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root/OpenMD/trunk/src/brains/SimInfo.cpp
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Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 555 by chuckv, Mon May 30 14:01:52 2005 UTC vs.
Revision 764 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"
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 64 | 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 80 | 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 105 | Line 120 | namespace oopse {
120          }
121  
122          nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
123 +
124          nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;            
125  
126          //calculate atoms in rigid bodies
# Line 121 | 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 335 | 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 346 | 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 357 | 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  
369 –    Molecule::RigidBodyIterator rbIter;
370 –    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 392 | 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();
500        b = bond->getAtomB()->getGlobalIndex();        
# Line 404 | 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 415 | 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  
426 –    Molecule::RigidBodyIterator rbIter;
427 –    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 462 | Line 592 | namespace oopse {
592      //setup fortran force field
593      /** @deprecate */    
594      int isError = 0;
595 <    initFortranFF( &fInfo_.SIM_uses_RF , &isError );
595 >    
596 >    setupElectrostaticSummationMethod( isError );
597 >    setupSwitchingFunction();
598 >
599      if(isError){
600        sprintf( painCave.errMsg,
601                 "ForceField error: There was an error initializing the forceField in fortran.\n" );
# Line 506 | 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 517 | Line 651 | namespace oopse {
651      int useDirectionalAtom = 0;    
652      int useElectrostatics = 0;
653      //usePBC and useRF are from simParams
654 <    int usePBC = simParams_->getPBC();
655 <    int useRF = simParams_->getUseRF();
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 575 | 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  
# Line 583 | Line 740 | namespace oopse {
740  
741      temp = useRF;
742      MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
743 <    
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 611 | Line 773 | namespace oopse {
773                  "\tsetting a dielectric constant!\n");
774          painCave.isFatal = 1;
775          simError();
776 <      }
615 <        
616 <    } else {
617 <      fInfo_.dielect = 0.0;
776 >      }      
777      }
778  
779    }
# Line 650 | 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 759 | Line 922 | namespace oopse {
922  
923   #endif
924  
925 <  double SimInfo::calcMaxCutoffRadius() {
763 <
764 <
765 <    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();
771 <
772 <    //query the max cutoff radius among these atom types
773 <    for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
774 <      cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
775 <    }
776 <
777 <    double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
778 < #ifdef IS_MPI
779 <    //pick the max cutoff radius among the processors
780 < #endif
781 <
782 <    return maxCutoffRadius;
783 <  }
784 <
785 <  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) {
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 {
935 >        if (myPolicy == "MAX") {
936 >          cp = MAX_CUTOFF_POLICY;
937 >        } else {
938 >          if (myPolicy == "TRADITIONAL") {            
939 >            cp = TRADITIONAL_CUTOFF_POLICY;
940 >          } else {
941 >            // throw error        
942 >            sprintf( painCave.errMsg,
943 >                     "SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
944 >            painCave.isFatal = 1;
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 <      if (!simParams_->haveRcut()){
960 <        sprintf(painCave.errMsg,
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;
977 >        painCave.isFatal = 0;
978          simError();
979 <        rcut = 15.0;
980 <      } else{
981 <        rcut = simParams_->getRcut();
982 <      }
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  
801 –      if (!simParams_->haveRsw()){
802 –        sprintf(painCave.errMsg,
803 –                "SimCreator Warning: No value was set for switchingRadius.\n"
804 –                "\tOOPSE will use a default value of\n"
805 –                "\t0.95 * cutoffRadius for the switchingRadius\n");
806 –        painCave.isFatal = 0;
807 –        simError();
808 –        rsw = 0.95 * rcut;
809 –      } else{
810 –        rsw = simParams_->getRsw();
1014        }
1015 +    }
1016 +  }
1017  
1018 <    } else {
1019 <      // if charge, dipole or reaction field is not used and the cutofff radius is not specified in
1020 <      //meta-data file, the maximum cutoff radius calculated from forcefiled will be used
1021 <        
1022 <      if (simParams_->haveRcut()) {
1023 <        rcut = simParams_->getRcut();
1024 <      } else {
820 <        //set cutoff radius to the maximum cutoff radius based on atom types in the whole system
821 <        rcut = calcMaxCutoffRadius();
822 <      }
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 <      if (simParams_->haveRsw()) {
1027 <        rsw  = simParams_->getRsw();
1028 <      } else {
1029 <        rsw = rcut;
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 == "SWITCHING_FUNCTION") {
1037 >          esm = SWITCHING_FUNCTION;
1038 >        } else {
1039 >          if (myMethod == "SHIFTED_POTENTIAL") {
1040 >            esm = SHIFTED_POTENTIAL;
1041 >          } else {
1042 >            if (myMethod == "SHIFTED_FORCE") {            
1043 >              esm = SHIFTED_FORCE;
1044 >            } else {
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      
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::setupCutoff() {
1103 <    getCutoff(rcut_, rsw_);    
835 <    double rnblist = rcut_ + 1; // skin of neighbor list
1102 >  void SimInfo::setupSwitchingFunction() {    
1103 >    int ft = CUBIC;
1104  
1105 <    //Pass these cutoff radius etc. to fortran. This function should be called once and only once
1106 <    notifyFortranCutoffs(&rcut_, &rsw_, &rnblist);
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) {
# Line 981 | Line 1268 | namespace oopse {
1268    
1269     /*
1270     Return intertia tensor for entire system and angular momentum Vector.
1271 +
1272 +
1273 +       [  Ixx -Ixy  -Ixz ]
1274 +  J =| -Iyx  Iyy  -Iyz |
1275 +       [ -Izx -Iyz   Izz ]
1276      */
1277  
1278     void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
# Line 1032 | Line 1324 | namespace oopse {
1324        inertiaTensor(0,1) = -xy;
1325        inertiaTensor(0,2) = -xz;
1326        inertiaTensor(1,0) = -xy;
1327 <      inertiaTensor(2,0) = xx + zz;
1327 >      inertiaTensor(1,1) = xx + zz;
1328        inertiaTensor(1,2) = -yz;
1329        inertiaTensor(2,0) = -xz;
1330        inertiaTensor(2,1) = -yz;
# Line 1060 | Line 1352 | namespace oopse {
1352        SimInfo::MoleculeIterator i;
1353        Molecule* mol;
1354        
1355 <      Vector3d thisq(0.0);
1356 <      Vector3d thisv(0.0);
1355 >      Vector3d thisr(0.0);
1356 >      Vector3d thisp(0.0);
1357        
1358 <      double thisMass = 0.0;
1358 >      double thisMass;
1359        
1360        for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {        
1361 <         thisq = mol->getCom()-com;
1362 <         thisv = mol->getComVel()-comVel;
1363 <         thisMass = mol->getMass();
1072 <         angularMomentum += cross( thisq, thisv ) * thisMass;
1361 >        thisMass = mol->getMass();
1362 >        thisr = mol->getCom()-com;
1363 >        thisp = (mol->getComVel()-comVel)*thisMass;
1364          
1365 +        angularMomentum += cross( thisr, thisp );
1366 +        
1367        }  
1368        
1369   #ifdef IS_MPI

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