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root/OpenMD/branches/development/src/brains/SimInfo.cpp
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Comparing branches/development/src/brains/SimInfo.cpp (file contents):
Revision 1505 by gezelter, Sun Oct 3 22:18:59 2010 UTC vs.
Revision 1530 by gezelter, Tue Dec 28 21:47:55 2010 UTC

# Line 55 | Line 55
55   #include "primitives/Molecule.hpp"
56   #include "primitives/StuntDouble.hpp"
57   #include "UseTheForce/fCutoffPolicy.h"
58 – #include "UseTheForce/DarkSide/fSwitchingFunctionType.h"
58   #include "UseTheForce/doForces_interface.h"
59   #include "UseTheForce/DarkSide/neighborLists_interface.h"
61 – #include "UseTheForce/DarkSide/switcheroo_interface.h"
60   #include "utils/MemoryUtils.hpp"
61   #include "utils/simError.h"
62   #include "selection/SelectionManager.hpp"
63   #include "io/ForceFieldOptions.hpp"
64   #include "UseTheForce/ForceField.hpp"
65 + #include "nonbonded/SwitchingFunction.hpp"
66  
67  
68   #ifdef IS_MPI
# Line 71 | Line 70
70   #include "UseTheForce/DarkSide/simParallel_interface.h"
71   #endif
72  
73 + using namespace std;
74   namespace OpenMD {
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 –    return result;
83 –  }
75    
76    SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
77      forceField_(ff), simParams_(simParams),
# Line 90 | Line 81 | namespace OpenMD {
81      nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
82      nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
83      nConstraints_(0), sman_(NULL), fortranInitialized_(false),
84 <    calcBoxDipole_(false), useAtomicVirial_(true) {
85 <
86 <
87 <      MoleculeStamp* molStamp;
88 <      int nMolWithSameStamp;
89 <      int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
90 <      int nGroups = 0;      //total cutoff groups defined in meta-data file
91 <      CutoffGroupStamp* cgStamp;    
92 <      RigidBodyStamp* rbStamp;
93 <      int nRigidAtoms = 0;
94 <
95 <      std::vector<Component*> components = simParams->getComponents();
84 >    calcBoxDipole_(false), useAtomicVirial_(true) {    
85 >    
86 >    MoleculeStamp* molStamp;
87 >    int nMolWithSameStamp;
88 >    int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
89 >    int nGroups = 0;       //total cutoff groups defined in meta-data file
90 >    CutoffGroupStamp* cgStamp;    
91 >    RigidBodyStamp* rbStamp;
92 >    int nRigidAtoms = 0;
93 >    
94 >    vector<Component*> components = simParams->getComponents();
95 >    
96 >    for (vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
97 >      molStamp = (*i)->getMoleculeStamp();
98 >      nMolWithSameStamp = (*i)->getNMol();
99        
100 <      for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
101 <        molStamp = (*i)->getMoleculeStamp();
102 <        nMolWithSameStamp = (*i)->getNMol();
103 <        
104 <        addMoleculeStamp(molStamp, nMolWithSameStamp);
105 <
106 <        //calculate atoms in molecules
107 <        nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;  
108 <
109 <        //calculate atoms in cutoff groups
110 <        int nAtomsInGroups = 0;
111 <        int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
118 <        
119 <        for (int j=0; j < nCutoffGroupsInStamp; j++) {
120 <          cgStamp = molStamp->getCutoffGroupStamp(j);
121 <          nAtomsInGroups += cgStamp->getNMembers();
122 <        }
123 <
124 <        nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
125 <
126 <        nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;            
127 <
128 <        //calculate atoms in rigid bodies
129 <        int nAtomsInRigidBodies = 0;
130 <        int nRigidBodiesInStamp = molStamp->getNRigidBodies();
131 <        
132 <        for (int j=0; j < nRigidBodiesInStamp; j++) {
133 <          rbStamp = molStamp->getRigidBodyStamp(j);
134 <          nAtomsInRigidBodies += rbStamp->getNMembers();
135 <        }
136 <
137 <        nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
138 <        nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;            
139 <        
100 >      addMoleculeStamp(molStamp, nMolWithSameStamp);
101 >      
102 >      //calculate atoms in molecules
103 >      nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;  
104 >      
105 >      //calculate atoms in cutoff groups
106 >      int nAtomsInGroups = 0;
107 >      int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
108 >      
109 >      for (int j=0; j < nCutoffGroupsInStamp; j++) {
110 >        cgStamp = molStamp->getCutoffGroupStamp(j);
111 >        nAtomsInGroups += cgStamp->getNMembers();
112        }
113 <
114 <      //every free atom (atom does not belong to cutoff groups) is a cutoff
115 <      //group therefore the total number of cutoff groups in the system is
116 <      //equal to the total number of atoms minus number of atoms belong to
117 <      //cutoff group defined in meta-data file plus the number of cutoff
118 <      //groups defined in meta-data file
119 <      nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
120 <
121 <      //every free atom (atom does not belong to rigid bodies) is an
122 <      //integrable object therefore the total number of integrable objects
123 <      //in the system is equal to the total number of atoms minus number of
124 <      //atoms belong to rigid body defined in meta-data file plus the number
125 <      //of rigid bodies defined in meta-data file
126 <      nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
127 <                                                + nGlobalRigidBodies_;
128 <  
129 <      nGlobalMols_ = molStampIds_.size();
130 <      molToProcMap_.resize(nGlobalMols_);
131 <    }
132 <
113 >      
114 >      nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
115 >      
116 >      nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;            
117 >      
118 >      //calculate atoms in rigid bodies
119 >      int nAtomsInRigidBodies = 0;
120 >      int nRigidBodiesInStamp = molStamp->getNRigidBodies();
121 >      
122 >      for (int j=0; j < nRigidBodiesInStamp; j++) {
123 >        rbStamp = molStamp->getRigidBodyStamp(j);
124 >        nAtomsInRigidBodies += rbStamp->getNMembers();
125 >      }
126 >      
127 >      nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
128 >      nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;            
129 >      
130 >    }
131 >    
132 >    //every free atom (atom does not belong to cutoff groups) is a cutoff
133 >    //group therefore the total number of cutoff groups in the system is
134 >    //equal to the total number of atoms minus number of atoms belong to
135 >    //cutoff group defined in meta-data file plus the number of cutoff
136 >    //groups defined in meta-data file
137 >    nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
138 >    
139 >    //every free atom (atom does not belong to rigid bodies) is an
140 >    //integrable object therefore the total number of integrable objects
141 >    //in the system is equal to the total number of atoms minus number of
142 >    //atoms belong to rigid body defined in meta-data file plus the number
143 >    //of rigid bodies defined in meta-data file
144 >    nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
145 >      + nGlobalRigidBodies_;
146 >    
147 >    nGlobalMols_ = molStampIds_.size();
148 >    molToProcMap_.resize(nGlobalMols_);
149 >  }
150 >  
151    SimInfo::~SimInfo() {
152 <    std::map<int, Molecule*>::iterator i;
152 >    map<int, Molecule*>::iterator i;
153      for (i = molecules_.begin(); i != molecules_.end(); ++i) {
154        delete i->second;
155      }
# Line 170 | Line 160 | namespace OpenMD {
160      delete forceField_;
161    }
162  
173 –  int SimInfo::getNGlobalConstraints() {
174 –    int nGlobalConstraints;
175 – #ifdef IS_MPI
176 –    MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
177 –                  MPI_COMM_WORLD);    
178 – #else
179 –    nGlobalConstraints =  nConstraints_;
180 – #endif
181 –    return nGlobalConstraints;
182 –  }
163  
164    bool SimInfo::addMolecule(Molecule* mol) {
165      MoleculeIterator i;
166 <
166 >    
167      i = molecules_.find(mol->getGlobalIndex());
168      if (i == molecules_.end() ) {
169 <
170 <      molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
171 <        
169 >      
170 >      molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
171 >      
172        nAtoms_ += mol->getNAtoms();
173        nBonds_ += mol->getNBonds();
174        nBends_ += mol->getNBends();
# Line 198 | Line 178 | namespace OpenMD {
178        nIntegrableObjects_ += mol->getNIntegrableObjects();
179        nCutoffGroups_ += mol->getNCutoffGroups();
180        nConstraints_ += mol->getNConstraintPairs();
181 <
181 >      
182        addInteractionPairs(mol);
183 <  
183 >      
184        return true;
185      } else {
186        return false;
187      }
188    }
189 <
189 >  
190    bool SimInfo::removeMolecule(Molecule* mol) {
191      MoleculeIterator i;
192      i = molecules_.find(mol->getGlobalIndex());
# Line 234 | Line 214 | namespace OpenMD {
214      } else {
215        return false;
216      }
237 –
238 –
217    }    
218  
219          
# Line 253 | Line 231 | namespace OpenMD {
231    void SimInfo::calcNdf() {
232      int ndf_local;
233      MoleculeIterator i;
234 <    std::vector<StuntDouble*>::iterator j;
234 >    vector<StuntDouble*>::iterator j;
235      Molecule* mol;
236      StuntDouble* integrableObject;
237  
# Line 304 | Line 282 | namespace OpenMD {
282      int ndfRaw_local;
283  
284      MoleculeIterator i;
285 <    std::vector<StuntDouble*>::iterator j;
285 >    vector<StuntDouble*>::iterator j;
286      Molecule* mol;
287      StuntDouble* integrableObject;
288  
# Line 353 | Line 331 | namespace OpenMD {
331  
332    void SimInfo::addInteractionPairs(Molecule* mol) {
333      ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
334 <    std::vector<Bond*>::iterator bondIter;
335 <    std::vector<Bend*>::iterator bendIter;
336 <    std::vector<Torsion*>::iterator torsionIter;
337 <    std::vector<Inversion*>::iterator inversionIter;
334 >    vector<Bond*>::iterator bondIter;
335 >    vector<Bend*>::iterator bendIter;
336 >    vector<Torsion*>::iterator torsionIter;
337 >    vector<Inversion*>::iterator inversionIter;
338      Bond* bond;
339      Bend* bend;
340      Torsion* torsion;
# Line 374 | Line 352 | namespace OpenMD {
352      // always be excluded.  These are done at the bottom of this
353      // function.
354  
355 <    std::map<int, std::set<int> > atomGroups;
355 >    map<int, set<int> > atomGroups;
356      Molecule::RigidBodyIterator rbIter;
357      RigidBody* rb;
358      Molecule::IntegrableObjectIterator ii;
# Line 386 | Line 364 | namespace OpenMD {
364        
365        if (integrableObject->isRigidBody()) {
366          rb = static_cast<RigidBody*>(integrableObject);
367 <        std::vector<Atom*> atoms = rb->getAtoms();
368 <        std::set<int> rigidAtoms;
367 >        vector<Atom*> atoms = rb->getAtoms();
368 >        set<int> rigidAtoms;
369          for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
370            rigidAtoms.insert(atoms[i]->getGlobalIndex());
371          }
372          for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
373 <          atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
373 >          atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
374          }      
375        } else {
376 <        std::set<int> oneAtomSet;
376 >        set<int> oneAtomSet;
377          oneAtomSet.insert(integrableObject->getGlobalIndex());
378 <        atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));        
378 >        atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));        
379        }
380      }  
381            
# Line 500 | Line 478 | namespace OpenMD {
478  
479      for (rb = mol->beginRigidBody(rbIter); rb != NULL;
480           rb = mol->nextRigidBody(rbIter)) {
481 <      std::vector<Atom*> atoms = rb->getAtoms();
481 >      vector<Atom*> atoms = rb->getAtoms();
482        for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
483          for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
484            a = atoms[i]->getGlobalIndex();
# Line 514 | Line 492 | namespace OpenMD {
492  
493    void SimInfo::removeInteractionPairs(Molecule* mol) {
494      ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
495 <    std::vector<Bond*>::iterator bondIter;
496 <    std::vector<Bend*>::iterator bendIter;
497 <    std::vector<Torsion*>::iterator torsionIter;
498 <    std::vector<Inversion*>::iterator inversionIter;
495 >    vector<Bond*>::iterator bondIter;
496 >    vector<Bend*>::iterator bendIter;
497 >    vector<Torsion*>::iterator torsionIter;
498 >    vector<Inversion*>::iterator inversionIter;
499      Bond* bond;
500      Bend* bend;
501      Torsion* torsion;
# Line 527 | Line 505 | namespace OpenMD {
505      int c;
506      int d;
507  
508 <    std::map<int, std::set<int> > atomGroups;
508 >    map<int, set<int> > atomGroups;
509      Molecule::RigidBodyIterator rbIter;
510      RigidBody* rb;
511      Molecule::IntegrableObjectIterator ii;
# Line 539 | Line 517 | namespace OpenMD {
517        
518        if (integrableObject->isRigidBody()) {
519          rb = static_cast<RigidBody*>(integrableObject);
520 <        std::vector<Atom*> atoms = rb->getAtoms();
521 <        std::set<int> rigidAtoms;
520 >        vector<Atom*> atoms = rb->getAtoms();
521 >        set<int> rigidAtoms;
522          for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
523            rigidAtoms.insert(atoms[i]->getGlobalIndex());
524          }
525          for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
526 <          atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
526 >          atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
527          }      
528        } else {
529 <        std::set<int> oneAtomSet;
529 >        set<int> oneAtomSet;
530          oneAtomSet.insert(integrableObject->getGlobalIndex());
531 <        atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));        
531 >        atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));        
532        }
533      }  
534  
# Line 653 | Line 631 | namespace OpenMD {
631  
632      for (rb = mol->beginRigidBody(rbIter); rb != NULL;
633           rb = mol->nextRigidBody(rbIter)) {
634 <      std::vector<Atom*> atoms = rb->getAtoms();
634 >      vector<Atom*> atoms = rb->getAtoms();
635        for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
636          for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
637            a = atoms[i]->getGlobalIndex();
# Line 676 | Line 654 | namespace OpenMD {
654      molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
655    }
656  
679 –  void SimInfo::update() {
657  
658 <    setupSimType();
658 >  /**
659 >   * update
660 >   *
661 >   *  Performs the global checks and variable settings after the objects have been
662 >   *  created.
663 >   *
664 >   */
665 >  void SimInfo::update() {
666 >    
667 >    setupSimVariables();
668 >    setupCutoffs();
669 >    setupSwitching();
670 >    setupElectrostatics();
671 >    setupNeighborlists();
672  
673   #ifdef IS_MPI
674      setupFortranParallel();
675   #endif
686 –
676      setupFortranSim();
677 +    fortranInitialized_ = true;
678  
689 –    //setup fortran force field
690 –    /** @deprecate */    
691 –    int isError = 0;
692 –    
693 –    setupCutoff();
694 –    
695 –    setupElectrostaticSummationMethod( isError );
696 –    setupSwitchingFunction();
697 –    setupAccumulateBoxDipole();
698 –
699 –    if(isError){
700 –      sprintf( painCave.errMsg,
701 –               "ForceField error: There was an error initializing the forceField in fortran.\n" );
702 –      painCave.isFatal = 1;
703 –      simError();
704 –    }
705 –
679      calcNdf();
680      calcNdfRaw();
681      calcNdfTrans();
709 –
710 –    fortranInitialized_ = true;
682    }
683 <
684 <  std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
683 >  
684 >  set<AtomType*> SimInfo::getSimulatedAtomTypes() {
685      SimInfo::MoleculeIterator mi;
686      Molecule* mol;
687      Molecule::AtomIterator ai;
688      Atom* atom;
689 <    std::set<AtomType*> atomTypes;
690 <
691 <    for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
721 <
689 >    set<AtomType*> atomTypes;
690 >    
691 >    for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {      
692        for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
693          atomTypes.insert(atom->getAtomType());
694 <      }
695 <        
726 <    }
727 <
694 >      }      
695 >    }    
696      return atomTypes;        
697    }
698  
699 <  void SimInfo::setupSimType() {
700 <    std::set<AtomType*>::iterator i;
701 <    std::set<AtomType*> atomTypes;
702 <    atomTypes = getUniqueAtomTypes();
699 >  /**
700 >   * setupCutoffs
701 >   *
702 >   * Sets the values of cutoffRadius and cutoffMethod
703 >   *
704 >   * cutoffRadius : realType
705 >   *  If the cutoffRadius was explicitly set, use that value.
706 >   *  If the cutoffRadius was not explicitly set:
707 >   *      Are there electrostatic atoms?  Use 12.0 Angstroms.
708 >   *      No electrostatic atoms?  Poll the atom types present in the
709 >   *      simulation for suggested cutoff values (e.g. 2.5 * sigma).
710 >   *      Use the maximum suggested value that was found.
711 >   *
712 >   * cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE, SHIFTED_POTENTIAL)
713 >   *      If cutoffMethod was explicitly set, use that choice.
714 >   *      If cutoffMethod was not explicitly set, use SHIFTED_FORCE
715 >   */
716 >  void SimInfo::setupCutoffs() {
717      
718 <    int useLennardJones = 0;
719 <    int useElectrostatic = 0;
720 <    int useEAM = 0;
721 <    int useSC = 0;
722 <    int useCharge = 0;
723 <    int useDirectional = 0;
724 <    int useDipole = 0;
725 <    int useGayBerne = 0;
726 <    int useSticky = 0;
727 <    int useStickyPower = 0;
728 <    int useShape = 0;
729 <    int useFLARB = 0; //it is not in AtomType yet
730 <    int useDirectionalAtom = 0;    
731 <    int useElectrostatics = 0;
732 <    //usePBC and useRF are from simParams
733 <    int usePBC = simParams_->getUsePeriodicBoundaryConditions();
734 <    int useRF;
735 <    int useSF;
736 <    int useSP;
737 <    int useBoxDipole;
718 >    if (simParams_->haveCutoffRadius()) {
719 >      cutoffRadius_ = simParams_->getCutoffRadius();
720 >    } else {      
721 >      if (usesElectrostaticAtoms_) {
722 >        sprintf(painCave.errMsg,
723 >                "SimInfo: No value was set for the cutoffRadius.\n"
724 >                "\tOpenMD will use a default value of 12.0 angstroms"
725 >                "\tfor the cutoffRadius.\n");
726 >        painCave.isFatal = 0;
727 >        painCave.severity = OPENMD_INFO;
728 >        simError();
729 >        cutoffRadius_ = 12.0;
730 >      } else {
731 >        RealType thisCut;
732 >        set<AtomType*>::iterator i;
733 >        set<AtomType*> atomTypes;
734 >        atomTypes = getSimulatedAtomTypes();        
735 >        for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
736 >          thisCut = InteractionManager::Instance()->getSuggestedCutoffRadius((*i));
737 >          cutoffRadius_ = max(thisCut, cutoffRadius_);
738 >        }
739 >        sprintf(painCave.errMsg,
740 >                "SimInfo: No value was set for the cutoffRadius.\n"
741 >                "\tOpenMD will use %lf angstroms.\n",
742 >                cutoffRadius_);
743 >        painCave.isFatal = 0;
744 >        painCave.severity = OPENMD_INFO;
745 >        simError();
746 >      }            
747 >    }
748  
749 <    std::string myMethod;
749 >    InteractionManager::Instance()->setCutoffRadius(cutoffRadius_);
750  
751 <    // set the useRF logical
752 <    useRF = 0;
753 <    useSF = 0;
754 <    useSP = 0;
755 <    useBoxDipole = 0;
756 <
757 <    if (simParams_->haveElectrostaticSummationMethod()) {
758 <      std::string myMethod = simParams_->getElectrostaticSummationMethod();
759 <      toUpper(myMethod);
760 <      if (myMethod == "REACTION_FIELD"){
761 <        useRF = 1;
762 <      } else if (myMethod == "SHIFTED_FORCE"){
763 <        useSF = 1;
764 <      } else if (myMethod == "SHIFTED_POTENTIAL"){
765 <        useSP = 1;
751 >    map<string, CutoffMethod> stringToCutoffMethod;
752 >    stringToCutoffMethod["HARD"] = HARD;
753 >    stringToCutoffMethod["SWITCHING_FUNCTION"] = SWITCHING_FUNCTION;
754 >    stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;    
755 >    stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
756 >  
757 >    if (simParams_->haveCutoffMethod()) {
758 >      string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
759 >      map<string, CutoffMethod>::iterator i;
760 >      i = stringToCutoffMethod.find(cutMeth);
761 >      if (i == stringToCutoffMethod.end()) {
762 >        sprintf(painCave.errMsg,
763 >                "SimInfo: Could not find chosen cutoffMethod %s\n"
764 >                "\tShould be one of: "
765 >                "HARD, SWITCHING_FUNCTION, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n",
766 >                cutMeth.c_str());
767 >        painCave.isFatal = 1;
768 >        painCave.severity = OPENMD_ERROR;
769 >        simError();
770 >      } else {
771 >        cutoffMethod_ = i->second;
772        }
773 +    } else {
774 +      sprintf(painCave.errMsg,
775 +              "SimInfo: No value was set for the cutoffMethod.\n"
776 +              "\tOpenMD will use SHIFTED_FORCE.\n");
777 +        painCave.isFatal = 0;
778 +        painCave.severity = OPENMD_INFO;
779 +        simError();
780 +        cutoffMethod_ = SHIFTED_FORCE;        
781      }
782 +
783 +    InteractionManager::Instance()->setCutoffMethod(cutoffMethod_);
784 +  }
785 +  
786 +  /**
787 +   * setupSwitching
788 +   *
789 +   * Sets the values of switchingRadius and
790 +   *  If the switchingRadius was explicitly set, use that value (but check it)
791 +   *  If the switchingRadius was not explicitly set: use 0.85 * cutoffRadius_
792 +   */
793 +  void SimInfo::setupSwitching() {
794      
795 <    if (simParams_->haveAccumulateBoxDipole())
796 <      if (simParams_->getAccumulateBoxDipole())
797 <        useBoxDipole = 1;
795 >    if (simParams_->haveSwitchingRadius()) {
796 >      switchingRadius_ = simParams_->getSwitchingRadius();
797 >      if (switchingRadius_ > cutoffRadius_) {        
798 >        sprintf(painCave.errMsg,
799 >                "SimInfo: switchingRadius (%f) is larger than cutoffRadius(%f)\n",
800 >                switchingRadius_, cutoffRadius_);
801 >        painCave.isFatal = 1;
802 >        painCave.severity = OPENMD_ERROR;
803 >        simError();
804 >      }
805 >    } else {      
806 >      switchingRadius_ = 0.85 * cutoffRadius_;
807 >      sprintf(painCave.errMsg,
808 >              "SimInfo: No value was set for the switchingRadius.\n"
809 >              "\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
810 >              "\tswitchingRadius = %f. for this simulation\n", switchingRadius_);
811 >      painCave.isFatal = 0;
812 >      painCave.severity = OPENMD_WARNING;
813 >      simError();
814 >    }          
815 >  
816 >    InteractionManager::Instance()->setSwitchingRadius(switchingRadius_);
817  
818 +    SwitchingFunctionType ft;
819 +    
820 +    if (simParams_->haveSwitchingFunctionType()) {
821 +      string funcType = simParams_->getSwitchingFunctionType();
822 +      toUpper(funcType);
823 +      if (funcType == "CUBIC") {
824 +        ft = cubic;
825 +      } else {
826 +        if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
827 +          ft = fifth_order_poly;
828 +        } else {
829 +          // throw error        
830 +          sprintf( painCave.errMsg,
831 +                   "SimInfo : Unknown switchingFunctionType. (Input file specified %s .)\n"
832 +                   "\tswitchingFunctionType must be one of: "
833 +                   "\"cubic\" or \"fifth_order_polynomial\".",
834 +                   funcType.c_str() );
835 +          painCave.isFatal = 1;
836 +          painCave.severity = OPENMD_ERROR;
837 +          simError();
838 +        }          
839 +      }
840 +    }
841 +
842 +    InteractionManager::Instance()->setSwitchingFunctionType(ft);
843 +  }
844 +
845 +  /**
846 +   * setupSkinThickness
847 +   *
848 +   *  If the skinThickness was explicitly set, use that value (but check it)
849 +   *  If the skinThickness was not explicitly set: use 1.0 angstroms
850 +   */
851 +  void SimInfo::setupSkinThickness() {    
852 +    if (simParams_->haveSkinThickness()) {
853 +      skinThickness_ = simParams_->getSkinThickness();
854 +    } else {      
855 +      skinThickness_ = 1.0;
856 +      sprintf(painCave.errMsg,
857 +              "SimInfo Warning: No value was set for the skinThickness.\n"
858 +              "\tOpenMD will use a default value of %f Angstroms\n"
859 +              "\tfor this simulation\n", skinThickness_);
860 +      painCave.isFatal = 0;
861 +      simError();
862 +    }            
863 +  }
864 +
865 +  void SimInfo::setupSimType() {
866 +    set<AtomType*>::iterator i;
867 +    set<AtomType*> atomTypes;
868 +    atomTypes = getSimulatedAtomTypes();
869 +
870      useAtomicVirial_ = simParams_->getUseAtomicVirial();
871  
872 +    int usesElectrostatic = 0;
873 +    int usesMetallic = 0;
874 +    int usesDirectional = 0;
875      //loop over all of the atom types
876      for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
877 <      useLennardJones |= (*i)->isLennardJones();
878 <      useElectrostatic |= (*i)->isElectrostatic();
879 <      useEAM |= (*i)->isEAM();
788 <      useSC |= (*i)->isSC();
789 <      useCharge |= (*i)->isCharge();
790 <      useDirectional |= (*i)->isDirectional();
791 <      useDipole |= (*i)->isDipole();
792 <      useGayBerne |= (*i)->isGayBerne();
793 <      useSticky |= (*i)->isSticky();
794 <      useStickyPower |= (*i)->isStickyPower();
795 <      useShape |= (*i)->isShape();
877 >      usesElectrostatic |= (*i)->isElectrostatic();
878 >      usesMetallic |= (*i)->isMetal();
879 >      usesDirectional |= (*i)->isDirectional();
880      }
881  
798 –    if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
799 –      useDirectionalAtom = 1;
800 –    }
801 –
802 –    if (useCharge || useDipole) {
803 –      useElectrostatics = 1;
804 –    }
805 –
882   #ifdef IS_MPI    
883      int temp;
884 +    temp = usesDirectional;
885 +    MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
886  
887 <    temp = usePBC;
888 <    MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
887 >    temp = usesMetallic;
888 >    MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
889  
890 <    temp = useDirectionalAtom;
891 <    MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
814 <
815 <    temp = useLennardJones;
816 <    MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
817 <
818 <    temp = useElectrostatics;
819 <    MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
820 <
821 <    temp = useCharge;
822 <    MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
823 <
824 <    temp = useDipole;
825 <    MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
826 <
827 <    temp = useSticky;
828 <    MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
829 <
830 <    temp = useStickyPower;
831 <    MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
832 <    
833 <    temp = useGayBerne;
834 <    MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
835 <
836 <    temp = useEAM;
837 <    MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
838 <
839 <    temp = useSC;
840 <    MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
841 <    
842 <    temp = useShape;
843 <    MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);  
844 <
845 <    temp = useFLARB;
846 <    MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
847 <
848 <    temp = useRF;
849 <    MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
850 <
851 <    temp = useSF;
852 <    MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);  
853 <
854 <    temp = useSP;
855 <    MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
856 <
857 <    temp = useBoxDipole;
858 <    MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
859 <
860 <    temp = useAtomicVirial_;
861 <    MPI_Allreduce(&temp, &useAtomicVirial_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
862 <
890 >    temp = usesElectrostatic;
891 >    MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
892   #endif
893 <    fInfo_.SIM_uses_PBC = usePBC;    
894 <    fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
895 <    fInfo_.SIM_uses_LennardJones = useLennardJones;
896 <    fInfo_.SIM_uses_Electrostatics = useElectrostatics;    
897 <    fInfo_.SIM_uses_Charges = useCharge;
898 <    fInfo_.SIM_uses_Dipoles = useDipole;
870 <    fInfo_.SIM_uses_Sticky = useSticky;
871 <    fInfo_.SIM_uses_StickyPower = useStickyPower;
872 <    fInfo_.SIM_uses_GayBerne = useGayBerne;
873 <    fInfo_.SIM_uses_EAM = useEAM;
874 <    fInfo_.SIM_uses_SC = useSC;
875 <    fInfo_.SIM_uses_Shapes = useShape;
876 <    fInfo_.SIM_uses_FLARB = useFLARB;
877 <    fInfo_.SIM_uses_RF = useRF;
878 <    fInfo_.SIM_uses_SF = useSF;
879 <    fInfo_.SIM_uses_SP = useSP;
880 <    fInfo_.SIM_uses_BoxDipole = useBoxDipole;
881 <    fInfo_.SIM_uses_AtomicVirial = useAtomicVirial_;
893 >    fInfo_.SIM_uses_PBC = usesPeriodicBoundaries_;    
894 >    fInfo_.SIM_uses_DirectionalAtoms = usesDirectionalAtoms_;
895 >    fInfo_.SIM_uses_MetallicAtoms = usesMetallicAtoms_;
896 >    fInfo_.SIM_requires_SkipCorrection = usesElectrostaticAtoms_;
897 >    fInfo_.SIM_requires_SelfCorrection = usesElectrostaticAtoms_;
898 >    fInfo_.SIM_uses_AtomicVirial = usesAtomicVirial_;
899    }
900  
901    void SimInfo::setupFortranSim() {
902      int isError;
903      int nExclude, nOneTwo, nOneThree, nOneFour;
904 <    std::vector<int> fortranGlobalGroupMembership;
904 >    vector<int> fortranGlobalGroupMembership;
905      
906 +    notifyFortranSkinThickness(&skinThickness_);
907 +
908 +    int ljsp = cutoffMethod_ == SHIFTED_POTENTIAL ? 1 : 0;
909 +    int ljsf = cutoffMethod_ == SHIFTED_FORCE ? 1 : 0;
910 +    notifyFortranCutoffs(&cutoffRadius_, &switchingRadius_, &ljsp, &ljsf);
911 +
912      isError = 0;
913  
914      //globalGroupMembership_ is filled by SimCreator    
# Line 894 | Line 917 | namespace OpenMD {
917      }
918  
919      //calculate mass ratio of cutoff group
920 <    std::vector<RealType> mfact;
920 >    vector<RealType> mfact;
921      SimInfo::MoleculeIterator mi;
922      Molecule* mol;
923      Molecule::CutoffGroupIterator ci;
# Line 921 | Line 944 | namespace OpenMD {
944      }
945  
946      //fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
947 <    std::vector<int> identArray;
947 >    vector<int> identArray;
948  
949      //to avoid memory reallocation, reserve enough space identArray
950      identArray.reserve(getNAtoms());
# Line 934 | Line 957 | namespace OpenMD {
957  
958      //fill molMembershipArray
959      //molMembershipArray is filled by SimCreator    
960 <    std::vector<int> molMembershipArray(nGlobalAtoms_);
960 >    vector<int> molMembershipArray(nGlobalAtoms_);
961      for (int i = 0; i < nGlobalAtoms_; i++) {
962        molMembershipArray[i] = globalMolMembership_[i] + 1;
963      }
# Line 987 | Line 1010 | namespace OpenMD {
1010    void SimInfo::setupFortranParallel() {
1011   #ifdef IS_MPI    
1012      //SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
1013 <    std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
1014 <    std::vector<int> localToGlobalCutoffGroupIndex;
1013 >    vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
1014 >    vector<int> localToGlobalCutoffGroupIndex;
1015      SimInfo::MoleculeIterator mi;
1016      Molecule::AtomIterator ai;
1017      Molecule::CutoffGroupIterator ci;
# Line 1038 | Line 1061 | namespace OpenMD {
1061      errorCheckPoint();
1062  
1063   #endif
1041 –  }
1042 –
1043 –  void SimInfo::setupCutoff() {          
1044 –    
1045 –    ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
1046 –
1047 –    // Check the cutoff policy
1048 –    int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
1049 –
1050 –    // Set LJ shifting bools to false
1051 –    ljsp_ = 0;
1052 –    ljsf_ = 0;
1053 –
1054 –    std::string myPolicy;
1055 –    if (forceFieldOptions_.haveCutoffPolicy()){
1056 –      myPolicy = forceFieldOptions_.getCutoffPolicy();
1057 –    }else if (simParams_->haveCutoffPolicy()) {
1058 –      myPolicy = simParams_->getCutoffPolicy();
1059 –    }
1060 –
1061 –    if (!myPolicy.empty()){
1062 –      toUpper(myPolicy);
1063 –      if (myPolicy == "MIX") {
1064 –        cp = MIX_CUTOFF_POLICY;
1065 –      } else {
1066 –        if (myPolicy == "MAX") {
1067 –          cp = MAX_CUTOFF_POLICY;
1068 –        } else {
1069 –          if (myPolicy == "TRADITIONAL") {            
1070 –            cp = TRADITIONAL_CUTOFF_POLICY;
1071 –          } else {
1072 –            // throw error        
1073 –            sprintf( painCave.errMsg,
1074 –                     "SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
1075 –            painCave.isFatal = 1;
1076 –            simError();
1077 –          }    
1078 –        }          
1079 –      }
1080 –    }          
1081 –    notifyFortranCutoffPolicy(&cp);
1082 –
1083 –    // Check the Skin Thickness for neighborlists
1084 –    RealType skin;
1085 –    if (simParams_->haveSkinThickness()) {
1086 –      skin = simParams_->getSkinThickness();
1087 –      notifyFortranSkinThickness(&skin);
1088 –    }            
1089 –        
1090 –    // Check if the cutoff was set explicitly:
1091 –    if (simParams_->haveCutoffRadius()) {
1092 –      rcut_ = simParams_->getCutoffRadius();
1093 –      if (simParams_->haveSwitchingRadius()) {
1094 –        rsw_  = simParams_->getSwitchingRadius();
1095 –      } else {
1096 –        if (fInfo_.SIM_uses_Charges |
1097 –            fInfo_.SIM_uses_Dipoles |
1098 –            fInfo_.SIM_uses_RF) {
1099 –          
1100 –          rsw_ = 0.85 * rcut_;
1101 –          sprintf(painCave.errMsg,
1102 –                  "SimCreator Warning: No value was set for the switchingRadius.\n"
1103 –                  "\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
1104 –                  "\tswitchingRadius = %f. for this simulation\n", rsw_);
1105 –        painCave.isFatal = 0;
1106 –        simError();
1107 –        } else {
1108 –          rsw_ = rcut_;
1109 –          sprintf(painCave.errMsg,
1110 –                  "SimCreator Warning: No value was set for the switchingRadius.\n"
1111 –                  "\tOpenMD will use the same value as the cutoffRadius.\n"
1112 –                  "\tswitchingRadius = %f. for this simulation\n", rsw_);
1113 –          painCave.isFatal = 0;
1114 –          simError();
1115 –        }
1116 –      }
1117 –
1118 –      if (simParams_->haveElectrostaticSummationMethod()) {
1119 –        std::string myMethod = simParams_->getElectrostaticSummationMethod();
1120 –        toUpper(myMethod);
1121 –        
1122 –        if (myMethod == "SHIFTED_POTENTIAL") {
1123 –          ljsp_ = 1;
1124 –        } else if (myMethod == "SHIFTED_FORCE") {
1125 –          ljsf_ = 1;
1126 –        }
1127 –      }
1128 –
1129 –      notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1130 –      
1131 –    } else {
1132 –      
1133 –      // For electrostatic atoms, we'll assume a large safe value:
1134 –      if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
1135 –        sprintf(painCave.errMsg,
1136 –                "SimCreator Warning: No value was set for the cutoffRadius.\n"
1137 –                "\tOpenMD will use a default value of 15.0 angstroms"
1138 –                "\tfor the cutoffRadius.\n");
1139 –        painCave.isFatal = 0;
1140 –        simError();
1141 –        rcut_ = 15.0;
1142 –      
1143 –        if (simParams_->haveElectrostaticSummationMethod()) {
1144 –          std::string myMethod = simParams_->getElectrostaticSummationMethod();
1145 –          toUpper(myMethod);
1146 –          
1147 –          // For the time being, we're tethering the LJ shifted behavior to the
1148 –          // electrostaticSummationMethod keyword options
1149 –          if (myMethod == "SHIFTED_POTENTIAL") {
1150 –            ljsp_ = 1;
1151 –          } else if (myMethod == "SHIFTED_FORCE") {
1152 –            ljsf_ = 1;
1153 –          }
1154 –          if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1155 –            if (simParams_->haveSwitchingRadius()){
1156 –              sprintf(painCave.errMsg,
1157 –                      "SimInfo Warning: A value was set for the switchingRadius\n"
1158 –                      "\teven though the electrostaticSummationMethod was\n"
1159 –                      "\tset to %s\n", myMethod.c_str());
1160 –              painCave.isFatal = 1;
1161 –              simError();            
1162 –            }
1163 –          }
1164 –        }
1165 –      
1166 –        if (simParams_->haveSwitchingRadius()){
1167 –          rsw_ = simParams_->getSwitchingRadius();
1168 –        } else {        
1169 –          sprintf(painCave.errMsg,
1170 –                  "SimCreator Warning: No value was set for switchingRadius.\n"
1171 –                  "\tOpenMD will use a default value of\n"
1172 –                  "\t0.85 * cutoffRadius for the switchingRadius\n");
1173 –          painCave.isFatal = 0;
1174 –          simError();
1175 –          rsw_ = 0.85 * rcut_;
1176 –        }
1177 –
1178 –        Electrostatic::setElectrostaticCutoffRadius(rcut_, rsw_);
1179 –        notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1180 –
1181 –      } else {
1182 –        // We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1183 –        // We'll punt and let fortran figure out the cutoffs later.
1184 –        
1185 –        notifyFortranYouAreOnYourOwn();
1186 –
1187 –      }
1188 –    }
1064    }
1065  
1191 –  void SimInfo::setupElectrostaticSummationMethod( int isError ) {    
1192 –    
1193 –    int errorOut;
1194 –    ElectrostaticSummationMethod esm = NONE;
1195 –    ElectrostaticScreeningMethod sm = UNDAMPED;
1196 –    RealType alphaVal;
1197 –    RealType dielectric;
1198 –    
1199 –    errorOut = isError;
1066  
1201 –    if (simParams_->haveElectrostaticSummationMethod()) {
1202 –      std::string myMethod = simParams_->getElectrostaticSummationMethod();
1203 –      toUpper(myMethod);
1204 –      if (myMethod == "NONE") {
1205 –        esm = NONE;
1206 –      } else {
1207 –        if (myMethod == "SWITCHING_FUNCTION") {
1208 –          esm = SWITCHING_FUNCTION;
1209 –        } else {
1210 –          if (myMethod == "SHIFTED_POTENTIAL") {
1211 –            esm = SHIFTED_POTENTIAL;
1212 –          } else {
1213 –            if (myMethod == "SHIFTED_FORCE") {            
1214 –              esm = SHIFTED_FORCE;
1215 –            } else {
1216 –              if (myMethod == "REACTION_FIELD") {
1217 –                esm = REACTION_FIELD;
1218 –                dielectric = simParams_->getDielectric();
1219 –                if (!simParams_->haveDielectric()) {
1220 –                  // throw warning
1221 –                  sprintf( painCave.errMsg,
1222 –                           "SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
1223 –                           "\tA default value of %f will be used for the dielectric.\n", dielectric);
1224 –                  painCave.isFatal = 0;
1225 –                  simError();
1226 –                }
1227 –              } else {
1228 –                // throw error        
1229 –                sprintf( painCave.errMsg,
1230 –                         "SimInfo error: Unknown electrostaticSummationMethod.\n"
1231 –                         "\t(Input file specified %s .)\n"
1232 –                         "\telectrostaticSummationMethod must be one of: \"none\",\n"
1233 –                         "\t\"shifted_potential\", \"shifted_force\", or \n"
1234 –                         "\t\"reaction_field\".\n", myMethod.c_str() );
1235 –                painCave.isFatal = 1;
1236 –                simError();
1237 –              }    
1238 –            }          
1239 –          }
1240 –        }
1241 –      }
1242 –    }
1243 –    
1244 –    if (simParams_->haveElectrostaticScreeningMethod()) {
1245 –      std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1246 –      toUpper(myScreen);
1247 –      if (myScreen == "UNDAMPED") {
1248 –        sm = UNDAMPED;
1249 –      } else {
1250 –        if (myScreen == "DAMPED") {
1251 –          sm = DAMPED;
1252 –          if (!simParams_->haveDampingAlpha()) {
1253 –            // first set a cutoff dependent alpha value
1254 –            // we assume alpha depends linearly with rcut from 0 to 20.5 ang
1255 –            alphaVal = 0.5125 - rcut_* 0.025;
1256 –            // for values rcut > 20.5, alpha is zero
1257 –            if (alphaVal < 0) alphaVal = 0;
1258 –
1259 –            // throw warning
1260 –            sprintf( painCave.errMsg,
1261 –                     "SimInfo warning: dampingAlpha was not specified in the input file.\n"
1262 –                     "\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1263 –            painCave.isFatal = 0;
1264 –            simError();
1265 –          } else {
1266 –            alphaVal = simParams_->getDampingAlpha();
1267 –          }
1268 –          
1269 –        } else {
1270 –          // throw error        
1271 –          sprintf( painCave.errMsg,
1272 –                   "SimInfo error: Unknown electrostaticScreeningMethod.\n"
1273 –                   "\t(Input file specified %s .)\n"
1274 –                   "\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1275 –                   "or \"damped\".\n", myScreen.c_str() );
1276 –          painCave.isFatal = 1;
1277 –          simError();
1278 –        }
1279 –      }
1280 –    }
1281 –    
1282 –
1283 –    Electrostatic::setElectrostaticSummationMethod( esm );
1284 –    Electrostatic::setElectrostaticScreeningMethod( sm );
1285 –    Electrostatic::setDampingAlpha( alphaVal );
1286 –    Electrostatic::setReactionFieldDielectric( dielectric );
1287 –    initFortranFF( &errorOut );
1288 –  }
1289 –
1067    void SimInfo::setupSwitchingFunction() {    
1291 –    int ft = CUBIC;
1068  
1293 –    if (simParams_->haveSwitchingFunctionType()) {
1294 –      std::string funcType = simParams_->getSwitchingFunctionType();
1295 –      toUpper(funcType);
1296 –      if (funcType == "CUBIC") {
1297 –        ft = CUBIC;
1298 –      } else {
1299 –        if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1300 –          ft = FIFTH_ORDER_POLY;
1301 –        } else {
1302 –          // throw error        
1303 –          sprintf( painCave.errMsg,
1304 –                   "SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1305 –          painCave.isFatal = 1;
1306 –          simError();
1307 –        }          
1308 –      }
1309 –    }
1310 –
1311 –    // send switching function notification to switcheroo
1312 –    setFunctionType(&ft);
1313 –
1069    }
1070  
1071    void SimInfo::setupAccumulateBoxDipole() {    
# Line 1318 | Line 1073 | namespace OpenMD {
1073      // we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1074      if ( simParams_->haveAccumulateBoxDipole() )
1075        if ( simParams_->getAccumulateBoxDipole() ) {
1321 –        setAccumulateBoxDipole();
1076          calcBoxDipole_ = true;
1077        }
1078  
# Line 1328 | Line 1082 | namespace OpenMD {
1082      properties_.addProperty(genData);  
1083    }
1084  
1085 <  void SimInfo::removeProperty(const std::string& propName) {
1085 >  void SimInfo::removeProperty(const string& propName) {
1086      properties_.removeProperty(propName);  
1087    }
1088  
# Line 1336 | Line 1090 | namespace OpenMD {
1090      properties_.clearProperties();
1091    }
1092  
1093 <  std::vector<std::string> SimInfo::getPropertyNames() {
1093 >  vector<string> SimInfo::getPropertyNames() {
1094      return properties_.getPropertyNames();  
1095    }
1096        
1097 <  std::vector<GenericData*> SimInfo::getProperties() {
1097 >  vector<GenericData*> SimInfo::getProperties() {
1098      return properties_.getProperties();
1099    }
1100  
1101 <  GenericData* SimInfo::getPropertyByName(const std::string& propName) {
1101 >  GenericData* SimInfo::getPropertyByName(const string& propName) {
1102      return properties_.getPropertyByName(propName);
1103    }
1104  
# Line 1427 | Line 1181 | namespace OpenMD {
1181  
1182    }        
1183  
1184 <  std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1184 >  ostream& operator <<(ostream& o, SimInfo& info) {
1185  
1186      return o;
1187    }
# Line 1577 | Line 1331 | namespace OpenMD {
1331      return IOIndexToIntegrableObject.at(index);
1332    }
1333    
1334 <  void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1334 >  void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1335      IOIndexToIntegrableObject= v;
1336    }
1337  
# Line 1619 | Line 1373 | namespace OpenMD {
1373      return;
1374    }
1375   /*
1376 <   void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1376 >   void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1377        assert( v.size() == nAtoms_ + nRigidBodies_);
1378        sdByGlobalIndex_ = v;
1379      }
# Line 1629 | Line 1383 | namespace OpenMD {
1383        return sdByGlobalIndex_.at(index);
1384      }  
1385   */  
1386 +  int SimInfo::getNGlobalConstraints() {
1387 +    int nGlobalConstraints;
1388 + #ifdef IS_MPI
1389 +    MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1390 +                  MPI_COMM_WORLD);    
1391 + #else
1392 +    nGlobalConstraints =  nConstraints_;
1393 + #endif
1394 +    return nGlobalConstraints;
1395 +  }
1396 +
1397   }//end namespace OpenMD
1398  

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