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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 557 by chuckv, Tue May 31 22:31:54 2005 UTC vs.
Revision 879 by chrisfen, Wed Feb 1 21:06:43 2006 UTC

# Line 48 | Line 48
48  
49   #include <algorithm>
50   #include <set>
51 + #include <map>
52  
53   #include "brains/SimInfo.hpp"
54   #include "math/Vector3.hpp"
55   #include "primitives/Molecule.hpp"
56 + #include "UseTheForce/fCutoffPolicy.h"
57 + #include "UseTheForce/DarkSide/fElectrostaticSummationMethod.h"
58 + #include "UseTheForce/DarkSide/fElectrostaticScreeningMethod.h"
59 + #include "UseTheForce/DarkSide/fSwitchingFunctionType.h"
60   #include "UseTheForce/doForces_interface.h"
61 < #include "UseTheForce/notifyCutoffs_interface.h"
61 > #include "UseTheForce/DarkSide/electrostatic_interface.h"
62 > #include "UseTheForce/DarkSide/switcheroo_interface.h"
63   #include "utils/MemoryUtils.hpp"
64   #include "utils/simError.h"
65   #include "selection/SelectionManager.hpp"
66 + #include "io/ForceFieldOptions.hpp"
67 + #include "UseTheForce/ForceField.hpp"
68  
69   #ifdef IS_MPI
70   #include "UseTheForce/mpiComponentPlan.h"
# Line 64 | 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 75 | Line 91 | namespace oopse {
91      nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
92      sman_(NULL), fortranInitialized_(false) {
93  
78 –            
79 –      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  
97 –
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 112 | 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 121 | 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 148 | Line 166 | namespace oopse {
166      }
167      molecules_.clear();
168        
151 –    delete stamps_;
169      delete sman_;
170      delete simParams_;
171      delete forceField_;
# Line 255 | 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 335 | 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 346 | 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 357 | 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  
369 –    Molecule::RigidBodyIterator rbIter;
370 –    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 392 | 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 404 | 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 415 | 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  
426 –    Molecule::RigidBodyIterator rbIter;
427 –    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 462 | Line 590 | namespace oopse {
590      //setup fortran force field
591      /** @deprecate */    
592      int isError = 0;
593 <    initFortranFF( &fInfo_.SIM_uses_RF , &isError );
593 >    
594 >    setupElectrostaticSummationMethod( isError );
595 >    setupSwitchingFunction();
596 >
597      if(isError){
598        sprintf( painCave.errMsg,
599                 "ForceField error: There was an error initializing the forceField in fortran.\n" );
# Line 506 | 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 517 | 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 575 | 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 583 | Line 738 | namespace oopse {
738  
739      temp = useRF;
740      MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
741 <    
741 >
742 >    temp = useSF;
743 >    MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
744 >
745   #endif
746  
747      fInfo_.SIM_uses_PBC = usePBC;    
# Line 596 | 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 611 | Line 771 | namespace oopse {
771                  "\tsetting a dielectric constant!\n");
772          painCave.isFatal = 1;
773          simError();
774 <      }
615 <        
616 <    } else {
617 <      fInfo_.dielect = 0.0;
774 >      }      
775      }
776  
777    }
# Line 650 | 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 759 | Line 920 | namespace oopse {
920  
921   #endif
922  
923 <  double SimInfo::calcMaxCutoffRadius() {
923 >  void SimInfo::setupCutoff() {          
924 >    
925 >    ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
926  
927 <
928 <    std::set<AtomType*> atomTypes;
766 <    std::set<AtomType*>::iterator i;
767 <    std::vector<double> cutoffRadius;
768 <
769 <    //get the unique atom types
770 <    atomTypes = getUniqueAtomTypes();
927 >    // Check the cutoff policy
928 >    int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
929  
930 <    //query the max cutoff radius among these atom types
931 <    for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
932 <      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      }
936  
937 <    double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
938 < #ifdef IS_MPI
939 <    //pick the max cutoff radius among the processors
940 < #endif
937 >    if (!myPolicy.empty()){
938 >      toUpper(myPolicy);
939 >      if (myPolicy == "MIX") {
940 >        cp = MIX_CUTOFF_POLICY;
941 >      } else {
942 >        if (myPolicy == "MAX") {
943 >          cp = MAX_CUTOFF_POLICY;
944 >        } else {
945 >          if (myPolicy == "TRADITIONAL") {            
946 >            cp = TRADITIONAL_CUTOFF_POLICY;
947 >          } else {
948 >            // throw error        
949 >            sprintf( painCave.errMsg,
950 >                     "SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
951 >            painCave.isFatal = 1;
952 >            simError();
953 >          }    
954 >        }          
955 >      }
956 >    }          
957 >    notifyFortranCutoffPolicy(&cp);
958  
959 <    return maxCutoffRadius;
960 <  }
961 <
962 <  void SimInfo::getCutoff(double& rcut, double& rsw) {
963 <    
964 <    if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
959 >    // Check the Skin Thickness for neighborlists
960 >    double skin;
961 >    if (simParams_->haveSkinThickness()) {
962 >      skin = simParams_->getSkinThickness();
963 >      notifyFortranSkinThickness(&skin);
964 >    }            
965          
966 <      if (!simParams_->haveRcut()){
967 <        sprintf(painCave.errMsg,
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 percent of the cutoffRadius.\n"
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 >      
994 >      notifyFortranCutoffs(&rcut_, &rsw_);
995 >      
996 >    } else {
997 >      
998 >      // For electrostatic atoms, we'll assume a large safe value:
999 >      if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
1000 >        sprintf(painCave.errMsg,
1001                  "SimCreator Warning: No value was set for the cutoffRadius.\n"
1002                  "\tOOPSE will use a default value of 15.0 angstroms"
1003                  "\tfor the cutoffRadius.\n");
1004 <        painCave.isFatal = 0;
1004 >        painCave.isFatal = 0;
1005          simError();
1006 <        rcut = 15.0;
1007 <      } else{
1008 <        rcut = simParams_->getRcut();
1006 >        rcut_ = 15.0;
1007 >      
1008 >        if (simParams_->haveElectrostaticSummationMethod()) {
1009 >          std::string myMethod = simParams_->getElectrostaticSummationMethod();
1010 >          toUpper(myMethod);
1011 >          if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1012 >            if (simParams_->haveSwitchingRadius()){
1013 >              sprintf(painCave.errMsg,
1014 >                      "SimInfo Warning: A value was set for the switchingRadius\n"
1015 >                      "\teven though the electrostaticSummationMethod was\n"
1016 >                      "\tset to %s\n", myMethod.c_str());
1017 >              painCave.isFatal = 1;
1018 >              simError();            
1019 >            }
1020 >          }
1021 >        }
1022 >      
1023 >        if (simParams_->haveSwitchingRadius()){
1024 >          rsw_ = simParams_->getSwitchingRadius();
1025 >        } else {        
1026 >          sprintf(painCave.errMsg,
1027 >                  "SimCreator Warning: No value was set for switchingRadius.\n"
1028 >                  "\tOOPSE will use a default value of\n"
1029 >                  "\t0.85 * cutoffRadius for the switchingRadius\n");
1030 >          painCave.isFatal = 0;
1031 >          simError();
1032 >          rsw_ = 0.85 * rcut_;
1033 >        }
1034 >        notifyFortranCutoffs(&rcut_, &rsw_);
1035 >      } else {
1036 >        // We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1037 >        // We'll punt and let fortran figure out the cutoffs later.
1038 >        
1039 >        notifyFortranYouAreOnYourOwn();
1040 >
1041        }
1042 +    }
1043 +  }
1044  
1045 <      if (!simParams_->haveRsw()){
1046 <        sprintf(painCave.errMsg,
1047 <                "SimCreator Warning: No value was set for switchingRadius.\n"
1048 <                "\tOOPSE will use a default value of\n"
1049 <                "\t0.95 * cutoffRadius for the switchingRadius\n");
1050 <        painCave.isFatal = 0;
1051 <        simError();
808 <        rsw = 0.95 * rcut;
809 <      } else{
810 <        rsw = simParams_->getRsw();
811 <      }
1045 >  void SimInfo::setupElectrostaticSummationMethod( int isError ) {    
1046 >    
1047 >    int errorOut;
1048 >    int esm =  NONE;
1049 >    int sm = UNDAMPED;
1050 >    double alphaVal;
1051 >    double dielectric;
1052  
1053 <    } else {
1054 <      // if charge, dipole or reaction field is not used and the cutofff radius is not specified in
1055 <      //meta-data file, the maximum cutoff radius calculated from forcefiled will be used
816 <        
817 <      if (simParams_->haveRcut()) {
818 <        rcut = simParams_->getRcut();
819 <      } else {
820 <        //set cutoff radius to the maximum cutoff radius based on atom types in the whole system
821 <        rcut = calcMaxCutoffRadius();
822 <      }
1053 >    errorOut = isError;
1054 >    alphaVal = simParams_->getDampingAlpha();
1055 >    dielectric = simParams_->getDielectric();
1056  
1057 <      if (simParams_->haveRsw()) {
1058 <        rsw  = simParams_->getRsw();
1057 >    if (simParams_->haveElectrostaticSummationMethod()) {
1058 >      std::string myMethod = simParams_->getElectrostaticSummationMethod();
1059 >      toUpper(myMethod);
1060 >      if (myMethod == "NONE") {
1061 >        esm = NONE;
1062        } else {
1063 <        rsw = rcut;
1063 >        if (myMethod == "SWITCHING_FUNCTION") {
1064 >          esm = SWITCHING_FUNCTION;
1065 >        } else {
1066 >          if (myMethod == "SHIFTED_POTENTIAL") {
1067 >            esm = SHIFTED_POTENTIAL;
1068 >          } else {
1069 >            if (myMethod == "SHIFTED_FORCE") {            
1070 >              esm = SHIFTED_FORCE;
1071 >            } else {
1072 >              if (myMethod == "REACTION_FIELD") {            
1073 >                esm = REACTION_FIELD;
1074 >              } else {
1075 >                // throw error        
1076 >                sprintf( painCave.errMsg,
1077 >                         "SimInfo error: Unknown electrostaticSummationMethod.\n"
1078 >                         "\t(Input file specified %s .)\n"
1079 >                         "\telectrostaticSummationMethod must be one of: \"none\",\n"
1080 >                         "\t\"shifted_potential\", \"shifted_force\", or \n"
1081 >                         "\t\"reaction_field\".\n", myMethod.c_str() );
1082 >                painCave.isFatal = 1;
1083 >                simError();
1084 >              }    
1085 >            }          
1086 >          }
1087 >        }
1088        }
1089 +    }
1090      
1091 +    if (simParams_->haveElectrostaticScreeningMethod()) {
1092 +      std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1093 +      toUpper(myScreen);
1094 +      if (myScreen == "UNDAMPED") {
1095 +        sm = UNDAMPED;
1096 +      } else {
1097 +        if (myScreen == "DAMPED") {
1098 +          sm = DAMPED;
1099 +          if (!simParams_->haveDampingAlpha()) {
1100 +            //throw error
1101 +            sprintf( painCave.errMsg,
1102 +                     "SimInfo warning: dampingAlpha was not specified in the input file.\n"
1103 +                     "\tA default value of %f (1/ang) will be used.\n", alphaVal);
1104 +            painCave.isFatal = 0;
1105 +            simError();
1106 +          }
1107 +        } else {
1108 +          // throw error        
1109 +          sprintf( painCave.errMsg,
1110 +                   "SimInfo error: Unknown electrostaticScreeningMethod.\n"
1111 +                   "\t(Input file specified %s .)\n"
1112 +                   "\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1113 +                   "or \"damped\".\n", myScreen.c_str() );
1114 +          painCave.isFatal = 1;
1115 +          simError();
1116 +        }
1117 +      }
1118      }
1119 +    
1120 +    // let's pass some summation method variables to fortran
1121 +    setElectrostaticSummationMethod( &esm );
1122 +    setFortranElectrostaticMethod( &esm );
1123 +    setScreeningMethod( &sm );
1124 +    setDampingAlpha( &alphaVal );
1125 +    setReactionFieldDielectric( &dielectric );
1126 +    initFortranFF( &errorOut );
1127    }
1128  
1129 <  void SimInfo::setupCutoff() {
1130 <    getCutoff(rcut_, rsw_);    
835 <    double rnblist = rcut_ + 1; // skin of neighbor list
1129 >  void SimInfo::setupSwitchingFunction() {    
1130 >    int ft = CUBIC;
1131  
1132 <    //Pass these cutoff radius etc. to fortran. This function should be called once and only once
1133 <    notifyFortranCutoffs(&rcut_, &rsw_, &rnblist);
1132 >    if (simParams_->haveSwitchingFunctionType()) {
1133 >      std::string funcType = simParams_->getSwitchingFunctionType();
1134 >      toUpper(funcType);
1135 >      if (funcType == "CUBIC") {
1136 >        ft = CUBIC;
1137 >      } else {
1138 >        if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1139 >          ft = FIFTH_ORDER_POLY;
1140 >        } else {
1141 >          // throw error        
1142 >          sprintf( painCave.errMsg,
1143 >                   "SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1144 >          painCave.isFatal = 1;
1145 >          simError();
1146 >        }          
1147 >      }
1148 >    }
1149 >
1150 >    // send switching function notification to switcheroo
1151 >    setFunctionType(&ft);
1152 >
1153    }
1154  
1155    void SimInfo::addProperty(GenericData* genData) {

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