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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 726 by chrisfen, Fri Nov 11 15:22:11 2005 UTC vs.
Revision 1078 by gezelter, Wed Oct 18 21:58:48 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 "primitives/StuntDouble.hpp"
57   #include "UseTheForce/fCutoffPolicy.h"
58   #include "UseTheForce/DarkSide/fElectrostaticSummationMethod.h"
59   #include "UseTheForce/DarkSide/fElectrostaticScreeningMethod.h"
60   #include "UseTheForce/DarkSide/fSwitchingFunctionType.h"
61   #include "UseTheForce/doForces_interface.h"
62   #include "UseTheForce/DarkSide/electrostatic_interface.h"
61 – #include "UseTheForce/notifyCutoffs_interface.h"
63   #include "UseTheForce/DarkSide/switcheroo_interface.h"
64   #include "utils/MemoryUtils.hpp"
65   #include "utils/simError.h"
66   #include "selection/SelectionManager.hpp"
67 + #include "io/ForceFieldOptions.hpp"
68 + #include "UseTheForce/ForceField.hpp"
69  
70   #ifdef IS_MPI
71   #include "UseTheForce/mpiComponentPlan.h"
# Line 70 | Line 73 | namespace oopse {
73   #endif
74  
75   namespace oopse {
76 +  std::set<int> getRigidSet(int index, std::map<int, std::set<int> >& container) {
77 +    std::map<int, std::set<int> >::iterator i = container.find(index);
78 +    std::set<int> result;
79 +    if (i != container.end()) {
80 +        result = i->second;
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),
86 <    ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
83 >    return result;
84 >  }
85 >  
86 >  SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
87 >    forceField_(ff), simParams_(simParams),
88 >    ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
89      nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
90      nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
91      nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nRigidBodies_(0),
92      nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
93 <    sman_(NULL), fortranInitialized_(false) {
93 >    sman_(NULL), fortranInitialized_(false), calcBoxDipole_(false) {
94  
84 –            
85 –      std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
95        MoleculeStamp* molStamp;
96        int nMolWithSameStamp;
97        int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
# Line 90 | Line 99 | namespace oopse {
99        CutoffGroupStamp* cgStamp;    
100        RigidBodyStamp* rbStamp;
101        int nRigidAtoms = 0;
102 <    
103 <      for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
104 <        molStamp = i->first;
105 <        nMolWithSameStamp = i->second;
102 >      std::vector<Component*> components = simParams->getComponents();
103 >      
104 >      for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
105 >        molStamp = (*i)->getMoleculeStamp();
106 >        nMolWithSameStamp = (*i)->getNMol();
107          
108          addMoleculeStamp(molStamp, nMolWithSameStamp);
109  
110          //calculate atoms in molecules
111          nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;  
112  
103 –
113          //calculate atoms in cutoff groups
114          int nAtomsInGroups = 0;
115          int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
116          
117          for (int j=0; j < nCutoffGroupsInStamp; j++) {
118 <          cgStamp = molStamp->getCutoffGroup(j);
118 >          cgStamp = molStamp->getCutoffGroupStamp(j);
119            nAtomsInGroups += cgStamp->getNMembers();
120          }
121  
# Line 119 | Line 128 | namespace oopse {
128          int nRigidBodiesInStamp = molStamp->getNRigidBodies();
129          
130          for (int j=0; j < nRigidBodiesInStamp; j++) {
131 <          rbStamp = molStamp->getRigidBody(j);
131 >          rbStamp = molStamp->getRigidBodyStamp(j);
132            nAtomsInRigidBodies += rbStamp->getNMembers();
133          }
134  
# Line 158 | Line 167 | namespace oopse {
167      }
168      molecules_.clear();
169        
161 –    delete stamps_;
170      delete sman_;
171      delete simParams_;
172      delete forceField_;
# Line 265 | Line 273 | namespace oopse {
273            }
274          }
275              
276 <      }//end for (integrableObject)
277 <    }// end for (mol)
276 >      }
277 >    }
278      
279      // n_constraints is local, so subtract them on each processor
280      ndf_local -= nConstraints_;
# Line 283 | Line 291 | namespace oopse {
291  
292    }
293  
294 +  int SimInfo::getFdf() {
295 + #ifdef IS_MPI
296 +    MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
297 + #else
298 +    fdf_ = fdf_local;
299 + #endif
300 +    return fdf_;
301 +  }
302 +    
303    void SimInfo::calcNdfRaw() {
304      int ndfRaw_local;
305  
# Line 345 | Line 362 | namespace oopse {
362      int b;
363      int c;
364      int d;
365 +
366 +    std::map<int, std::set<int> > atomGroups;
367 +
368 +    Molecule::RigidBodyIterator rbIter;
369 +    RigidBody* rb;
370 +    Molecule::IntegrableObjectIterator ii;
371 +    StuntDouble* integrableObject;
372 +    
373 +    for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
374 +           integrableObject = mol->nextIntegrableObject(ii)) {
375 +
376 +      if (integrableObject->isRigidBody()) {
377 +          rb = static_cast<RigidBody*>(integrableObject);
378 +          std::vector<Atom*> atoms = rb->getAtoms();
379 +          std::set<int> rigidAtoms;
380 +          for (int i = 0; i < atoms.size(); ++i) {
381 +            rigidAtoms.insert(atoms[i]->getGlobalIndex());
382 +          }
383 +          for (int i = 0; i < atoms.size(); ++i) {
384 +            atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
385 +          }      
386 +      } else {
387 +        std::set<int> oneAtomSet;
388 +        oneAtomSet.insert(integrableObject->getGlobalIndex());
389 +        atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));        
390 +      }
391 +    }  
392 +
393      
394 +    
395      for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
396        a = bond->getAtomA()->getGlobalIndex();
397        b = bond->getAtomB()->getGlobalIndex();        
# Line 356 | Line 402 | namespace oopse {
402        a = bend->getAtomA()->getGlobalIndex();
403        b = bend->getAtomB()->getGlobalIndex();        
404        c = bend->getAtomC()->getGlobalIndex();
405 +      std::set<int> rigidSetA = getRigidSet(a, atomGroups);
406 +      std::set<int> rigidSetB = getRigidSet(b, atomGroups);
407 +      std::set<int> rigidSetC = getRigidSet(c, atomGroups);
408  
409 <      exclude_.addPair(a, b);
410 <      exclude_.addPair(a, c);
411 <      exclude_.addPair(b, c);        
409 >      exclude_.addPairs(rigidSetA, rigidSetB);
410 >      exclude_.addPairs(rigidSetA, rigidSetC);
411 >      exclude_.addPairs(rigidSetB, rigidSetC);
412 >      
413 >      //exclude_.addPair(a, b);
414 >      //exclude_.addPair(a, c);
415 >      //exclude_.addPair(b, c);        
416      }
417  
418      for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
# Line 367 | Line 420 | namespace oopse {
420        b = torsion->getAtomB()->getGlobalIndex();        
421        c = torsion->getAtomC()->getGlobalIndex();        
422        d = torsion->getAtomD()->getGlobalIndex();        
423 +      std::set<int> rigidSetA = getRigidSet(a, atomGroups);
424 +      std::set<int> rigidSetB = getRigidSet(b, atomGroups);
425 +      std::set<int> rigidSetC = getRigidSet(c, atomGroups);
426 +      std::set<int> rigidSetD = getRigidSet(d, atomGroups);
427  
428 +      exclude_.addPairs(rigidSetA, rigidSetB);
429 +      exclude_.addPairs(rigidSetA, rigidSetC);
430 +      exclude_.addPairs(rigidSetA, rigidSetD);
431 +      exclude_.addPairs(rigidSetB, rigidSetC);
432 +      exclude_.addPairs(rigidSetB, rigidSetD);
433 +      exclude_.addPairs(rigidSetC, rigidSetD);
434 +
435 +      /*
436 +      exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
437 +      exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
438 +      exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
439 +      exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
440 +      exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
441 +      exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
442 +        
443 +      
444        exclude_.addPair(a, b);
445        exclude_.addPair(a, c);
446        exclude_.addPair(a, d);
447        exclude_.addPair(b, c);
448        exclude_.addPair(b, d);
449        exclude_.addPair(c, d);        
450 +      */
451      }
452  
379 –    Molecule::RigidBodyIterator rbIter;
380 –    RigidBody* rb;
453      for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
454        std::vector<Atom*> atoms = rb->getAtoms();
455        for (int i = 0; i < atoms.size() -1 ; ++i) {
# Line 402 | Line 474 | namespace oopse {
474      int b;
475      int c;
476      int d;
477 +
478 +    std::map<int, std::set<int> > atomGroups;
479 +
480 +    Molecule::RigidBodyIterator rbIter;
481 +    RigidBody* rb;
482 +    Molecule::IntegrableObjectIterator ii;
483 +    StuntDouble* integrableObject;
484      
485 +    for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
486 +           integrableObject = mol->nextIntegrableObject(ii)) {
487 +
488 +      if (integrableObject->isRigidBody()) {
489 +          rb = static_cast<RigidBody*>(integrableObject);
490 +          std::vector<Atom*> atoms = rb->getAtoms();
491 +          std::set<int> rigidAtoms;
492 +          for (int i = 0; i < atoms.size(); ++i) {
493 +            rigidAtoms.insert(atoms[i]->getGlobalIndex());
494 +          }
495 +          for (int i = 0; i < atoms.size(); ++i) {
496 +            atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
497 +          }      
498 +      } else {
499 +        std::set<int> oneAtomSet;
500 +        oneAtomSet.insert(integrableObject->getGlobalIndex());
501 +        atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));        
502 +      }
503 +    }  
504 +
505 +    
506      for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
507        a = bond->getAtomA()->getGlobalIndex();
508        b = bond->getAtomB()->getGlobalIndex();        
# Line 414 | Line 514 | namespace oopse {
514        b = bend->getAtomB()->getGlobalIndex();        
515        c = bend->getAtomC()->getGlobalIndex();
516  
517 <      exclude_.removePair(a, b);
518 <      exclude_.removePair(a, c);
519 <      exclude_.removePair(b, c);        
517 >      std::set<int> rigidSetA = getRigidSet(a, atomGroups);
518 >      std::set<int> rigidSetB = getRigidSet(b, atomGroups);
519 >      std::set<int> rigidSetC = getRigidSet(c, atomGroups);
520 >
521 >      exclude_.removePairs(rigidSetA, rigidSetB);
522 >      exclude_.removePairs(rigidSetA, rigidSetC);
523 >      exclude_.removePairs(rigidSetB, rigidSetC);
524 >      
525 >      //exclude_.removePair(a, b);
526 >      //exclude_.removePair(a, c);
527 >      //exclude_.removePair(b, c);        
528      }
529  
530      for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
# Line 425 | Line 533 | namespace oopse {
533        c = torsion->getAtomC()->getGlobalIndex();        
534        d = torsion->getAtomD()->getGlobalIndex();        
535  
536 +      std::set<int> rigidSetA = getRigidSet(a, atomGroups);
537 +      std::set<int> rigidSetB = getRigidSet(b, atomGroups);
538 +      std::set<int> rigidSetC = getRigidSet(c, atomGroups);
539 +      std::set<int> rigidSetD = getRigidSet(d, atomGroups);
540 +
541 +      exclude_.removePairs(rigidSetA, rigidSetB);
542 +      exclude_.removePairs(rigidSetA, rigidSetC);
543 +      exclude_.removePairs(rigidSetA, rigidSetD);
544 +      exclude_.removePairs(rigidSetB, rigidSetC);
545 +      exclude_.removePairs(rigidSetB, rigidSetD);
546 +      exclude_.removePairs(rigidSetC, rigidSetD);
547 +
548 +      /*
549 +      exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
550 +      exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
551 +      exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
552 +      exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
553 +      exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
554 +      exclude_.removePairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
555 +
556 +      
557        exclude_.removePair(a, b);
558        exclude_.removePair(a, c);
559        exclude_.removePair(a, d);
560        exclude_.removePair(b, c);
561        exclude_.removePair(b, d);
562        exclude_.removePair(c, d);        
563 +      */
564      }
565  
436 –    Molecule::RigidBodyIterator rbIter;
437 –    RigidBody* rb;
566      for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
567        std::vector<Atom*> atoms = rb->getAtoms();
568        for (int i = 0; i < atoms.size() -1 ; ++i) {
# Line 473 | Line 601 | namespace oopse {
601      /** @deprecate */    
602      int isError = 0;
603      
604 +    setupCutoff();
605 +    
606      setupElectrostaticSummationMethod( isError );
607      setupSwitchingFunction();
608 +    setupAccumulateBoxDipole();
609  
610      if(isError){
611        sprintf( painCave.errMsg,
# Line 482 | Line 613 | namespace oopse {
613        painCave.isFatal = 1;
614        simError();
615      }
485 –  
486 –    
487 –    setupCutoff();
616  
617      calcNdf();
618      calcNdfRaw();
# Line 519 | Line 647 | namespace oopse {
647      int useLennardJones = 0;
648      int useElectrostatic = 0;
649      int useEAM = 0;
650 +    int useSC = 0;
651      int useCharge = 0;
652      int useDirectional = 0;
653      int useDipole = 0;
# Line 533 | Line 662 | namespace oopse {
662      int usePBC = simParams_->getUsePeriodicBoundaryConditions();
663      int useRF;
664      int useSF;
665 +    int useSP;
666 +    int useBoxDipole;
667      std::string myMethod;
668  
669      // set the useRF logical
670      useRF = 0;
671      useSF = 0;
672 +    useSP = 0;
673  
674  
675      if (simParams_->haveElectrostaticSummationMethod()) {
676        std::string myMethod = simParams_->getElectrostaticSummationMethod();
677        toUpper(myMethod);
678 <      if (myMethod == "REACTION_FIELD") {
679 <        useRF=1;
680 <      } else {
681 <        if (myMethod == "SHIFTED_FORCE") {
682 <          useSF = 1;
683 <        }
678 >      if (myMethod == "REACTION_FIELD"){
679 >        useRF = 1;
680 >      } else if (myMethod == "SHIFTED_FORCE"){
681 >        useSF = 1;
682 >      } else if (myMethod == "SHIFTED_POTENTIAL"){
683 >        useSP = 1;
684        }
685      }
686 +    
687 +    if (simParams_->haveAccumulateBoxDipole())
688 +      if (simParams_->getAccumulateBoxDipole())
689 +        useBoxDipole = 1;
690  
691      //loop over all of the atom types
692      for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
693        useLennardJones |= (*i)->isLennardJones();
694        useElectrostatic |= (*i)->isElectrostatic();
695        useEAM |= (*i)->isEAM();
696 +      useSC |= (*i)->isSC();
697        useCharge |= (*i)->isCharge();
698        useDirectional |= (*i)->isDirectional();
699        useDipole |= (*i)->isDipole();
# Line 607 | Line 744 | namespace oopse {
744      temp = useEAM;
745      MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
746  
747 +    temp = useSC;
748 +    MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
749 +    
750      temp = useShape;
751      MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);  
752  
# Line 617 | Line 757 | namespace oopse {
757      MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
758  
759      temp = useSF;
760 <    MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
760 >    MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);  
761  
762 +    temp = useSP;
763 +    MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
764 +
765 +    temp = useBoxDipole;
766 +    MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
767 +
768   #endif
769  
770      fInfo_.SIM_uses_PBC = usePBC;    
# Line 631 | Line 777 | namespace oopse {
777      fInfo_.SIM_uses_StickyPower = useStickyPower;
778      fInfo_.SIM_uses_GayBerne = useGayBerne;
779      fInfo_.SIM_uses_EAM = useEAM;
780 +    fInfo_.SIM_uses_SC = useSC;
781      fInfo_.SIM_uses_Shapes = useShape;
782      fInfo_.SIM_uses_FLARB = useFLARB;
783      fInfo_.SIM_uses_RF = useRF;
784      fInfo_.SIM_uses_SF = useSF;
785 <
786 <    if( myMethod == "REACTION_FIELD") {
640 <      
641 <      if (simParams_->haveDielectric()) {
642 <        fInfo_.dielect = simParams_->getDielectric();
643 <      } else {
644 <        sprintf(painCave.errMsg,
645 <                "SimSetup Error: No Dielectric constant was set.\n"
646 <                "\tYou are trying to use Reaction Field without"
647 <                "\tsetting a dielectric constant!\n");
648 <        painCave.isFatal = 1;
649 <        simError();
650 <      }      
651 <    }
652 <
785 >    fInfo_.SIM_uses_SP = useSP;
786 >    fInfo_.SIM_uses_BoxDipole = useBoxDipole;
787    }
788  
789    void SimInfo::setupFortranSim() {
# Line 666 | Line 800 | namespace oopse {
800      }
801  
802      //calculate mass ratio of cutoff group
803 <    std::vector<double> mfact;
803 >    std::vector<RealType> mfact;
804      SimInfo::MoleculeIterator mi;
805      Molecule* mol;
806      Molecule::CutoffGroupIterator ci;
807      CutoffGroup* cg;
808      Molecule::AtomIterator ai;
809      Atom* atom;
810 <    double totalMass;
810 >    RealType totalMass;
811  
812      //to avoid memory reallocation, reserve enough space for mfact
813      mfact.reserve(getNCutoffGroups());
# Line 796 | Line 930 | namespace oopse {
930  
931   #endif
932  
933 <  double SimInfo::calcMaxCutoffRadius() {
933 >  void SimInfo::setupCutoff() {          
934 >    
935 >    ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
936  
937 +    // Check the cutoff policy
938 +    int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
939  
940 <    std::set<AtomType*> atomTypes;
941 <    std::set<AtomType*>::iterator i;
942 <    std::vector<double> cutoffRadius;
943 <
944 <    //get the unique atom types
807 <    atomTypes = getUniqueAtomTypes();
808 <
809 <    //query the max cutoff radius among these atom types
810 <    for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
811 <      cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
940 >    std::string myPolicy;
941 >    if (forceFieldOptions_.haveCutoffPolicy()){
942 >      myPolicy = forceFieldOptions_.getCutoffPolicy();
943 >    }else if (simParams_->haveCutoffPolicy()) {
944 >      myPolicy = simParams_->getCutoffPolicy();
945      }
946  
947 <    double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
815 < #ifdef IS_MPI
816 <    //pick the max cutoff radius among the processors
817 < #endif
818 <
819 <    return maxCutoffRadius;
820 <  }
821 <
822 <  void SimInfo::getCutoff(double& rcut, double& rsw) {
823 <    
824 <    if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
825 <        
826 <      if (!simParams_->haveCutoffRadius()){
827 <        sprintf(painCave.errMsg,
828 <                "SimCreator Warning: No value was set for the cutoffRadius.\n"
829 <                "\tOOPSE will use a default value of 15.0 angstroms"
830 <                "\tfor the cutoffRadius.\n");
831 <        painCave.isFatal = 0;
832 <        simError();
833 <        rcut = 15.0;
834 <      } else{
835 <        rcut = simParams_->getCutoffRadius();
836 <      }
837 <
838 <      if (!simParams_->haveSwitchingRadius()){
839 <        sprintf(painCave.errMsg,
840 <                "SimCreator Warning: No value was set for switchingRadius.\n"
841 <                "\tOOPSE will use a default value of\n"
842 <                "\t0.85 * cutoffRadius for the switchingRadius\n");
843 <        painCave.isFatal = 0;
844 <        simError();
845 <        rsw = 0.85 * rcut;
846 <      } else{
847 <        rsw = simParams_->getSwitchingRadius();
848 <      }
849 <
850 <    } else {
851 <      // if charge, dipole or reaction field is not used and the cutofff radius is not specified in
852 <      //meta-data file, the maximum cutoff radius calculated from forcefiled will be used
853 <        
854 <      if (simParams_->haveCutoffRadius()) {
855 <        rcut = simParams_->getCutoffRadius();
856 <      } else {
857 <        //set cutoff radius to the maximum cutoff radius based on atom types in the whole system
858 <        rcut = calcMaxCutoffRadius();
859 <      }
860 <
861 <      if (simParams_->haveSwitchingRadius()) {
862 <        rsw  = simParams_->getSwitchingRadius();
863 <      } else {
864 <        rsw = rcut;
865 <      }
866 <    
867 <    }
868 <  }
869 <
870 <  void SimInfo::setupCutoff() {    
871 <    getCutoff(rcut_, rsw_);    
872 <    double rnblist = rcut_ + 1; // skin of neighbor list
873 <
874 <    //Pass these cutoff radius etc. to fortran. This function should be called once and only once
875 <    
876 <    int cp =  TRADITIONAL_CUTOFF_POLICY;
877 <    if (simParams_->haveCutoffPolicy()) {
878 <      std::string myPolicy = simParams_->getCutoffPolicy();
947 >    if (!myPolicy.empty()){
948        toUpper(myPolicy);
949        if (myPolicy == "MIX") {
950          cp = MIX_CUTOFF_POLICY;
# Line 894 | Line 963 | namespace oopse {
963            }    
964          }          
965        }
966 <    }
966 >    }          
967 >    notifyFortranCutoffPolicy(&cp);
968  
969 <
969 >    // Check the Skin Thickness for neighborlists
970 >    RealType skin;
971      if (simParams_->haveSkinThickness()) {
972 <      double skinThickness = simParams_->getSkinThickness();
973 <    }
972 >      skin = simParams_->getSkinThickness();
973 >      notifyFortranSkinThickness(&skin);
974 >    }            
975 >        
976 >    // Check if the cutoff was set explicitly:
977 >    if (simParams_->haveCutoffRadius()) {
978 >      rcut_ = simParams_->getCutoffRadius();
979 >      if (simParams_->haveSwitchingRadius()) {
980 >        rsw_  = simParams_->getSwitchingRadius();
981 >      } else {
982 >        if (fInfo_.SIM_uses_Charges |
983 >            fInfo_.SIM_uses_Dipoles |
984 >            fInfo_.SIM_uses_RF) {
985 >          
986 >          rsw_ = 0.85 * rcut_;
987 >          sprintf(painCave.errMsg,
988 >                  "SimCreator Warning: No value was set for the switchingRadius.\n"
989 >                  "\tOOPSE will use a default value of 85 percent of the cutoffRadius.\n"
990 >                  "\tswitchingRadius = %f. for this simulation\n", rsw_);
991 >        painCave.isFatal = 0;
992 >        simError();
993 >        } else {
994 >          rsw_ = rcut_;
995 >          sprintf(painCave.errMsg,
996 >                  "SimCreator Warning: No value was set for the switchingRadius.\n"
997 >                  "\tOOPSE will use the same value as the cutoffRadius.\n"
998 >                  "\tswitchingRadius = %f. for this simulation\n", rsw_);
999 >          painCave.isFatal = 0;
1000 >          simError();
1001 >        }
1002 >      }
1003 >      
1004 >      notifyFortranCutoffs(&rcut_, &rsw_);
1005 >      
1006 >    } else {
1007 >      
1008 >      // For electrostatic atoms, we'll assume a large safe value:
1009 >      if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
1010 >        sprintf(painCave.errMsg,
1011 >                "SimCreator Warning: No value was set for the cutoffRadius.\n"
1012 >                "\tOOPSE will use a default value of 15.0 angstroms"
1013 >                "\tfor the cutoffRadius.\n");
1014 >        painCave.isFatal = 0;
1015 >        simError();
1016 >        rcut_ = 15.0;
1017 >      
1018 >        if (simParams_->haveElectrostaticSummationMethod()) {
1019 >          std::string myMethod = simParams_->getElectrostaticSummationMethod();
1020 >          toUpper(myMethod);
1021 >          if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1022 >            if (simParams_->haveSwitchingRadius()){
1023 >              sprintf(painCave.errMsg,
1024 >                      "SimInfo Warning: A value was set for the switchingRadius\n"
1025 >                      "\teven though the electrostaticSummationMethod was\n"
1026 >                      "\tset to %s\n", myMethod.c_str());
1027 >              painCave.isFatal = 1;
1028 >              simError();            
1029 >            }
1030 >          }
1031 >        }
1032 >      
1033 >        if (simParams_->haveSwitchingRadius()){
1034 >          rsw_ = simParams_->getSwitchingRadius();
1035 >        } else {        
1036 >          sprintf(painCave.errMsg,
1037 >                  "SimCreator Warning: No value was set for switchingRadius.\n"
1038 >                  "\tOOPSE will use a default value of\n"
1039 >                  "\t0.85 * cutoffRadius for the switchingRadius\n");
1040 >          painCave.isFatal = 0;
1041 >          simError();
1042 >          rsw_ = 0.85 * rcut_;
1043 >        }
1044 >        notifyFortranCutoffs(&rcut_, &rsw_);
1045 >      } else {
1046 >        // We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1047 >        // We'll punt and let fortran figure out the cutoffs later.
1048 >        
1049 >        notifyFortranYouAreOnYourOwn();
1050  
1051 <    notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp);
1052 <    // also send cutoff notification to electrostatics
906 <    setElectrostaticCutoffRadius(&rcut_, &rsw_);
1051 >      }
1052 >    }
1053    }
1054  
1055    void SimInfo::setupElectrostaticSummationMethod( int isError ) {    
# Line 911 | Line 1057 | namespace oopse {
1057      int errorOut;
1058      int esm =  NONE;
1059      int sm = UNDAMPED;
1060 <    double alphaVal;
1061 <    double dielectric;
1062 <
1060 >    RealType alphaVal;
1061 >    RealType dielectric;
1062 >    
1063      errorOut = isError;
918 –    alphaVal = simParams_->getDampingAlpha();
919 –    dielectric = simParams_->getDielectric();
1064  
1065      if (simParams_->haveElectrostaticSummationMethod()) {
1066        std::string myMethod = simParams_->getElectrostaticSummationMethod();
# Line 933 | Line 1077 | namespace oopse {
1077              if (myMethod == "SHIFTED_FORCE") {            
1078                esm = SHIFTED_FORCE;
1079              } else {
1080 <              if (myMethod == "REACTION_FIELD") {            
1080 >              if (myMethod == "REACTION_FIELD") {
1081                  esm = REACTION_FIELD;
1082 +                dielectric = simParams_->getDielectric();
1083 +                if (!simParams_->haveDielectric()) {
1084 +                  // throw warning
1085 +                  sprintf( painCave.errMsg,
1086 +                           "SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
1087 +                           "\tA default value of %f will be used for the dielectric.\n", dielectric);
1088 +                  painCave.isFatal = 0;
1089 +                  simError();
1090 +                }
1091                } else {
1092                  // throw error        
1093                  sprintf( painCave.errMsg,
1094 <                         "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() );
1094 >                         "SimInfo error: Unknown electrostaticSummationMethod.\n"
1095 >                         "\t(Input file specified %s .)\n"
1096 >                         "\telectrostaticSummationMethod must be one of: \"none\",\n"
1097 >                         "\t\"shifted_potential\", \"shifted_force\", or \n"
1098 >                         "\t\"reaction_field\".\n", myMethod.c_str() );
1099                  painCave.isFatal = 1;
1100                  simError();
1101                }    
# Line 957 | Line 1114 | namespace oopse {
1114          if (myScreen == "DAMPED") {
1115            sm = DAMPED;
1116            if (!simParams_->haveDampingAlpha()) {
1117 <            //throw error
1117 >            // first set a cutoff dependent alpha value
1118 >            // we assume alpha depends linearly with rcut from 0 to 20.5 ang
1119 >            alphaVal = 0.5125 - rcut_* 0.025;
1120 >            // for values rcut > 20.5, alpha is zero
1121 >            if (alphaVal < 0) alphaVal = 0;
1122 >
1123 >            // throw warning
1124              sprintf( painCave.errMsg,
1125 <                     "SimInfo warning: dampingAlpha was not specified in the input file. A default value of %f (1/ang) will be used.", alphaVal);
1125 >                     "SimInfo warning: dampingAlpha was not specified in the input file.\n"
1126 >                     "\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1127              painCave.isFatal = 0;
1128              simError();
1129            }
1130          } else {
1131            // throw error        
1132            sprintf( painCave.errMsg,
1133 <                   "SimInfo error: Unknown electrostaticScreeningMethod. (Input file specified %s .)\n\telectrostaticScreeningMethod must be one of: \"undamped\" or \"damped\".", myScreen.c_str() );
1133 >                   "SimInfo error: Unknown electrostaticScreeningMethod.\n"
1134 >                   "\t(Input file specified %s .)\n"
1135 >                   "\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1136 >                   "or \"damped\".\n", myScreen.c_str() );
1137            painCave.isFatal = 1;
1138            simError();
1139          }
# Line 975 | Line 1142 | namespace oopse {
1142      
1143      // let's pass some summation method variables to fortran
1144      setElectrostaticSummationMethod( &esm );
1145 +    setFortranElectrostaticMethod( &esm );
1146      setScreeningMethod( &sm );
1147      setDampingAlpha( &alphaVal );
1148      setReactionFieldDielectric( &dielectric );
1149 <    initFortranFF( &esm, &errorOut );
1149 >    initFortranFF( &errorOut );
1150    }
1151  
1152    void SimInfo::setupSwitchingFunction() {    
# Line 1007 | Line 1175 | namespace oopse {
1175  
1176    }
1177  
1178 +  void SimInfo::setupAccumulateBoxDipole() {    
1179 +
1180 +    // we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1181 +    if ( simParams_->haveAccumulateBoxDipole() )
1182 +      if ( simParams_->getAccumulateBoxDipole() ) {
1183 +        setAccumulateBoxDipole();
1184 +        calcBoxDipole_ = true;
1185 +      }
1186 +
1187 +  }
1188 +
1189    void SimInfo::addProperty(GenericData* genData) {
1190      properties_.addProperty(genData);  
1191    }
# Line 1063 | Line 1242 | namespace oopse {
1242      Molecule* mol;
1243  
1244      Vector3d comVel(0.0);
1245 <    double totalMass = 0.0;
1245 >    RealType totalMass = 0.0;
1246      
1247  
1248      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1249 <      double mass = mol->getMass();
1249 >      RealType mass = mol->getMass();
1250        totalMass += mass;
1251        comVel += mass * mol->getComVel();
1252      }  
1253  
1254   #ifdef IS_MPI
1255 <    double tmpMass = totalMass;
1255 >    RealType tmpMass = totalMass;
1256      Vector3d tmpComVel(comVel);    
1257 <    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1258 <    MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1257 >    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1258 >    MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1259   #endif
1260  
1261      comVel /= totalMass;
# Line 1089 | Line 1268 | namespace oopse {
1268      Molecule* mol;
1269  
1270      Vector3d com(0.0);
1271 <    double totalMass = 0.0;
1271 >    RealType totalMass = 0.0;
1272      
1273      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1274 <      double mass = mol->getMass();
1274 >      RealType mass = mol->getMass();
1275        totalMass += mass;
1276        com += mass * mol->getCom();
1277      }  
1278  
1279   #ifdef IS_MPI
1280 <    double tmpMass = totalMass;
1280 >    RealType tmpMass = totalMass;
1281      Vector3d tmpCom(com);    
1282 <    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1283 <    MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1282 >    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1283 >    MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1284   #endif
1285  
1286      com /= totalMass;
# Line 1125 | Line 1304 | namespace oopse {
1304        Molecule* mol;
1305        
1306      
1307 <      double totalMass = 0.0;
1307 >      RealType totalMass = 0.0;
1308      
1309  
1310        for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1311 <         double mass = mol->getMass();
1311 >         RealType mass = mol->getMass();
1312           totalMass += mass;
1313           com += mass * mol->getCom();
1314           comVel += mass * mol->getComVel();          
1315        }  
1316        
1317   #ifdef IS_MPI
1318 <      double tmpMass = totalMass;
1318 >      RealType tmpMass = totalMass;
1319        Vector3d tmpCom(com);  
1320        Vector3d tmpComVel(comVel);
1321 <      MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1322 <      MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1323 <      MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1321 >      MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1322 >      MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1323 >      MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1324   #endif
1325        
1326        com /= totalMass;
# Line 1160 | Line 1339 | namespace oopse {
1339     void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1340        
1341  
1342 <      double xx = 0.0;
1343 <      double yy = 0.0;
1344 <      double zz = 0.0;
1345 <      double xy = 0.0;
1346 <      double xz = 0.0;
1347 <      double yz = 0.0;
1342 >      RealType xx = 0.0;
1343 >      RealType yy = 0.0;
1344 >      RealType zz = 0.0;
1345 >      RealType xy = 0.0;
1346 >      RealType xz = 0.0;
1347 >      RealType yz = 0.0;
1348        Vector3d com(0.0);
1349        Vector3d comVel(0.0);
1350        
# Line 1177 | Line 1356 | namespace oopse {
1356        Vector3d thisq(0.0);
1357        Vector3d thisv(0.0);
1358  
1359 <      double thisMass = 0.0;
1359 >      RealType thisMass = 0.0;
1360      
1361        
1362        
# Line 1215 | Line 1394 | namespace oopse {
1394   #ifdef IS_MPI
1395        Mat3x3d tmpI(inertiaTensor);
1396        Vector3d tmpAngMom;
1397 <      MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1398 <      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1397 >      MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1398 >      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1399   #endif
1400                
1401        return;
# Line 1237 | Line 1416 | namespace oopse {
1416        Vector3d thisr(0.0);
1417        Vector3d thisp(0.0);
1418        
1419 <      double thisMass;
1419 >      RealType thisMass;
1420        
1421        for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {        
1422          thisMass = mol->getMass();
# Line 1250 | Line 1429 | namespace oopse {
1429        
1430   #ifdef IS_MPI
1431        Vector3d tmpAngMom;
1432 <      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1432 >      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1433   #endif
1434        
1435        return angularMomentum;
1436     }
1437    
1438 <  
1438 >  StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1439 >    return IOIndexToIntegrableObject.at(index);
1440 >  }
1441 >  
1442 >  void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1443 >    IOIndexToIntegrableObject= v;
1444 >  }
1445 >
1446 > /*
1447 >   void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1448 >      assert( v.size() == nAtoms_ + nRigidBodies_);
1449 >      sdByGlobalIndex_ = v;
1450 >    }
1451 >
1452 >    StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1453 >      //assert(index < nAtoms_ + nRigidBodies_);
1454 >      return sdByGlobalIndex_.at(index);
1455 >    }  
1456 > */  
1457   }//end namespace oopse
1458  

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