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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 1465 by chuckv, Fri Jul 9 23:08:25 2010 UTC vs.
Revision 1528 by gezelter, Fri Dec 17 20:11:05 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/fElectrostaticSummationMethod.h"
59 – #include "UseTheForce/DarkSide/fElectrostaticScreeningMethod.h"
58   #include "UseTheForce/DarkSide/fSwitchingFunctionType.h"
59   #include "UseTheForce/doForces_interface.h"
60   #include "UseTheForce/DarkSide/neighborLists_interface.h"
63 – #include "UseTheForce/DarkSide/electrostatic_interface.h"
61   #include "UseTheForce/DarkSide/switcheroo_interface.h"
62   #include "utils/MemoryUtils.hpp"
63   #include "utils/simError.h"
64   #include "selection/SelectionManager.hpp"
65   #include "io/ForceFieldOptions.hpp"
66   #include "UseTheForce/ForceField.hpp"
67 + #include "nonbonded/InteractionManager.hpp"
68  
69  
70   #ifdef IS_MPI
# Line 74 | Line 72
72   #include "UseTheForce/DarkSide/simParallel_interface.h"
73   #endif
74  
75 + using namespace std;
76   namespace OpenMD {
78 –  std::set<int> getRigidSet(int index, std::map<int, std::set<int> >& container) {
79 –    std::map<int, std::set<int> >::iterator i = container.find(index);
80 –    std::set<int> result;
81 –    if (i != container.end()) {
82 –        result = i->second;
83 –    }
84 –
85 –    return result;
86 –  }
77    
78    SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
79      forceField_(ff), simParams_(simParams),
# Line 93 | Line 83 | namespace OpenMD {
83      nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
84      nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
85      nConstraints_(0), sman_(NULL), fortranInitialized_(false),
86 <    calcBoxDipole_(false), useAtomicVirial_(true) {
87 <
88 <
89 <      MoleculeStamp* molStamp;
90 <      int nMolWithSameStamp;
91 <      int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
92 <      int nGroups = 0;      //total cutoff groups defined in meta-data file
93 <      CutoffGroupStamp* cgStamp;    
94 <      RigidBodyStamp* rbStamp;
95 <      int nRigidAtoms = 0;
96 <
97 <      std::vector<Component*> components = simParams->getComponents();
86 >    calcBoxDipole_(false), useAtomicVirial_(true) {    
87 >    
88 >    MoleculeStamp* molStamp;
89 >    int nMolWithSameStamp;
90 >    int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
91 >    int nGroups = 0;       //total cutoff groups defined in meta-data file
92 >    CutoffGroupStamp* cgStamp;    
93 >    RigidBodyStamp* rbStamp;
94 >    int nRigidAtoms = 0;
95 >    
96 >    vector<Component*> components = simParams->getComponents();
97 >    
98 >    for (vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
99 >      molStamp = (*i)->getMoleculeStamp();
100 >      nMolWithSameStamp = (*i)->getNMol();
101        
102 <      for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
103 <        molStamp = (*i)->getMoleculeStamp();
104 <        nMolWithSameStamp = (*i)->getNMol();
105 <        
106 <        addMoleculeStamp(molStamp, nMolWithSameStamp);
107 <
108 <        //calculate atoms in molecules
109 <        nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;  
110 <
111 <        //calculate atoms in cutoff groups
112 <        int nAtomsInGroups = 0;
113 <        int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
121 <        
122 <        for (int j=0; j < nCutoffGroupsInStamp; j++) {
123 <          cgStamp = molStamp->getCutoffGroupStamp(j);
124 <          nAtomsInGroups += cgStamp->getNMembers();
125 <        }
126 <
127 <        nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
128 <
129 <        nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;            
130 <
131 <        //calculate atoms in rigid bodies
132 <        int nAtomsInRigidBodies = 0;
133 <        int nRigidBodiesInStamp = molStamp->getNRigidBodies();
134 <        
135 <        for (int j=0; j < nRigidBodiesInStamp; j++) {
136 <          rbStamp = molStamp->getRigidBodyStamp(j);
137 <          nAtomsInRigidBodies += rbStamp->getNMembers();
138 <        }
139 <
140 <        nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
141 <        nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;            
142 <        
102 >      addMoleculeStamp(molStamp, nMolWithSameStamp);
103 >      
104 >      //calculate atoms in molecules
105 >      nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;  
106 >      
107 >      //calculate atoms in cutoff groups
108 >      int nAtomsInGroups = 0;
109 >      int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
110 >      
111 >      for (int j=0; j < nCutoffGroupsInStamp; j++) {
112 >        cgStamp = molStamp->getCutoffGroupStamp(j);
113 >        nAtomsInGroups += cgStamp->getNMembers();
114        }
115 <
116 <      //every free atom (atom does not belong to cutoff groups) is a cutoff
117 <      //group therefore the total number of cutoff groups in the system is
118 <      //equal to the total number of atoms minus number of atoms belong to
119 <      //cutoff group defined in meta-data file plus the number of cutoff
120 <      //groups defined in meta-data file
121 <      nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
122 <
123 <      //every free atom (atom does not belong to rigid bodies) is an
124 <      //integrable object therefore the total number of integrable objects
125 <      //in the system is equal to the total number of atoms minus number of
126 <      //atoms belong to rigid body defined in meta-data file plus the number
127 <      //of rigid bodies defined in meta-data file
128 <      nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
129 <                                                + nGlobalRigidBodies_;
130 <  
131 <      nGlobalMols_ = molStampIds_.size();
132 <      molToProcMap_.resize(nGlobalMols_);
133 <    }
134 <
115 >      
116 >      nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
117 >      
118 >      nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;            
119 >      
120 >      //calculate atoms in rigid bodies
121 >      int nAtomsInRigidBodies = 0;
122 >      int nRigidBodiesInStamp = molStamp->getNRigidBodies();
123 >      
124 >      for (int j=0; j < nRigidBodiesInStamp; j++) {
125 >        rbStamp = molStamp->getRigidBodyStamp(j);
126 >        nAtomsInRigidBodies += rbStamp->getNMembers();
127 >      }
128 >      
129 >      nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
130 >      nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;            
131 >      
132 >    }
133 >    
134 >    //every free atom (atom does not belong to cutoff groups) is a cutoff
135 >    //group therefore the total number of cutoff groups in the system is
136 >    //equal to the total number of atoms minus number of atoms belong to
137 >    //cutoff group defined in meta-data file plus the number of cutoff
138 >    //groups defined in meta-data file
139 >    nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
140 >    
141 >    //every free atom (atom does not belong to rigid bodies) is an
142 >    //integrable object therefore the total number of integrable objects
143 >    //in the system is equal to the total number of atoms minus number of
144 >    //atoms belong to rigid body defined in meta-data file plus the number
145 >    //of rigid bodies defined in meta-data file
146 >    nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
147 >      + nGlobalRigidBodies_;
148 >    
149 >    nGlobalMols_ = molStampIds_.size();
150 >    molToProcMap_.resize(nGlobalMols_);
151 >  }
152 >  
153    SimInfo::~SimInfo() {
154 <    std::map<int, Molecule*>::iterator i;
154 >    map<int, Molecule*>::iterator i;
155      for (i = molecules_.begin(); i != molecules_.end(); ++i) {
156        delete i->second;
157      }
# Line 173 | Line 162 | namespace OpenMD {
162      delete forceField_;
163    }
164  
176 –  int SimInfo::getNGlobalConstraints() {
177 –    int nGlobalConstraints;
178 – #ifdef IS_MPI
179 –    MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
180 –                  MPI_COMM_WORLD);    
181 – #else
182 –    nGlobalConstraints =  nConstraints_;
183 – #endif
184 –    return nGlobalConstraints;
185 –  }
165  
166    bool SimInfo::addMolecule(Molecule* mol) {
167      MoleculeIterator i;
168 <
168 >    
169      i = molecules_.find(mol->getGlobalIndex());
170      if (i == molecules_.end() ) {
171 <
172 <      molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
173 <        
171 >      
172 >      molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
173 >      
174        nAtoms_ += mol->getNAtoms();
175        nBonds_ += mol->getNBonds();
176        nBends_ += mol->getNBends();
# Line 201 | Line 180 | namespace OpenMD {
180        nIntegrableObjects_ += mol->getNIntegrableObjects();
181        nCutoffGroups_ += mol->getNCutoffGroups();
182        nConstraints_ += mol->getNConstraintPairs();
183 <
183 >      
184        addInteractionPairs(mol);
185 <  
185 >      
186        return true;
187      } else {
188        return false;
189      }
190    }
191 <
191 >  
192    bool SimInfo::removeMolecule(Molecule* mol) {
193      MoleculeIterator i;
194      i = molecules_.find(mol->getGlobalIndex());
# Line 237 | Line 216 | namespace OpenMD {
216      } else {
217        return false;
218      }
240 –
241 –
219    }    
220  
221          
# Line 256 | Line 233 | namespace OpenMD {
233    void SimInfo::calcNdf() {
234      int ndf_local;
235      MoleculeIterator i;
236 <    std::vector<StuntDouble*>::iterator j;
236 >    vector<StuntDouble*>::iterator j;
237      Molecule* mol;
238      StuntDouble* integrableObject;
239  
# Line 307 | Line 284 | namespace OpenMD {
284      int ndfRaw_local;
285  
286      MoleculeIterator i;
287 <    std::vector<StuntDouble*>::iterator j;
287 >    vector<StuntDouble*>::iterator j;
288      Molecule* mol;
289      StuntDouble* integrableObject;
290  
# Line 356 | Line 333 | namespace OpenMD {
333  
334    void SimInfo::addInteractionPairs(Molecule* mol) {
335      ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
336 <    std::vector<Bond*>::iterator bondIter;
337 <    std::vector<Bend*>::iterator bendIter;
338 <    std::vector<Torsion*>::iterator torsionIter;
339 <    std::vector<Inversion*>::iterator inversionIter;
336 >    vector<Bond*>::iterator bondIter;
337 >    vector<Bend*>::iterator bendIter;
338 >    vector<Torsion*>::iterator torsionIter;
339 >    vector<Inversion*>::iterator inversionIter;
340      Bond* bond;
341      Bend* bend;
342      Torsion* torsion;
# Line 377 | Line 354 | namespace OpenMD {
354      // always be excluded.  These are done at the bottom of this
355      // function.
356  
357 <    std::map<int, std::set<int> > atomGroups;
357 >    map<int, set<int> > atomGroups;
358      Molecule::RigidBodyIterator rbIter;
359      RigidBody* rb;
360      Molecule::IntegrableObjectIterator ii;
# Line 389 | Line 366 | namespace OpenMD {
366        
367        if (integrableObject->isRigidBody()) {
368          rb = static_cast<RigidBody*>(integrableObject);
369 <        std::vector<Atom*> atoms = rb->getAtoms();
370 <        std::set<int> rigidAtoms;
369 >        vector<Atom*> atoms = rb->getAtoms();
370 >        set<int> rigidAtoms;
371          for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
372            rigidAtoms.insert(atoms[i]->getGlobalIndex());
373          }
374          for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
375 <          atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
375 >          atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
376          }      
377        } else {
378 <        std::set<int> oneAtomSet;
378 >        set<int> oneAtomSet;
379          oneAtomSet.insert(integrableObject->getGlobalIndex());
380 <        atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));        
380 >        atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));        
381        }
382      }  
383            
# Line 503 | Line 480 | namespace OpenMD {
480  
481      for (rb = mol->beginRigidBody(rbIter); rb != NULL;
482           rb = mol->nextRigidBody(rbIter)) {
483 <      std::vector<Atom*> atoms = rb->getAtoms();
483 >      vector<Atom*> atoms = rb->getAtoms();
484        for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
485          for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
486            a = atoms[i]->getGlobalIndex();
# Line 517 | Line 494 | namespace OpenMD {
494  
495    void SimInfo::removeInteractionPairs(Molecule* mol) {
496      ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
497 <    std::vector<Bond*>::iterator bondIter;
498 <    std::vector<Bend*>::iterator bendIter;
499 <    std::vector<Torsion*>::iterator torsionIter;
500 <    std::vector<Inversion*>::iterator inversionIter;
497 >    vector<Bond*>::iterator bondIter;
498 >    vector<Bend*>::iterator bendIter;
499 >    vector<Torsion*>::iterator torsionIter;
500 >    vector<Inversion*>::iterator inversionIter;
501      Bond* bond;
502      Bend* bend;
503      Torsion* torsion;
# Line 530 | Line 507 | namespace OpenMD {
507      int c;
508      int d;
509  
510 <    std::map<int, std::set<int> > atomGroups;
510 >    map<int, set<int> > atomGroups;
511      Molecule::RigidBodyIterator rbIter;
512      RigidBody* rb;
513      Molecule::IntegrableObjectIterator ii;
# Line 542 | Line 519 | namespace OpenMD {
519        
520        if (integrableObject->isRigidBody()) {
521          rb = static_cast<RigidBody*>(integrableObject);
522 <        std::vector<Atom*> atoms = rb->getAtoms();
523 <        std::set<int> rigidAtoms;
522 >        vector<Atom*> atoms = rb->getAtoms();
523 >        set<int> rigidAtoms;
524          for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
525            rigidAtoms.insert(atoms[i]->getGlobalIndex());
526          }
527          for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
528 <          atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
528 >          atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
529          }      
530        } else {
531 <        std::set<int> oneAtomSet;
531 >        set<int> oneAtomSet;
532          oneAtomSet.insert(integrableObject->getGlobalIndex());
533 <        atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));        
533 >        atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));        
534        }
535      }  
536  
# Line 656 | Line 633 | namespace OpenMD {
633  
634      for (rb = mol->beginRigidBody(rbIter); rb != NULL;
635           rb = mol->nextRigidBody(rbIter)) {
636 <      std::vector<Atom*> atoms = rb->getAtoms();
636 >      vector<Atom*> atoms = rb->getAtoms();
637        for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
638          for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
639            a = atoms[i]->getGlobalIndex();
# Line 682 | Line 659 | namespace OpenMD {
659    void SimInfo::update() {
660  
661      setupSimType();
662 +    setupCutoffRadius();
663 +    setupSwitchingRadius();
664 +    setupCutoffMethod();
665 +    setupSkinThickness();
666 +    setupSwitchingFunction();
667 +    setupAccumulateBoxDipole();
668  
669   #ifdef IS_MPI
670      setupFortranParallel();
671   #endif
689 –
672      setupFortranSim();
673 +    fortranInitialized_ = true;
674  
692 –    //setup fortran force field
693 –    /** @deprecate */    
694 –    int isError = 0;
695 –    
696 –    setupCutoff();
697 –    
698 –    setupElectrostaticSummationMethod( isError );
699 –    setupSwitchingFunction();
700 –    setupAccumulateBoxDipole();
701 –
702 –    if(isError){
703 –      sprintf( painCave.errMsg,
704 –               "ForceField error: There was an error initializing the forceField in fortran.\n" );
705 –      painCave.isFatal = 1;
706 –      simError();
707 –    }
708 –
675      calcNdf();
676      calcNdfRaw();
677      calcNdfTrans();
712 –
713 –    fortranInitialized_ = true;
678    }
679 <
680 <  std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
679 >  
680 >  set<AtomType*> SimInfo::getSimulatedAtomTypes() {
681      SimInfo::MoleculeIterator mi;
682      Molecule* mol;
683      Molecule::AtomIterator ai;
684      Atom* atom;
685 <    std::set<AtomType*> atomTypes;
686 <
685 >    set<AtomType*> atomTypes;
686 >    
687      for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
688 <
688 >      
689        for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
690          atomTypes.insert(atom->getAtomType());
691        }
692 <        
692 >      
693      }
694 <
694 >    
695      return atomTypes;        
696    }
697  
698 <  void SimInfo::setupSimType() {
699 <    std::set<AtomType*>::iterator i;
700 <    std::set<AtomType*> atomTypes;
701 <    atomTypes = getUniqueAtomTypes();
698 >  /**
699 >   * setupCutoffRadius
700 >   *
701 >   *  If the cutoffRadius was explicitly set, use that value.
702 >   *  If the cutoffRadius was not explicitly set:
703 >   *      Are there electrostatic atoms?  Use 12.0 Angstroms.
704 >   *      No electrostatic atoms?  Poll the atom types present in the
705 >   *      simulation for suggested cutoff values (e.g. 2.5 * sigma).
706 >   *      Use the maximum suggested value that was found.
707 >   */
708 >  void SimInfo::setupCutoffRadius() {
709      
710 <    int useLennardJones = 0;
711 <    int useElectrostatic = 0;
712 <    int useEAM = 0;
713 <    int useSC = 0;
714 <    int useCharge = 0;
715 <    int useDirectional = 0;
716 <    int useDipole = 0;
717 <    int useGayBerne = 0;
718 <    int useSticky = 0;
719 <    int useStickyPower = 0;
720 <    int useShape = 0;
721 <    int useFLARB = 0; //it is not in AtomType yet
722 <    int useDirectionalAtom = 0;    
723 <    int useElectrostatics = 0;
724 <    //usePBC and useRF are from simParams
725 <    int usePBC = simParams_->getUsePeriodicBoundaryConditions();
726 <    int useRF;
727 <    int useSF;
728 <    int useSP;
729 <    int useBoxDipole;
730 <
731 <    std::string myMethod;
732 <
733 <    // set the useRF logical
734 <    useRF = 0;
735 <    useSF = 0;
736 <    useSP = 0;
737 <    useBoxDipole = 0;
710 >    if (simParams_->haveCutoffRadius()) {
711 >      cutoffRadius_ = simParams_->getCutoffRadius();
712 >    } else {      
713 >      if (usesElectrostaticAtoms_) {
714 >        sprintf(painCave.errMsg,
715 >                "SimInfo Warning: No value was set for the cutoffRadius.\n"
716 >                "\tOpenMD will use a default value of 12.0 angstroms"
717 >                "\tfor the cutoffRadius.\n");
718 >        painCave.isFatal = 0;
719 >        simError();
720 >        cutoffRadius_ = 12.0;
721 >      } else {
722 >        RealType thisCut;
723 >        set<AtomType*>::iterator i;
724 >        set<AtomType*> atomTypes;
725 >        atomTypes = getSimulatedAtomTypes();        
726 >        for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
727 >          thisCut = InteractionManager::Instance()->getSuggestedCutoffRadius((*i));
728 >          cutoffRadius_ = max(thisCut, cutoffRadius_);
729 >        }
730 >        sprintf(painCave.errMsg,
731 >                "SimInfo Warning: No value was set for the cutoffRadius.\n"
732 >                "\tOpenMD will use %lf angstroms.\n",
733 >                cutoffRadius_);
734 >        painCave.isFatal = 0;
735 >        simError();
736 >      }            
737 >    }
738  
739 +    InteractionManager::Instance()->setCutoffRadius(cutoffRadius_);
740 +  }
741 +  
742 +  /**
743 +   * setupSwitchingRadius
744 +   *
745 +   *  If the switchingRadius was explicitly set, use that value (but check it)
746 +   *  If the switchingRadius was not explicitly set: use 0.85 * cutoffRadius_
747 +   */
748 +  void SimInfo::setupSwitchingRadius() {
749 +    
750 +    if (simParams_->haveSwitchingRadius()) {
751 +      switchingRadius_ = simParams_->getSwitchingRadius();
752 +      if (switchingRadius_ > cutoffRadius_) {        
753 +        sprintf(painCave.errMsg,
754 +                "SimInfo Error: switchingRadius (%f) is larger than cutoffRadius(%f)\n",
755 +                switchingRadius_, cutoffRadius_);
756 +        painCave.isFatal = 1;
757 +        simError();
758  
769 –    if (simParams_->haveElectrostaticSummationMethod()) {
770 –      std::string myMethod = simParams_->getElectrostaticSummationMethod();
771 –      toUpper(myMethod);
772 –      if (myMethod == "REACTION_FIELD"){
773 –        useRF = 1;
774 –      } else if (myMethod == "SHIFTED_FORCE"){
775 –        useSF = 1;
776 –      } else if (myMethod == "SHIFTED_POTENTIAL"){
777 –        useSP = 1;
759        }
760 <    }
761 <    
762 <    if (simParams_->haveAccumulateBoxDipole())
763 <      if (simParams_->getAccumulateBoxDipole())
764 <        useBoxDipole = 1;
760 >    } else {      
761 >      switchingRadius_ = 0.85 * cutoffRadius_;
762 >      sprintf(painCave.errMsg,
763 >              "SimInfo Warning: No value was set for the switchingRadius.\n"
764 >              "\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
765 >              "\tswitchingRadius = %f. for this simulation\n", switchingRadius_);
766 >      painCave.isFatal = 0;
767 >      simError();
768 >    }            
769 >    InteractionManager::Instance()->setSwitchingRadius(switchingRadius_);
770 >  }
771  
772 +  /**
773 +   * setupSkinThickness
774 +   *
775 +   *  If the skinThickness was explicitly set, use that value (but check it)
776 +   *  If the skinThickness was not explicitly set: use 1.0 angstroms
777 +   */
778 +  void SimInfo::setupSkinThickness() {    
779 +    if (simParams_->haveSkinThickness()) {
780 +      skinThickness_ = simParams_->getSkinThickness();
781 +    } else {      
782 +      skinThickness_ = 1.0;
783 +      sprintf(painCave.errMsg,
784 +              "SimInfo Warning: No value was set for the skinThickness.\n"
785 +              "\tOpenMD will use a default value of %f Angstroms\n"
786 +              "\tfor this simulation\n", skinThickness_);
787 +      painCave.isFatal = 0;
788 +      simError();
789 +    }            
790 +  }
791 +
792 +  void SimInfo::setupSimType() {
793 +    set<AtomType*>::iterator i;
794 +    set<AtomType*> atomTypes;
795 +    atomTypes = getSimulatedAtomTypes();
796 +
797      useAtomicVirial_ = simParams_->getUseAtomicVirial();
798  
799 +    int usesElectrostatic = 0;
800 +    int usesMetallic = 0;
801 +    int usesDirectional = 0;
802      //loop over all of the atom types
803      for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
804 <      useLennardJones |= (*i)->isLennardJones();
805 <      useElectrostatic |= (*i)->isElectrostatic();
806 <      useEAM |= (*i)->isEAM();
792 <      useSC |= (*i)->isSC();
793 <      useCharge |= (*i)->isCharge();
794 <      useDirectional |= (*i)->isDirectional();
795 <      useDipole |= (*i)->isDipole();
796 <      useGayBerne |= (*i)->isGayBerne();
797 <      useSticky |= (*i)->isSticky();
798 <      useStickyPower |= (*i)->isStickyPower();
799 <      useShape |= (*i)->isShape();
804 >      usesElectrostatic |= (*i)->isElectrostatic();
805 >      usesMetallic |= (*i)->isMetal();
806 >      usesDirectional |= (*i)->isDirectional();
807      }
808  
802 –    if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
803 –      useDirectionalAtom = 1;
804 –    }
805 –
806 –    if (useCharge || useDipole) {
807 –      useElectrostatics = 1;
808 –    }
809 –
809   #ifdef IS_MPI    
810      int temp;
811 +    temp = usesDirectional;
812 +    MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
813  
814 <    temp = usePBC;
815 <    MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
814 >    temp = usesMetallic;
815 >    MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
816  
817 <    temp = useDirectionalAtom;
818 <    MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
818 <
819 <    temp = useLennardJones;
820 <    MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
821 <
822 <    temp = useElectrostatics;
823 <    MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
824 <
825 <    temp = useCharge;
826 <    MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
827 <
828 <    temp = useDipole;
829 <    MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
830 <
831 <    temp = useSticky;
832 <    MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
833 <
834 <    temp = useStickyPower;
835 <    MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
836 <    
837 <    temp = useGayBerne;
838 <    MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
839 <
840 <    temp = useEAM;
841 <    MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
842 <
843 <    temp = useSC;
844 <    MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
845 <    
846 <    temp = useShape;
847 <    MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);  
848 <
849 <    temp = useFLARB;
850 <    MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
851 <
852 <    temp = useRF;
853 <    MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
854 <
855 <    temp = useSF;
856 <    MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);  
857 <
858 <    temp = useSP;
859 <    MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
860 <
861 <    temp = useBoxDipole;
862 <    MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
863 <
864 <    temp = useAtomicVirial_;
865 <    MPI_Allreduce(&temp, &useAtomicVirial_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
866 <
817 >    temp = usesElectrostatic;
818 >    MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
819   #endif
820 <
821 <    fInfo_.SIM_uses_PBC = usePBC;    
822 <    fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
823 <    fInfo_.SIM_uses_LennardJones = useLennardJones;
824 <    fInfo_.SIM_uses_Electrostatics = useElectrostatics;    
825 <    fInfo_.SIM_uses_Charges = useCharge;
874 <    fInfo_.SIM_uses_Dipoles = useDipole;
875 <    fInfo_.SIM_uses_Sticky = useSticky;
876 <    fInfo_.SIM_uses_StickyPower = useStickyPower;
877 <    fInfo_.SIM_uses_GayBerne = useGayBerne;
878 <    fInfo_.SIM_uses_EAM = useEAM;
879 <    fInfo_.SIM_uses_SC = useSC;
880 <    fInfo_.SIM_uses_Shapes = useShape;
881 <    fInfo_.SIM_uses_FLARB = useFLARB;
882 <    fInfo_.SIM_uses_RF = useRF;
883 <    fInfo_.SIM_uses_SF = useSF;
884 <    fInfo_.SIM_uses_SP = useSP;
885 <    fInfo_.SIM_uses_BoxDipole = useBoxDipole;
886 <    fInfo_.SIM_uses_AtomicVirial = useAtomicVirial_;
820 >    fInfo_.SIM_uses_PBC = usesPeriodicBoundaries_;    
821 >    fInfo_.SIM_uses_DirectionalAtoms = usesDirectionalAtoms_;
822 >    fInfo_.SIM_uses_MetallicAtoms = usesMetallicAtoms_;
823 >    fInfo_.SIM_requires_SkipCorrection = usesElectrostaticAtoms_;
824 >    fInfo_.SIM_requires_SelfCorrection = usesElectrostaticAtoms_;
825 >    fInfo_.SIM_uses_AtomicVirial = usesAtomicVirial_;
826    }
827  
828    void SimInfo::setupFortranSim() {
829      int isError;
830      int nExclude, nOneTwo, nOneThree, nOneFour;
831 <    std::vector<int> fortranGlobalGroupMembership;
831 >    vector<int> fortranGlobalGroupMembership;
832      
833 +    notifyFortranSkinThickness(&skinThickness_);
834 +
835 +    int ljsp = cutoffMethod_ == SHIFTED_POTENTIAL ? 1 : 0;
836 +    int ljsf = cutoffMethod_ == SHIFTED_FORCE ? 1 : 0;
837 +    notifyFortranCutoffs(&cutoffRadius_, &switchingRadius_, &ljsp, &ljsf);
838 +
839      isError = 0;
840  
841      //globalGroupMembership_ is filled by SimCreator    
# Line 899 | Line 844 | namespace OpenMD {
844      }
845  
846      //calculate mass ratio of cutoff group
847 <    std::vector<RealType> mfact;
847 >    vector<RealType> mfact;
848      SimInfo::MoleculeIterator mi;
849      Molecule* mol;
850      Molecule::CutoffGroupIterator ci;
# Line 926 | Line 871 | namespace OpenMD {
871      }
872  
873      //fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
874 <    std::vector<int> identArray;
874 >    vector<int> identArray;
875  
876      //to avoid memory reallocation, reserve enough space identArray
877      identArray.reserve(getNAtoms());
# Line 939 | Line 884 | namespace OpenMD {
884  
885      //fill molMembershipArray
886      //molMembershipArray is filled by SimCreator    
887 <    std::vector<int> molMembershipArray(nGlobalAtoms_);
887 >    vector<int> molMembershipArray(nGlobalAtoms_);
888      for (int i = 0; i < nGlobalAtoms_; i++) {
889        molMembershipArray[i] = globalMolMembership_[i] + 1;
890      }
# Line 992 | Line 937 | namespace OpenMD {
937    void SimInfo::setupFortranParallel() {
938   #ifdef IS_MPI    
939      //SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
940 <    std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
941 <    std::vector<int> localToGlobalCutoffGroupIndex;
940 >    vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
941 >    vector<int> localToGlobalCutoffGroupIndex;
942      SimInfo::MoleculeIterator mi;
943      Molecule::AtomIterator ai;
944      Molecule::CutoffGroupIterator ci;
# Line 1045 | Line 990 | namespace OpenMD {
990   #endif
991    }
992  
1048 –  void SimInfo::setupCutoff() {          
1049 –    
1050 –    ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
993  
994 <    // Check the cutoff policy
995 <    int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
1054 <
1055 <    // Set LJ shifting bools to false
1056 <    ljsp_ = 0;
1057 <    ljsf_ = 0;
1058 <
1059 <    std::string myPolicy;
1060 <    if (forceFieldOptions_.haveCutoffPolicy()){
1061 <      myPolicy = forceFieldOptions_.getCutoffPolicy();
1062 <    }else if (simParams_->haveCutoffPolicy()) {
1063 <      myPolicy = simParams_->getCutoffPolicy();
1064 <    }
1065 <
1066 <    if (!myPolicy.empty()){
1067 <      toUpper(myPolicy);
1068 <      if (myPolicy == "MIX") {
1069 <        cp = MIX_CUTOFF_POLICY;
1070 <      } else {
1071 <        if (myPolicy == "MAX") {
1072 <          cp = MAX_CUTOFF_POLICY;
1073 <        } else {
1074 <          if (myPolicy == "TRADITIONAL") {            
1075 <            cp = TRADITIONAL_CUTOFF_POLICY;
1076 <          } else {
1077 <            // throw error        
1078 <            sprintf( painCave.errMsg,
1079 <                     "SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
1080 <            painCave.isFatal = 1;
1081 <            simError();
1082 <          }    
1083 <        }          
1084 <      }
1085 <    }          
1086 <    notifyFortranCutoffPolicy(&cp);
1087 <
1088 <    // Check the Skin Thickness for neighborlists
1089 <    RealType skin;
1090 <    if (simParams_->haveSkinThickness()) {
1091 <      skin = simParams_->getSkinThickness();
1092 <      notifyFortranSkinThickness(&skin);
1093 <    }            
1094 <        
1095 <    // Check if the cutoff was set explicitly:
1096 <    if (simParams_->haveCutoffRadius()) {
1097 <      rcut_ = simParams_->getCutoffRadius();
1098 <      if (simParams_->haveSwitchingRadius()) {
1099 <        rsw_  = simParams_->getSwitchingRadius();
1100 <      } else {
1101 <        if (fInfo_.SIM_uses_Charges |
1102 <            fInfo_.SIM_uses_Dipoles |
1103 <            fInfo_.SIM_uses_RF) {
1104 <          
1105 <          rsw_ = 0.85 * rcut_;
1106 <          sprintf(painCave.errMsg,
1107 <                  "SimCreator Warning: No value was set for the switchingRadius.\n"
1108 <                  "\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
1109 <                  "\tswitchingRadius = %f. for this simulation\n", rsw_);
1110 <        painCave.isFatal = 0;
1111 <        simError();
1112 <        } else {
1113 <          rsw_ = rcut_;
1114 <          sprintf(painCave.errMsg,
1115 <                  "SimCreator Warning: No value was set for the switchingRadius.\n"
1116 <                  "\tOpenMD will use the same value as the cutoffRadius.\n"
1117 <                  "\tswitchingRadius = %f. for this simulation\n", rsw_);
1118 <          painCave.isFatal = 0;
1119 <          simError();
1120 <        }
1121 <      }
1122 <
1123 <      if (simParams_->haveElectrostaticSummationMethod()) {
1124 <        std::string myMethod = simParams_->getElectrostaticSummationMethod();
1125 <        toUpper(myMethod);
1126 <        
1127 <        if (myMethod == "SHIFTED_POTENTIAL") {
1128 <          ljsp_ = 1;
1129 <        } else if (myMethod == "SHIFTED_FORCE") {
1130 <          ljsf_ = 1;
1131 <        }
1132 <      }
1133 <
1134 <      notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1135 <      
1136 <    } else {
1137 <      
1138 <      // For electrostatic atoms, we'll assume a large safe value:
1139 <      if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
1140 <        sprintf(painCave.errMsg,
1141 <                "SimCreator Warning: No value was set for the cutoffRadius.\n"
1142 <                "\tOpenMD will use a default value of 15.0 angstroms"
1143 <                "\tfor the cutoffRadius.\n");
1144 <        painCave.isFatal = 0;
1145 <        simError();
1146 <        rcut_ = 15.0;
1147 <      
1148 <        if (simParams_->haveElectrostaticSummationMethod()) {
1149 <          std::string myMethod = simParams_->getElectrostaticSummationMethod();
1150 <          toUpper(myMethod);
1151 <      
1152 <      // For the time being, we're tethering the LJ shifted behavior to the
1153 <      // electrostaticSummationMethod keyword options
1154 <          if (myMethod == "SHIFTED_POTENTIAL") {
1155 <            ljsp_ = 1;
1156 <          } else if (myMethod == "SHIFTED_FORCE") {
1157 <            ljsf_ = 1;
1158 <          }
1159 <          if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1160 <            if (simParams_->haveSwitchingRadius()){
1161 <              sprintf(painCave.errMsg,
1162 <                      "SimInfo Warning: A value was set for the switchingRadius\n"
1163 <                      "\teven though the electrostaticSummationMethod was\n"
1164 <                      "\tset to %s\n", myMethod.c_str());
1165 <              painCave.isFatal = 1;
1166 <              simError();            
1167 <            }
1168 <          }
1169 <        }
1170 <      
1171 <        if (simParams_->haveSwitchingRadius()){
1172 <          rsw_ = simParams_->getSwitchingRadius();
1173 <        } else {        
1174 <          sprintf(painCave.errMsg,
1175 <                  "SimCreator Warning: No value was set for switchingRadius.\n"
1176 <                  "\tOpenMD will use a default value of\n"
1177 <                  "\t0.85 * cutoffRadius for the switchingRadius\n");
1178 <          painCave.isFatal = 0;
1179 <          simError();
1180 <          rsw_ = 0.85 * rcut_;
1181 <        }
1182 <
1183 <        notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1184 <
1185 <      } else {
1186 <        // We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1187 <        // We'll punt and let fortran figure out the cutoffs later.
1188 <        
1189 <        notifyFortranYouAreOnYourOwn();
1190 <
1191 <      }
1192 <    }
1193 <  }
1194 <
1195 <  void SimInfo::setupElectrostaticSummationMethod( int isError ) {    
1196 <    
1197 <    int errorOut;
1198 <    int esm =  NONE;
1199 <    int sm = UNDAMPED;
1200 <    RealType alphaVal;
1201 <    RealType dielectric;
994 >  void SimInfo::setupSwitchingFunction() {    
995 >    int ft = CUBIC;
996      
997 <    errorOut = isError;
998 <
1205 <    if (simParams_->haveElectrostaticSummationMethod()) {
1206 <      std::string myMethod = simParams_->getElectrostaticSummationMethod();
1207 <      toUpper(myMethod);
1208 <      if (myMethod == "NONE") {
1209 <        esm = NONE;
1210 <      } else {
1211 <        if (myMethod == "SWITCHING_FUNCTION") {
1212 <          esm = SWITCHING_FUNCTION;
1213 <        } else {
1214 <          if (myMethod == "SHIFTED_POTENTIAL") {
1215 <            esm = SHIFTED_POTENTIAL;
1216 <          } else {
1217 <            if (myMethod == "SHIFTED_FORCE") {            
1218 <              esm = SHIFTED_FORCE;
1219 <            } else {
1220 <              if (myMethod == "REACTION_FIELD") {
1221 <                esm = REACTION_FIELD;
1222 <                dielectric = simParams_->getDielectric();
1223 <                if (!simParams_->haveDielectric()) {
1224 <                  // throw warning
1225 <                  sprintf( painCave.errMsg,
1226 <                           "SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
1227 <                           "\tA default value of %f will be used for the dielectric.\n", dielectric);
1228 <                  painCave.isFatal = 0;
1229 <                  simError();
1230 <                }
1231 <              } else {
1232 <                // throw error        
1233 <                sprintf( painCave.errMsg,
1234 <                         "SimInfo error: Unknown electrostaticSummationMethod.\n"
1235 <                         "\t(Input file specified %s .)\n"
1236 <                         "\telectrostaticSummationMethod must be one of: \"none\",\n"
1237 <                         "\t\"shifted_potential\", \"shifted_force\", or \n"
1238 <                         "\t\"reaction_field\".\n", myMethod.c_str() );
1239 <                painCave.isFatal = 1;
1240 <                simError();
1241 <              }    
1242 <            }          
1243 <          }
1244 <        }
1245 <      }
1246 <    }
1247 <    
1248 <    if (simParams_->haveElectrostaticScreeningMethod()) {
1249 <      std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1250 <      toUpper(myScreen);
1251 <      if (myScreen == "UNDAMPED") {
1252 <        sm = UNDAMPED;
1253 <      } else {
1254 <        if (myScreen == "DAMPED") {
1255 <          sm = DAMPED;
1256 <          if (!simParams_->haveDampingAlpha()) {
1257 <            // first set a cutoff dependent alpha value
1258 <            // we assume alpha depends linearly with rcut from 0 to 20.5 ang
1259 <            alphaVal = 0.5125 - rcut_* 0.025;
1260 <            // for values rcut > 20.5, alpha is zero
1261 <            if (alphaVal < 0) alphaVal = 0;
1262 <
1263 <            // throw warning
1264 <            sprintf( painCave.errMsg,
1265 <                     "SimInfo warning: dampingAlpha was not specified in the input file.\n"
1266 <                     "\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1267 <            painCave.isFatal = 0;
1268 <            simError();
1269 <          } else {
1270 <            alphaVal = simParams_->getDampingAlpha();
1271 <          }
1272 <          
1273 <        } else {
1274 <          // throw error        
1275 <          sprintf( painCave.errMsg,
1276 <                   "SimInfo error: Unknown electrostaticScreeningMethod.\n"
1277 <                   "\t(Input file specified %s .)\n"
1278 <                   "\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1279 <                   "or \"damped\".\n", myScreen.c_str() );
1280 <          painCave.isFatal = 1;
1281 <          simError();
1282 <        }
1283 <      }
1284 <    }
1285 <    
1286 <    // let's pass some summation method variables to fortran
1287 <    setElectrostaticSummationMethod( &esm );
1288 <    setFortranElectrostaticMethod( &esm );
1289 <    setScreeningMethod( &sm );
1290 <    setDampingAlpha( &alphaVal );
1291 <    setReactionFieldDielectric( &dielectric );
1292 <    initFortranFF( &errorOut );
1293 <  }
1294 <
1295 <  void SimInfo::setupSwitchingFunction() {    
1296 <    int ft = CUBIC;
1297 <
1298 <    if (simParams_->haveSwitchingFunctionType()) {
1299 <      std::string funcType = simParams_->getSwitchingFunctionType();
997 >    if (simParams_->haveSwitchingFunctionType()) {
998 >      string funcType = simParams_->getSwitchingFunctionType();
999        toUpper(funcType);
1000        if (funcType == "CUBIC") {
1001          ft = CUBIC;
# Line 1323 | Line 1022 | namespace OpenMD {
1022      // we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1023      if ( simParams_->haveAccumulateBoxDipole() )
1024        if ( simParams_->getAccumulateBoxDipole() ) {
1326 –        setAccumulateBoxDipole();
1025          calcBoxDipole_ = true;
1026        }
1027  
# Line 1333 | Line 1031 | namespace OpenMD {
1031      properties_.addProperty(genData);  
1032    }
1033  
1034 <  void SimInfo::removeProperty(const std::string& propName) {
1034 >  void SimInfo::removeProperty(const string& propName) {
1035      properties_.removeProperty(propName);  
1036    }
1037  
# Line 1341 | Line 1039 | namespace OpenMD {
1039      properties_.clearProperties();
1040    }
1041  
1042 <  std::vector<std::string> SimInfo::getPropertyNames() {
1042 >  vector<string> SimInfo::getPropertyNames() {
1043      return properties_.getPropertyNames();  
1044    }
1045        
1046 <  std::vector<GenericData*> SimInfo::getProperties() {
1046 >  vector<GenericData*> SimInfo::getProperties() {
1047      return properties_.getProperties();
1048    }
1049  
1050 <  GenericData* SimInfo::getPropertyByName(const std::string& propName) {
1050 >  GenericData* SimInfo::getPropertyByName(const string& propName) {
1051      return properties_.getPropertyByName(propName);
1052    }
1053  
# Line 1432 | Line 1130 | namespace OpenMD {
1130  
1131    }        
1132  
1133 <  std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1133 >  ostream& operator <<(ostream& o, SimInfo& info) {
1134  
1135      return o;
1136    }
# Line 1475 | Line 1173 | namespace OpenMD {
1173  
1174  
1175         [  Ixx -Ixy  -Ixz ]
1176 <  J =| -Iyx  Iyy  -Iyz |
1176 >    J =| -Iyx  Iyy  -Iyz |
1177         [ -Izx -Iyz   Izz ]
1178      */
1179  
# Line 1582 | Line 1280 | namespace OpenMD {
1280      return IOIndexToIntegrableObject.at(index);
1281    }
1282    
1283 <  void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1283 >  void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1284      IOIndexToIntegrableObject= v;
1285    }
1286  
# Line 1624 | Line 1322 | namespace OpenMD {
1322      return;
1323    }
1324   /*
1325 <   void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1325 >   void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1326        assert( v.size() == nAtoms_ + nRigidBodies_);
1327        sdByGlobalIndex_ = v;
1328      }
# Line 1634 | Line 1332 | namespace OpenMD {
1332        return sdByGlobalIndex_.at(index);
1333      }  
1334   */  
1335 +  int SimInfo::getNGlobalConstraints() {
1336 +    int nGlobalConstraints;
1337 + #ifdef IS_MPI
1338 +    MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1339 +                  MPI_COMM_WORLD);    
1340 + #else
1341 +    nGlobalConstraints =  nConstraints_;
1342 + #endif
1343 +    return nGlobalConstraints;
1344 +  }
1345 +
1346   }//end namespace OpenMD
1347  

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