1043 | namespace oopse {
1043                } else {
1044                  // throw error        
1045                  sprintf( painCave.errMsg,
1046 <                         "SimInfo error: Unknown electrostaticSummationMethod. (Input file specified %s .)\n\telectrostaticSummationMethod must be one of: \"none\", \"shifted_potential\", \"shifted_force\", or \"reaction_field\".", myMethod.c_str() );
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                }    
# Line 945 | Line 1057 | namespace oopse {
1057        }
1058      }
1059      
1060 <    if (simParams_->haveScreeningMethod()) {
1061 <      std::string myScreen = simParams_->getScreeningMethod();
1060 >    if (simParams_->haveElectrostaticScreeningMethod()) {
1061 >      std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1062        toUpper(myScreen);
1063        if (myScreen == "UNDAMPED") {
1064          sm = UNDAMPED;
# Line 956 | Line 1068 | namespace oopse {
1068            if (!simParams_->haveDampingAlpha()) {
1069              //throw error
1070              sprintf( painCave.errMsg,
1071 <                     "SimInfo warning: dampingAlpha was not specified in the input file. A default value of %f (1/ang) will be used.", alphaVal);
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();
962 –          } else {
963 –            // throw error        
964 –            sprintf( painCave.errMsg,
965 –                     "SimInfo error: Unknown electrostaticSummationMethod. (Input file specified %s .)\n\telectrostaticSummationMethod must be one of: \"undamped\" or \"damped\".", myScreen.c_str() );
966 –            painCave.isFatal = 1;
967 –            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      setElectrostaticSummationMethod( &esm );
1091 +    notifyFortranElectrostaticMethod( &esm );
1092      setScreeningMethod( &sm );
1093      setDampingAlpha( &alphaVal );
1094      setReactionFieldDielectric( &dielectric );
1095 <    initFortranFF( &esm, &errorOut );
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) {

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