ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/OpenMD/branches/development/src/brains/SimInfo.cpp
(Generate patch)

Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 705 by chrisfen, Tue Nov 1 19:14:27 2005 UTC vs.
Revision 945 by gezelter, Tue Apr 25 02:09:01 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/DarkSide/electrostatic_interface.h"
62 < #include "UseTheForce/notifyCutoffs_interface.h"
62 > #include "UseTheForce/DarkSide/switcheroo_interface.h"
63   #include "utils/MemoryUtils.hpp"
64   #include "utils/simError.h"
65   #include "selection/SelectionManager.hpp"
66 + #include "io/ForceFieldOptions.hpp"
67 + #include "UseTheForce/ForceField.hpp"
68  
69   #ifdef IS_MPI
70   #include "UseTheForce/mpiComponentPlan.h"
# Line 67 | 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),
85 <    ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
82 >    return result;
83 >  }
84 >  
85 >  SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
86 >    forceField_(ff), simParams_(simParams),
87 >    ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
88      nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
89      nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
90      nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nRigidBodies_(0),
91      nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
92      sman_(NULL), fortranInitialized_(false) {
93  
81 –            
82 –      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
# Line 87 | Line 98 | namespace oopse {
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  
100 –
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  
# Line 116 | 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 155 | Line 166 | namespace oopse {
166      }
167      molecules_.clear();
168        
158 –    delete stamps_;
169      delete sman_;
170      delete simParams_;
171      delete forceField_;
# Line 262 | 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 280 | Line 290 | namespace oopse {
290  
291    }
292  
293 +  int SimInfo::getFdf() {
294 + #ifdef IS_MPI
295 +    MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
296 + #else
297 +    fdf_ = fdf_local;
298 + #endif
299 +    return fdf_;
300 +  }
301 +    
302    void SimInfo::calcNdfRaw() {
303      int ndfRaw_local;
304  
# Line 342 | Line 361 | namespace oopse {
361      int b;
362      int c;
363      int d;
364 +
365 +    std::map<int, std::set<int> > atomGroups;
366 +
367 +    Molecule::RigidBodyIterator rbIter;
368 +    RigidBody* rb;
369 +    Molecule::IntegrableObjectIterator ii;
370 +    StuntDouble* integrableObject;
371 +    
372 +    for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
373 +           integrableObject = mol->nextIntegrableObject(ii)) {
374 +
375 +      if (integrableObject->isRigidBody()) {
376 +          rb = static_cast<RigidBody*>(integrableObject);
377 +          std::vector<Atom*> atoms = rb->getAtoms();
378 +          std::set<int> rigidAtoms;
379 +          for (int i = 0; i < atoms.size(); ++i) {
380 +            rigidAtoms.insert(atoms[i]->getGlobalIndex());
381 +          }
382 +          for (int i = 0; i < atoms.size(); ++i) {
383 +            atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
384 +          }      
385 +      } else {
386 +        std::set<int> oneAtomSet;
387 +        oneAtomSet.insert(integrableObject->getGlobalIndex());
388 +        atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));        
389 +      }
390 +    }  
391 +
392      
393 +    
394      for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
395        a = bond->getAtomA()->getGlobalIndex();
396        b = bond->getAtomB()->getGlobalIndex();        
# Line 353 | Line 401 | namespace oopse {
401        a = bend->getAtomA()->getGlobalIndex();
402        b = bend->getAtomB()->getGlobalIndex();        
403        c = bend->getAtomC()->getGlobalIndex();
404 +      std::set<int> rigidSetA = getRigidSet(a, atomGroups);
405 +      std::set<int> rigidSetB = getRigidSet(b, atomGroups);
406 +      std::set<int> rigidSetC = getRigidSet(c, atomGroups);
407  
408 <      exclude_.addPair(a, b);
409 <      exclude_.addPair(a, c);
410 <      exclude_.addPair(b, c);        
408 >      exclude_.addPairs(rigidSetA, rigidSetB);
409 >      exclude_.addPairs(rigidSetA, rigidSetC);
410 >      exclude_.addPairs(rigidSetB, rigidSetC);
411 >      
412 >      //exclude_.addPair(a, b);
413 >      //exclude_.addPair(a, c);
414 >      //exclude_.addPair(b, c);        
415      }
416  
417      for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
# Line 364 | Line 419 | namespace oopse {
419        b = torsion->getAtomB()->getGlobalIndex();        
420        c = torsion->getAtomC()->getGlobalIndex();        
421        d = torsion->getAtomD()->getGlobalIndex();        
422 +      std::set<int> rigidSetA = getRigidSet(a, atomGroups);
423 +      std::set<int> rigidSetB = getRigidSet(b, atomGroups);
424 +      std::set<int> rigidSetC = getRigidSet(c, atomGroups);
425 +      std::set<int> rigidSetD = getRigidSet(d, atomGroups);
426  
427 +      exclude_.addPairs(rigidSetA, rigidSetB);
428 +      exclude_.addPairs(rigidSetA, rigidSetC);
429 +      exclude_.addPairs(rigidSetA, rigidSetD);
430 +      exclude_.addPairs(rigidSetB, rigidSetC);
431 +      exclude_.addPairs(rigidSetB, rigidSetD);
432 +      exclude_.addPairs(rigidSetC, rigidSetD);
433 +
434 +      /*
435 +      exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
436 +      exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
437 +      exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
438 +      exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
439 +      exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
440 +      exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
441 +        
442 +      
443        exclude_.addPair(a, b);
444        exclude_.addPair(a, c);
445        exclude_.addPair(a, d);
446        exclude_.addPair(b, c);
447        exclude_.addPair(b, d);
448        exclude_.addPair(c, d);        
449 +      */
450      }
451  
376 –    Molecule::RigidBodyIterator rbIter;
377 –    RigidBody* rb;
452      for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
453        std::vector<Atom*> atoms = rb->getAtoms();
454        for (int i = 0; i < atoms.size() -1 ; ++i) {
# Line 399 | Line 473 | namespace oopse {
473      int b;
474      int c;
475      int d;
476 +
477 +    std::map<int, std::set<int> > atomGroups;
478 +
479 +    Molecule::RigidBodyIterator rbIter;
480 +    RigidBody* rb;
481 +    Molecule::IntegrableObjectIterator ii;
482 +    StuntDouble* integrableObject;
483      
484 +    for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
485 +           integrableObject = mol->nextIntegrableObject(ii)) {
486 +
487 +      if (integrableObject->isRigidBody()) {
488 +          rb = static_cast<RigidBody*>(integrableObject);
489 +          std::vector<Atom*> atoms = rb->getAtoms();
490 +          std::set<int> rigidAtoms;
491 +          for (int i = 0; i < atoms.size(); ++i) {
492 +            rigidAtoms.insert(atoms[i]->getGlobalIndex());
493 +          }
494 +          for (int i = 0; i < atoms.size(); ++i) {
495 +            atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
496 +          }      
497 +      } else {
498 +        std::set<int> oneAtomSet;
499 +        oneAtomSet.insert(integrableObject->getGlobalIndex());
500 +        atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));        
501 +      }
502 +    }  
503 +
504 +    
505      for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
506        a = bond->getAtomA()->getGlobalIndex();
507        b = bond->getAtomB()->getGlobalIndex();        
# Line 411 | Line 513 | namespace oopse {
513        b = bend->getAtomB()->getGlobalIndex();        
514        c = bend->getAtomC()->getGlobalIndex();
515  
516 <      exclude_.removePair(a, b);
517 <      exclude_.removePair(a, c);
518 <      exclude_.removePair(b, c);        
516 >      std::set<int> rigidSetA = getRigidSet(a, atomGroups);
517 >      std::set<int> rigidSetB = getRigidSet(b, atomGroups);
518 >      std::set<int> rigidSetC = getRigidSet(c, atomGroups);
519 >
520 >      exclude_.removePairs(rigidSetA, rigidSetB);
521 >      exclude_.removePairs(rigidSetA, rigidSetC);
522 >      exclude_.removePairs(rigidSetB, rigidSetC);
523 >      
524 >      //exclude_.removePair(a, b);
525 >      //exclude_.removePair(a, c);
526 >      //exclude_.removePair(b, c);        
527      }
528  
529      for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
# Line 422 | Line 532 | namespace oopse {
532        c = torsion->getAtomC()->getGlobalIndex();        
533        d = torsion->getAtomD()->getGlobalIndex();        
534  
535 +      std::set<int> rigidSetA = getRigidSet(a, atomGroups);
536 +      std::set<int> rigidSetB = getRigidSet(b, atomGroups);
537 +      std::set<int> rigidSetC = getRigidSet(c, atomGroups);
538 +      std::set<int> rigidSetD = getRigidSet(d, atomGroups);
539 +
540 +      exclude_.removePairs(rigidSetA, rigidSetB);
541 +      exclude_.removePairs(rigidSetA, rigidSetC);
542 +      exclude_.removePairs(rigidSetA, rigidSetD);
543 +      exclude_.removePairs(rigidSetB, rigidSetC);
544 +      exclude_.removePairs(rigidSetB, rigidSetD);
545 +      exclude_.removePairs(rigidSetC, rigidSetD);
546 +
547 +      /*
548 +      exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
549 +      exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
550 +      exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
551 +      exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
552 +      exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
553 +      exclude_.removePairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
554 +
555 +      
556        exclude_.removePair(a, b);
557        exclude_.removePair(a, c);
558        exclude_.removePair(a, d);
559        exclude_.removePair(b, c);
560        exclude_.removePair(b, d);
561        exclude_.removePair(c, d);        
562 +      */
563      }
564  
433 –    Molecule::RigidBodyIterator rbIter;
434 –    RigidBody* rb;
565      for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
566        std::vector<Atom*> atoms = rb->getAtoms();
567        for (int i = 0; i < atoms.size() -1 ; ++i) {
# Line 471 | Line 601 | namespace oopse {
601      int isError = 0;
602      
603      setupElectrostaticSummationMethod( isError );
604 +    setupSwitchingFunction();
605  
606      if(isError){
607        sprintf( painCave.errMsg,
# Line 515 | Line 646 | namespace oopse {
646      int useLennardJones = 0;
647      int useElectrostatic = 0;
648      int useEAM = 0;
649 +    int useSC = 0;
650      int useCharge = 0;
651      int useDirectional = 0;
652      int useDipole = 0;
# Line 528 | Line 660 | namespace oopse {
660      //usePBC and useRF are from simParams
661      int usePBC = simParams_->getUsePeriodicBoundaryConditions();
662      int useRF;
663 <    int useDW;
663 >    int useSF;
664      std::string myMethod;
665  
666      // set the useRF logical
667      useRF = 0;
668 <    useDW = 0;
668 >    useSF = 0;
669  
670  
671      if (simParams_->haveElectrostaticSummationMethod()) {
# Line 542 | Line 674 | namespace oopse {
674        if (myMethod == "REACTION_FIELD") {
675          useRF=1;
676        } else {
677 <        if (myMethod == "DAMPED_WOLF") {
678 <          useDW = 1;
677 >        if (myMethod == "SHIFTED_FORCE") {
678 >          useSF = 1;
679          }
680        }
681      }
# Line 553 | Line 685 | namespace oopse {
685        useLennardJones |= (*i)->isLennardJones();
686        useElectrostatic |= (*i)->isElectrostatic();
687        useEAM |= (*i)->isEAM();
688 +      useSC |= (*i)->isSC();
689        useCharge |= (*i)->isCharge();
690        useDirectional |= (*i)->isDirectional();
691        useDipole |= (*i)->isDipole();
# Line 603 | Line 736 | namespace oopse {
736      temp = useEAM;
737      MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
738  
739 +    temp = useSC;
740 +    MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
741 +    
742      temp = useShape;
743      MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);  
744  
# Line 612 | Line 748 | namespace oopse {
748      temp = useRF;
749      MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
750  
751 <    temp = useDW;
752 <    MPI_Allreduce(&temp, &useDW, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
751 >    temp = useSF;
752 >    MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
753  
754   #endif
755  
# Line 627 | Line 763 | namespace oopse {
763      fInfo_.SIM_uses_StickyPower = useStickyPower;
764      fInfo_.SIM_uses_GayBerne = useGayBerne;
765      fInfo_.SIM_uses_EAM = useEAM;
766 +    fInfo_.SIM_uses_SC = useSC;
767      fInfo_.SIM_uses_Shapes = useShape;
768      fInfo_.SIM_uses_FLARB = useFLARB;
769      fInfo_.SIM_uses_RF = useRF;
770 <    fInfo_.SIM_uses_DampedWolf = useDW;
770 >    fInfo_.SIM_uses_SF = useSF;
771  
772      if( myMethod == "REACTION_FIELD") {
773        
# Line 792 | Line 929 | namespace oopse {
929  
930   #endif
931  
932 <  double SimInfo::calcMaxCutoffRadius() {
932 >  void SimInfo::setupCutoff() {          
933 >    
934 >    ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
935  
936 +    // Check the cutoff policy
937 +    int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
938  
939 <    std::set<AtomType*> atomTypes;
940 <    std::set<AtomType*>::iterator i;
941 <    std::vector<double> cutoffRadius;
942 <
943 <    //get the unique atom types
803 <    atomTypes = getUniqueAtomTypes();
804 <
805 <    //query the max cutoff radius among these atom types
806 <    for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
807 <      cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
939 >    std::string myPolicy;
940 >    if (forceFieldOptions_.haveCutoffPolicy()){
941 >      myPolicy = forceFieldOptions_.getCutoffPolicy();
942 >    }else if (simParams_->haveCutoffPolicy()) {
943 >      myPolicy = simParams_->getCutoffPolicy();
944      }
945  
946 <    double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
811 < #ifdef IS_MPI
812 <    //pick the max cutoff radius among the processors
813 < #endif
814 <
815 <    return maxCutoffRadius;
816 <  }
817 <
818 <  void SimInfo::getCutoff(double& rcut, double& rsw) {
819 <    
820 <    if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
821 <        
822 <      if (!simParams_->haveCutoffRadius()){
823 <        sprintf(painCave.errMsg,
824 <                "SimCreator Warning: No value was set for the cutoffRadius.\n"
825 <                "\tOOPSE will use a default value of 15.0 angstroms"
826 <                "\tfor the cutoffRadius.\n");
827 <        painCave.isFatal = 0;
828 <        simError();
829 <        rcut = 15.0;
830 <      } else{
831 <        rcut = simParams_->getCutoffRadius();
832 <      }
833 <
834 <      if (!simParams_->haveSwitchingRadius()){
835 <        sprintf(painCave.errMsg,
836 <                "SimCreator Warning: No value was set for switchingRadius.\n"
837 <                "\tOOPSE will use a default value of\n"
838 <                "\t0.85 * cutoffRadius for the switchingRadius\n");
839 <        painCave.isFatal = 0;
840 <        simError();
841 <        rsw = 0.85 * rcut;
842 <      } else{
843 <        rsw = simParams_->getSwitchingRadius();
844 <      }
845 <
846 <    } else {
847 <      // if charge, dipole or reaction field is not used and the cutofff radius is not specified in
848 <      //meta-data file, the maximum cutoff radius calculated from forcefiled will be used
849 <        
850 <      if (simParams_->haveCutoffRadius()) {
851 <        rcut = simParams_->getCutoffRadius();
852 <      } else {
853 <        //set cutoff radius to the maximum cutoff radius based on atom types in the whole system
854 <        rcut = calcMaxCutoffRadius();
855 <      }
856 <
857 <      if (simParams_->haveSwitchingRadius()) {
858 <        rsw  = simParams_->getSwitchingRadius();
859 <      } else {
860 <        rsw = rcut;
861 <      }
862 <    
863 <    }
864 <  }
865 <
866 <  void SimInfo::setupCutoff() {    
867 <    getCutoff(rcut_, rsw_);    
868 <    double rnblist = rcut_ + 1; // skin of neighbor list
869 <
870 <    //Pass these cutoff radius etc. to fortran. This function should be called once and only once
871 <    
872 <    int cp =  TRADITIONAL_CUTOFF_POLICY;
873 <    if (simParams_->haveCutoffPolicy()) {
874 <      std::string myPolicy = simParams_->getCutoffPolicy();
946 >    if (!myPolicy.empty()){
947        toUpper(myPolicy);
948        if (myPolicy == "MIX") {
949          cp = MIX_CUTOFF_POLICY;
# Line 890 | Line 962 | namespace oopse {
962            }    
963          }          
964        }
965 <    }
965 >    }          
966 >    notifyFortranCutoffPolicy(&cp);
967  
968 <
968 >    // Check the Skin Thickness for neighborlists
969 >    double skin;
970      if (simParams_->haveSkinThickness()) {
971 <      double skinThickness = simParams_->getSkinThickness();
972 <    }
971 >      skin = simParams_->getSkinThickness();
972 >      notifyFortranSkinThickness(&skin);
973 >    }            
974 >        
975 >    // Check if the cutoff was set explicitly:
976 >    if (simParams_->haveCutoffRadius()) {
977 >      rcut_ = simParams_->getCutoffRadius();
978 >      if (simParams_->haveSwitchingRadius()) {
979 >        rsw_  = simParams_->getSwitchingRadius();
980 >      } else {
981 >        if (fInfo_.SIM_uses_Charges |
982 >            fInfo_.SIM_uses_Dipoles |
983 >            fInfo_.SIM_uses_RF) {
984 >          
985 >          rsw_ = 0.85 * rcut_;
986 >          sprintf(painCave.errMsg,
987 >                  "SimCreator Warning: No value was set for the switchingRadius.\n"
988 >                  "\tOOPSE will use a default value of 85 percent of the cutoffRadius.\n"
989 >                  "\tswitchingRadius = %f. for this simulation\n", rsw_);
990 >        painCave.isFatal = 0;
991 >        simError();
992 >        } else {
993 >          rsw_ = rcut_;
994 >          sprintf(painCave.errMsg,
995 >                  "SimCreator Warning: No value was set for the switchingRadius.\n"
996 >                  "\tOOPSE will use the same value as the cutoffRadius.\n"
997 >                  "\tswitchingRadius = %f. for this simulation\n", rsw_);
998 >          painCave.isFatal = 0;
999 >          simError();
1000 >        }
1001 >      }
1002 >      
1003 >      notifyFortranCutoffs(&rcut_, &rsw_);
1004 >      
1005 >    } else {
1006 >      
1007 >      // For electrostatic atoms, we'll assume a large safe value:
1008 >      if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
1009 >        sprintf(painCave.errMsg,
1010 >                "SimCreator Warning: No value was set for the cutoffRadius.\n"
1011 >                "\tOOPSE will use a default value of 15.0 angstroms"
1012 >                "\tfor the cutoffRadius.\n");
1013 >        painCave.isFatal = 0;
1014 >        simError();
1015 >        rcut_ = 15.0;
1016 >      
1017 >        if (simParams_->haveElectrostaticSummationMethod()) {
1018 >          std::string myMethod = simParams_->getElectrostaticSummationMethod();
1019 >          toUpper(myMethod);
1020 >          if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1021 >            if (simParams_->haveSwitchingRadius()){
1022 >              sprintf(painCave.errMsg,
1023 >                      "SimInfo Warning: A value was set for the switchingRadius\n"
1024 >                      "\teven though the electrostaticSummationMethod was\n"
1025 >                      "\tset to %s\n", myMethod.c_str());
1026 >              painCave.isFatal = 1;
1027 >              simError();            
1028 >            }
1029 >          }
1030 >        }
1031 >      
1032 >        if (simParams_->haveSwitchingRadius()){
1033 >          rsw_ = simParams_->getSwitchingRadius();
1034 >        } else {        
1035 >          sprintf(painCave.errMsg,
1036 >                  "SimCreator Warning: No value was set for switchingRadius.\n"
1037 >                  "\tOOPSE will use a default value of\n"
1038 >                  "\t0.85 * cutoffRadius for the switchingRadius\n");
1039 >          painCave.isFatal = 0;
1040 >          simError();
1041 >          rsw_ = 0.85 * rcut_;
1042 >        }
1043 >        notifyFortranCutoffs(&rcut_, &rsw_);
1044 >      } else {
1045 >        // We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1046 >        // We'll punt and let fortran figure out the cutoffs later.
1047 >        
1048 >        notifyFortranYouAreOnYourOwn();
1049  
1050 <    notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp);
1051 <    // also send cutoff notification to electrostatics
902 <    setElectrostaticCutoffRadius(&rcut_, &rsw_);
1050 >      }
1051 >    }
1052    }
1053  
1054    void SimInfo::setupElectrostaticSummationMethod( int isError ) {    
1055      
1056      int errorOut;
1057      int esm =  NONE;
1058 +    int sm = UNDAMPED;
1059      double alphaVal;
1060      double dielectric;
1061  
# Line 919 | Line 1069 | namespace oopse {
1069        if (myMethod == "NONE") {
1070          esm = NONE;
1071        } else {
1072 <        if (myMethod == "UNDAMPED_WOLF") {
1073 <          esm = UNDAMPED_WOLF;
1072 >        if (myMethod == "SWITCHING_FUNCTION") {
1073 >          esm = SWITCHING_FUNCTION;
1074          } else {
1075 <          if (myMethod == "DAMPED_WOLF") {            
1076 <            esm = DAMPED_WOLF;
1077 <            if (!simParams_->haveDampingAlpha()) {
1078 <              //throw error
1079 <              sprintf( painCave.errMsg,
930 <                       "SimInfo warning: dampingAlpha was not specified in the input file. A default value of %f (1/ang) will be used for the Damped Wolf Method.", alphaVal);
931 <              painCave.isFatal = 0;
932 <              simError();
933 <            }
934 <          } else {
935 <            if (myMethod == "REACTION_FIELD") {      
936 <              esm = REACTION_FIELD;
1075 >          if (myMethod == "SHIFTED_POTENTIAL") {
1076 >            esm = SHIFTED_POTENTIAL;
1077 >          } else {
1078 >            if (myMethod == "SHIFTED_FORCE") {            
1079 >              esm = SHIFTED_FORCE;
1080              } else {
1081 <              // throw error        
1082 <              sprintf( painCave.errMsg,
1083 <                       "SimInfo error: Unknown electrostaticSummationMethod. (Input file specified %s .)\n\telectrostaticSummationMethod must be one of: \"none\", \"undamped_wolf\", \"damped_wolf\", or \"reaction_field\".", myMethod.c_str() );
1084 <              painCave.isFatal = 1;
1085 <              simError();
1086 <            }    
1087 <          }          
1081 >              if (myMethod == "REACTION_FIELD") {            
1082 >                esm = REACTION_FIELD;
1083 >              } else {
1084 >                // throw error        
1085 >                sprintf( painCave.errMsg,
1086 >                         "SimInfo error: Unknown electrostaticSummationMethod.\n"
1087 >                         "\t(Input file specified %s .)\n"
1088 >                         "\telectrostaticSummationMethod must be one of: \"none\",\n"
1089 >                         "\t\"shifted_potential\", \"shifted_force\", or \n"
1090 >                         "\t\"reaction_field\".\n", myMethod.c_str() );
1091 >                painCave.isFatal = 1;
1092 >                simError();
1093 >              }    
1094 >            }          
1095 >          }
1096 >        }
1097 >      }
1098 >    }
1099 >    
1100 >    if (simParams_->haveElectrostaticScreeningMethod()) {
1101 >      std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1102 >      toUpper(myScreen);
1103 >      if (myScreen == "UNDAMPED") {
1104 >        sm = UNDAMPED;
1105 >      } else {
1106 >        if (myScreen == "DAMPED") {
1107 >          sm = DAMPED;
1108 >          if (!simParams_->haveDampingAlpha()) {
1109 >            //throw error
1110 >            sprintf( painCave.errMsg,
1111 >                     "SimInfo warning: dampingAlpha was not specified in the input file.\n"
1112 >                     "\tA default value of %f (1/ang) will be used.\n", alphaVal);
1113 >            painCave.isFatal = 0;
1114 >            simError();
1115 >          }
1116 >        } else {
1117 >          // throw error        
1118 >          sprintf( painCave.errMsg,
1119 >                   "SimInfo error: Unknown electrostaticScreeningMethod.\n"
1120 >                   "\t(Input file specified %s .)\n"
1121 >                   "\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1122 >                   "or \"damped\".\n", myScreen.c_str() );
1123 >          painCave.isFatal = 1;
1124 >          simError();
1125          }
1126        }
1127      }
1128 +    
1129      // let's pass some summation method variables to fortran
1130      setElectrostaticSummationMethod( &esm );
1131 <    setDampedWolfAlpha( &alphaVal );
1131 >    setFortranElectrostaticMethod( &esm );
1132 >    setScreeningMethod( &sm );
1133 >    setDampingAlpha( &alphaVal );
1134      setReactionFieldDielectric( &dielectric );
1135 <    initFortranFF( &esm, &errorOut );
1135 >    initFortranFF( &errorOut );
1136 >  }
1137 >
1138 >  void SimInfo::setupSwitchingFunction() {    
1139 >    int ft = CUBIC;
1140 >
1141 >    if (simParams_->haveSwitchingFunctionType()) {
1142 >      std::string funcType = simParams_->getSwitchingFunctionType();
1143 >      toUpper(funcType);
1144 >      if (funcType == "CUBIC") {
1145 >        ft = CUBIC;
1146 >      } else {
1147 >        if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1148 >          ft = FIFTH_ORDER_POLY;
1149 >        } else {
1150 >          // throw error        
1151 >          sprintf( painCave.errMsg,
1152 >                   "SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1153 >          painCave.isFatal = 1;
1154 >          simError();
1155 >        }          
1156 >      }
1157 >    }
1158 >
1159 >    // send switching function notification to switcheroo
1160 >    setFunctionType(&ft);
1161 >
1162    }
1163  
1164    void SimInfo::addProperty(GenericData* genData) {

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines