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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 1503 by gezelter, Sat Oct 2 19:54:41 2010 UTC vs.
Revision 1549 by gezelter, Wed Apr 27 18:38:15 2011 UTC

# Line 54 | Line 54
54   #include "math/Vector3.hpp"
55   #include "primitives/Molecule.hpp"
56   #include "primitives/StuntDouble.hpp"
57 – #include "UseTheForce/fCutoffPolicy.h"
58 – #include "UseTheForce/DarkSide/fSwitchingFunctionType.h"
59 – #include "UseTheForce/doForces_interface.h"
57   #include "UseTheForce/DarkSide/neighborLists_interface.h"
58 < #include "UseTheForce/DarkSide/switcheroo_interface.h"
58 > #include "UseTheForce/doForces_interface.h"
59   #include "utils/MemoryUtils.hpp"
60   #include "utils/simError.h"
61   #include "selection/SelectionManager.hpp"
62   #include "io/ForceFieldOptions.hpp"
63   #include "UseTheForce/ForceField.hpp"
64 + #include "nonbonded/SwitchingFunction.hpp"
65  
68 –
66   #ifdef IS_MPI
67   #include "UseTheForce/mpiComponentPlan.h"
68   #include "UseTheForce/DarkSide/simParallel_interface.h"
69   #endif
70  
71 + using namespace std;
72   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 –  }
73    
74    SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
75      forceField_(ff), simParams_(simParams),
# Line 90 | Line 79 | namespace OpenMD {
79      nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
80      nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
81      nConstraints_(0), sman_(NULL), fortranInitialized_(false),
82 <    calcBoxDipole_(false), useAtomicVirial_(true) {
83 <
84 <
85 <      MoleculeStamp* molStamp;
86 <      int nMolWithSameStamp;
87 <      int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
88 <      int nGroups = 0;      //total cutoff groups defined in meta-data file
89 <      CutoffGroupStamp* cgStamp;    
90 <      RigidBodyStamp* rbStamp;
91 <      int nRigidAtoms = 0;
92 <
93 <      std::vector<Component*> components = simParams->getComponents();
82 >    calcBoxDipole_(false), useAtomicVirial_(true) {    
83 >    
84 >    MoleculeStamp* molStamp;
85 >    int nMolWithSameStamp;
86 >    int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
87 >    int nGroups = 0;       //total cutoff groups defined in meta-data file
88 >    CutoffGroupStamp* cgStamp;    
89 >    RigidBodyStamp* rbStamp;
90 >    int nRigidAtoms = 0;
91 >    
92 >    vector<Component*> components = simParams->getComponents();
93 >    
94 >    for (vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
95 >      molStamp = (*i)->getMoleculeStamp();
96 >      nMolWithSameStamp = (*i)->getNMol();
97        
98 <      for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
99 <        molStamp = (*i)->getMoleculeStamp();
100 <        nMolWithSameStamp = (*i)->getNMol();
101 <        
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();
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 <        
98 >      addMoleculeStamp(molStamp, nMolWithSameStamp);
99 >      
100 >      //calculate atoms in molecules
101 >      nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;  
102 >      
103 >      //calculate atoms in cutoff groups
104 >      int nAtomsInGroups = 0;
105 >      int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
106 >      
107 >      for (int j=0; j < nCutoffGroupsInStamp; j++) {
108 >        cgStamp = molStamp->getCutoffGroupStamp(j);
109 >        nAtomsInGroups += cgStamp->getNMembers();
110        }
111 <
112 <      //every free atom (atom does not belong to cutoff groups) is a cutoff
113 <      //group therefore the total number of cutoff groups in the system is
114 <      //equal to the total number of atoms minus number of atoms belong to
115 <      //cutoff group defined in meta-data file plus the number of cutoff
116 <      //groups defined in meta-data file
117 <      nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
118 <
119 <      //every free atom (atom does not belong to rigid bodies) is an
120 <      //integrable object therefore the total number of integrable objects
121 <      //in the system is equal to the total number of atoms minus number of
122 <      //atoms belong to rigid body defined in meta-data file plus the number
123 <      //of rigid bodies defined in meta-data file
124 <      nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
125 <                                                + nGlobalRigidBodies_;
126 <  
127 <      nGlobalMols_ = molStampIds_.size();
158 <      molToProcMap_.resize(nGlobalMols_);
111 >      
112 >      nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
113 >      
114 >      nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;            
115 >      
116 >      //calculate atoms in rigid bodies
117 >      int nAtomsInRigidBodies = 0;
118 >      int nRigidBodiesInStamp = molStamp->getNRigidBodies();
119 >      
120 >      for (int j=0; j < nRigidBodiesInStamp; j++) {
121 >        rbStamp = molStamp->getRigidBodyStamp(j);
122 >        nAtomsInRigidBodies += rbStamp->getNMembers();
123 >      }
124 >      
125 >      nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
126 >      nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;            
127 >      
128      }
129 +    
130 +    //every free atom (atom does not belong to cutoff groups) is a cutoff
131 +    //group therefore the total number of cutoff groups in the system is
132 +    //equal to the total number of atoms minus number of atoms belong to
133 +    //cutoff group defined in meta-data file plus the number of cutoff
134 +    //groups defined in meta-data file
135 +    std::cerr << "nGA = " << nGlobalAtoms_ << "\n";
136 +    std::cerr << "nCA = " << nCutoffAtoms << "\n";
137 +    std::cerr << "nG = " << nGroups << "\n";
138  
139 +    nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
140 +
141 +    std::cerr << "nGCG = " << nGlobalCutoffGroups_ << "\n";
142 +    
143 +    //every free atom (atom does not belong to rigid bodies) is an
144 +    //integrable object therefore the total number of integrable objects
145 +    //in the system is equal to the total number of atoms minus number of
146 +    //atoms belong to rigid body defined in meta-data file plus the number
147 +    //of rigid bodies defined in meta-data file
148 +    nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
149 +      + nGlobalRigidBodies_;
150 +    
151 +    nGlobalMols_ = molStampIds_.size();
152 +    molToProcMap_.resize(nGlobalMols_);
153 +  }
154 +  
155    SimInfo::~SimInfo() {
156 <    std::map<int, Molecule*>::iterator i;
156 >    map<int, Molecule*>::iterator i;
157      for (i = molecules_.begin(); i != molecules_.end(); ++i) {
158        delete i->second;
159      }
# Line 170 | Line 164 | namespace OpenMD {
164      delete forceField_;
165    }
166  
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 –  }
167  
168    bool SimInfo::addMolecule(Molecule* mol) {
169      MoleculeIterator i;
170 <
170 >    
171      i = molecules_.find(mol->getGlobalIndex());
172      if (i == molecules_.end() ) {
173 <
174 <      molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
175 <        
173 >      
174 >      molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
175 >      
176        nAtoms_ += mol->getNAtoms();
177        nBonds_ += mol->getNBonds();
178        nBends_ += mol->getNBends();
# Line 198 | Line 182 | namespace OpenMD {
182        nIntegrableObjects_ += mol->getNIntegrableObjects();
183        nCutoffGroups_ += mol->getNCutoffGroups();
184        nConstraints_ += mol->getNConstraintPairs();
185 <
185 >      
186        addInteractionPairs(mol);
187 <  
187 >      
188        return true;
189      } else {
190        return false;
191      }
192    }
193 <
193 >  
194    bool SimInfo::removeMolecule(Molecule* mol) {
195      MoleculeIterator i;
196      i = molecules_.find(mol->getGlobalIndex());
# Line 234 | Line 218 | namespace OpenMD {
218      } else {
219        return false;
220      }
237 –
238 –
221    }    
222  
223          
# Line 253 | Line 235 | namespace OpenMD {
235    void SimInfo::calcNdf() {
236      int ndf_local;
237      MoleculeIterator i;
238 <    std::vector<StuntDouble*>::iterator j;
238 >    vector<StuntDouble*>::iterator j;
239      Molecule* mol;
240      StuntDouble* integrableObject;
241  
# Line 304 | Line 286 | namespace OpenMD {
286      int ndfRaw_local;
287  
288      MoleculeIterator i;
289 <    std::vector<StuntDouble*>::iterator j;
289 >    vector<StuntDouble*>::iterator j;
290      Molecule* mol;
291      StuntDouble* integrableObject;
292  
# Line 353 | Line 335 | namespace OpenMD {
335  
336    void SimInfo::addInteractionPairs(Molecule* mol) {
337      ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
338 <    std::vector<Bond*>::iterator bondIter;
339 <    std::vector<Bend*>::iterator bendIter;
340 <    std::vector<Torsion*>::iterator torsionIter;
341 <    std::vector<Inversion*>::iterator inversionIter;
338 >    vector<Bond*>::iterator bondIter;
339 >    vector<Bend*>::iterator bendIter;
340 >    vector<Torsion*>::iterator torsionIter;
341 >    vector<Inversion*>::iterator inversionIter;
342      Bond* bond;
343      Bend* bend;
344      Torsion* torsion;
# Line 374 | Line 356 | namespace OpenMD {
356      // always be excluded.  These are done at the bottom of this
357      // function.
358  
359 <    std::map<int, std::set<int> > atomGroups;
359 >    map<int, set<int> > atomGroups;
360      Molecule::RigidBodyIterator rbIter;
361      RigidBody* rb;
362      Molecule::IntegrableObjectIterator ii;
# Line 386 | Line 368 | namespace OpenMD {
368        
369        if (integrableObject->isRigidBody()) {
370          rb = static_cast<RigidBody*>(integrableObject);
371 <        std::vector<Atom*> atoms = rb->getAtoms();
372 <        std::set<int> rigidAtoms;
371 >        vector<Atom*> atoms = rb->getAtoms();
372 >        set<int> rigidAtoms;
373          for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
374            rigidAtoms.insert(atoms[i]->getGlobalIndex());
375          }
376          for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
377 <          atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
377 >          atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
378          }      
379        } else {
380 <        std::set<int> oneAtomSet;
380 >        set<int> oneAtomSet;
381          oneAtomSet.insert(integrableObject->getGlobalIndex());
382 <        atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));        
382 >        atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));        
383        }
384      }  
385            
# Line 500 | Line 482 | namespace OpenMD {
482  
483      for (rb = mol->beginRigidBody(rbIter); rb != NULL;
484           rb = mol->nextRigidBody(rbIter)) {
485 <      std::vector<Atom*> atoms = rb->getAtoms();
485 >      vector<Atom*> atoms = rb->getAtoms();
486        for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
487          for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
488            a = atoms[i]->getGlobalIndex();
# Line 514 | Line 496 | namespace OpenMD {
496  
497    void SimInfo::removeInteractionPairs(Molecule* mol) {
498      ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
499 <    std::vector<Bond*>::iterator bondIter;
500 <    std::vector<Bend*>::iterator bendIter;
501 <    std::vector<Torsion*>::iterator torsionIter;
502 <    std::vector<Inversion*>::iterator inversionIter;
499 >    vector<Bond*>::iterator bondIter;
500 >    vector<Bend*>::iterator bendIter;
501 >    vector<Torsion*>::iterator torsionIter;
502 >    vector<Inversion*>::iterator inversionIter;
503      Bond* bond;
504      Bend* bend;
505      Torsion* torsion;
# Line 527 | Line 509 | namespace OpenMD {
509      int c;
510      int d;
511  
512 <    std::map<int, std::set<int> > atomGroups;
512 >    map<int, set<int> > atomGroups;
513      Molecule::RigidBodyIterator rbIter;
514      RigidBody* rb;
515      Molecule::IntegrableObjectIterator ii;
# Line 539 | Line 521 | namespace OpenMD {
521        
522        if (integrableObject->isRigidBody()) {
523          rb = static_cast<RigidBody*>(integrableObject);
524 <        std::vector<Atom*> atoms = rb->getAtoms();
525 <        std::set<int> rigidAtoms;
524 >        vector<Atom*> atoms = rb->getAtoms();
525 >        set<int> rigidAtoms;
526          for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
527            rigidAtoms.insert(atoms[i]->getGlobalIndex());
528          }
529          for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
530 <          atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
530 >          atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
531          }      
532        } else {
533 <        std::set<int> oneAtomSet;
533 >        set<int> oneAtomSet;
534          oneAtomSet.insert(integrableObject->getGlobalIndex());
535 <        atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));        
535 >        atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));        
536        }
537      }  
538  
# Line 653 | Line 635 | namespace OpenMD {
635  
636      for (rb = mol->beginRigidBody(rbIter); rb != NULL;
637           rb = mol->nextRigidBody(rbIter)) {
638 <      std::vector<Atom*> atoms = rb->getAtoms();
638 >      vector<Atom*> atoms = rb->getAtoms();
639        for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
640          for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
641            a = atoms[i]->getGlobalIndex();
# Line 676 | Line 658 | namespace OpenMD {
658      molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
659    }
660  
679 –  void SimInfo::update() {
661  
662 <    setupSimType();
663 <
664 < #ifdef IS_MPI
665 <    setupFortranParallel();
666 < #endif
667 <
668 <    setupFortranSim();
669 <
670 <    //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 <
662 >  /**
663 >   * update
664 >   *
665 >   *  Performs the global checks and variable settings after the
666 >   *  objects have been created.
667 >   *
668 >   */
669 >  void SimInfo::update() {  
670 >    setupSimVariables();
671      calcNdf();
672      calcNdfRaw();
673      calcNdfTrans();
709 –
710 –    fortranInitialized_ = true;
674    }
675 <
676 <  std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
675 >  
676 >  /**
677 >   * getSimulatedAtomTypes
678 >   *
679 >   * Returns an STL set of AtomType* that are actually present in this
680 >   * simulation.  Must query all processors to assemble this information.
681 >   *
682 >   */
683 >  set<AtomType*> SimInfo::getSimulatedAtomTypes() {
684      SimInfo::MoleculeIterator mi;
685      Molecule* mol;
686      Molecule::AtomIterator ai;
687      Atom* atom;
688 <    std::set<AtomType*> atomTypes;
689 <
690 <    for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
721 <
688 >    set<AtomType*> atomTypes;
689 >    
690 >    for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {      
691        for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
692          atomTypes.insert(atom->getAtomType());
693 <      }
694 <        
726 <    }
693 >      }      
694 >    }    
695  
696 <    return atomTypes;        
729 <  }
696 > #ifdef IS_MPI
697  
698 <  void SimInfo::setupSimType() {
699 <    std::set<AtomType*>::iterator i;
733 <    std::set<AtomType*> atomTypes;
734 <    atomTypes = getUniqueAtomTypes();
735 <    
736 <    int useLennardJones = 0;
737 <    int useElectrostatic = 0;
738 <    int useEAM = 0;
739 <    int useSC = 0;
740 <    int useCharge = 0;
741 <    int useDirectional = 0;
742 <    int useDipole = 0;
743 <    int useGayBerne = 0;
744 <    int useSticky = 0;
745 <    int useStickyPower = 0;
746 <    int useShape = 0;
747 <    int useFLARB = 0; //it is not in AtomType yet
748 <    int useDirectionalAtom = 0;    
749 <    int useElectrostatics = 0;
750 <    //usePBC and useRF are from simParams
751 <    int usePBC = simParams_->getUsePeriodicBoundaryConditions();
752 <    int useRF;
753 <    int useSF;
754 <    int useSP;
755 <    int useBoxDipole;
698 >    // loop over the found atom types on this processor, and add their
699 >    // numerical idents to a vector:
700  
701 <    std::string myMethod;
701 >    vector<int> foundTypes;
702 >    set<AtomType*>::iterator i;
703 >    for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
704 >      foundTypes.push_back( (*i)->getIdent() );
705  
706 <    // set the useRF logical
707 <    useRF = 0;
761 <    useSF = 0;
762 <    useSP = 0;
763 <    useBoxDipole = 0;
706 >    // count_local holds the number of found types on this processor
707 >    int count_local = foundTypes.size();
708  
709 +    // count holds the total number of found types on all processors
710 +    // (some will be redundant with the ones found locally):
711 +    int count;
712 +    MPI::COMM_WORLD.Allreduce(&count_local, &count, 1, MPI::INT, MPI::SUM);
713  
714 <    if (simParams_->haveElectrostaticSummationMethod()) {
715 <      std::string myMethod = simParams_->getElectrostaticSummationMethod();
716 <      toUpper(myMethod);
717 <      if (myMethod == "REACTION_FIELD"){
718 <        useRF = 1;
719 <      } else if (myMethod == "SHIFTED_FORCE"){
720 <        useSF = 1;
721 <      } else if (myMethod == "SHIFTED_POTENTIAL"){
722 <        useSP = 1;
723 <      }
724 <    }
714 >    // create a vector to hold the globally found types, and resize it:
715 >    vector<int> ftGlobal;
716 >    ftGlobal.resize(count);
717 >    vector<int> counts;
718 >
719 >    int nproc = MPI::COMM_WORLD.Get_size();
720 >    counts.resize(nproc);
721 >    vector<int> disps;
722 >    disps.resize(nproc);
723 >
724 >    // now spray out the foundTypes to all the other processors:
725      
726 <    if (simParams_->haveAccumulateBoxDipole())
727 <      if (simParams_->getAccumulateBoxDipole())
780 <        useBoxDipole = 1;
726 >    MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
727 >                               &ftGlobal[0], &counts[0], &disps[0], MPI::INT);
728  
729 +    // foundIdents is a stl set, so inserting an already found ident
730 +    // will have no effect.
731 +    set<int> foundIdents;
732 +    vector<int>::iterator j;
733 +    for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
734 +      foundIdents.insert((*j));
735 +    
736 +    // now iterate over the foundIdents and get the actual atom types
737 +    // that correspond to these:
738 +    set<int>::iterator it;
739 +    for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
740 +      atomTypes.insert( forceField_->getAtomType((*it)) );
741 +
742 + #endif
743 +    
744 +    return atomTypes;        
745 +  }
746 +
747 +  void SimInfo::setupSimVariables() {
748      useAtomicVirial_ = simParams_->getUseAtomicVirial();
749 +    // we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
750 +    calcBoxDipole_ = false;
751 +    if ( simParams_->haveAccumulateBoxDipole() )
752 +      if ( simParams_->getAccumulateBoxDipole() ) {
753 +        calcBoxDipole_ = true;      
754 +      }
755  
756 +    set<AtomType*>::iterator i;
757 +    set<AtomType*> atomTypes;
758 +    atomTypes = getSimulatedAtomTypes();    
759 +    int usesElectrostatic = 0;
760 +    int usesMetallic = 0;
761 +    int usesDirectional = 0;
762      //loop over all of the atom types
763      for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
764 <      useLennardJones |= (*i)->isLennardJones();
765 <      useElectrostatic |= (*i)->isElectrostatic();
766 <      useEAM |= (*i)->isEAM();
789 <      useSC |= (*i)->isSC();
790 <      useCharge |= (*i)->isCharge();
791 <      useDirectional |= (*i)->isDirectional();
792 <      useDipole |= (*i)->isDipole();
793 <      useGayBerne |= (*i)->isGayBerne();
794 <      useSticky |= (*i)->isSticky();
795 <      useStickyPower |= (*i)->isStickyPower();
796 <      useShape |= (*i)->isShape();
764 >      usesElectrostatic |= (*i)->isElectrostatic();
765 >      usesMetallic |= (*i)->isMetal();
766 >      usesDirectional |= (*i)->isDirectional();
767      }
768  
799 –    if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
800 –      useDirectionalAtom = 1;
801 –    }
802 –
803 –    if (useCharge || useDipole) {
804 –      useElectrostatics = 1;
805 –    }
806 –
769   #ifdef IS_MPI    
770      int temp;
771 +    temp = usesDirectional;
772 +    MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
773  
774 <    temp = usePBC;
775 <    MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
774 >    temp = usesMetallic;
775 >    MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
776  
777 <    temp = useDirectionalAtom;
778 <    MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
777 >    temp = usesElectrostatic;
778 >    MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
779 > #endif
780 >    fInfo_.SIM_uses_PBC = usesPeriodicBoundaries_;    
781 >    fInfo_.SIM_uses_DirectionalAtoms = usesDirectionalAtoms_;
782 >    fInfo_.SIM_uses_MetallicAtoms = usesMetallicAtoms_;
783 >    fInfo_.SIM_requires_SkipCorrection = usesElectrostaticAtoms_;
784 >    fInfo_.SIM_requires_SelfCorrection = usesElectrostaticAtoms_;
785 >    fInfo_.SIM_uses_AtomicVirial = usesAtomicVirial_;
786 >  }
787  
816 –    temp = useLennardJones;
817 –    MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
788  
789 <    temp = useElectrostatics;
790 <    MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
789 >  vector<int> SimInfo::getGlobalAtomIndices() {
790 >    SimInfo::MoleculeIterator mi;
791 >    Molecule* mol;
792 >    Molecule::AtomIterator ai;
793 >    Atom* atom;
794  
795 <    temp = useCharge;
796 <    MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
795 >    vector<int> GlobalAtomIndices(getNAtoms(), 0);
796 >    
797 >    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
798 >      
799 >      for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
800 >        GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
801 >      }
802 >    }
803 >    return GlobalAtomIndices;
804 >  }
805  
825 –    temp = useDipole;
826 –    MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
806  
807 <    temp = useSticky;
808 <    MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
809 <
810 <    temp = useStickyPower;
811 <    MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
833 <    
834 <    temp = useGayBerne;
835 <    MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
807 >  vector<int> SimInfo::getGlobalGroupIndices() {
808 >    SimInfo::MoleculeIterator mi;
809 >    Molecule* mol;
810 >    Molecule::CutoffGroupIterator ci;
811 >    CutoffGroup* cg;
812  
813 <    temp = useEAM;
838 <    MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
839 <
840 <    temp = useSC;
841 <    MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
813 >    vector<int> GlobalGroupIndices;
814      
815 <    temp = useShape;
816 <    MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);  
817 <
818 <    temp = useFLARB;
819 <    MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
820 <
821 <    temp = useRF;
822 <    MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
823 <
824 <    temp = useSF;
853 <    MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);  
854 <
855 <    temp = useSP;
856 <    MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
857 <
858 <    temp = useBoxDipole;
859 <    MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
860 <
861 <    temp = useAtomicVirial_;
862 <    MPI_Allreduce(&temp, &useAtomicVirial_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
863 <
864 < #endif
865 <
866 <    fInfo_.SIM_uses_PBC = usePBC;    
867 <    fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
868 <    fInfo_.SIM_uses_LennardJones = useLennardJones;
869 <    fInfo_.SIM_uses_Electrostatics = useElectrostatics;    
870 <    fInfo_.SIM_uses_Charges = useCharge;
871 <    fInfo_.SIM_uses_Dipoles = useDipole;
872 <    fInfo_.SIM_uses_Sticky = useSticky;
873 <    fInfo_.SIM_uses_StickyPower = useStickyPower;
874 <    fInfo_.SIM_uses_GayBerne = useGayBerne;
875 <    fInfo_.SIM_uses_EAM = useEAM;
876 <    fInfo_.SIM_uses_SC = useSC;
877 <    fInfo_.SIM_uses_Shapes = useShape;
878 <    fInfo_.SIM_uses_FLARB = useFLARB;
879 <    fInfo_.SIM_uses_RF = useRF;
880 <    fInfo_.SIM_uses_SF = useSF;
881 <    fInfo_.SIM_uses_SP = useSP;
882 <    fInfo_.SIM_uses_BoxDipole = useBoxDipole;
883 <    fInfo_.SIM_uses_AtomicVirial = useAtomicVirial_;
815 >    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
816 >      
817 >      //local index of cutoff group is trivial, it only depends on the
818 >      //order of travesing
819 >      for (cg = mol->beginCutoffGroup(ci); cg != NULL;
820 >           cg = mol->nextCutoffGroup(ci)) {
821 >        GlobalGroupIndices.push_back(cg->getGlobalIndex());
822 >      }        
823 >    }
824 >    return GlobalGroupIndices;
825    }
826  
827 <  void SimInfo::setupFortranSim() {
827 >
828 >  void SimInfo::setupFortran() {
829      int isError;
830      int nExclude, nOneTwo, nOneThree, nOneFour;
831 <    std::vector<int> fortranGlobalGroupMembership;
831 >    vector<int> fortranGlobalGroupMembership;
832      
833      isError = 0;
834  
# Line 896 | Line 838 | namespace OpenMD {
838      }
839  
840      //calculate mass ratio of cutoff group
841 <    std::vector<RealType> mfact;
841 >    vector<RealType> mfact;
842      SimInfo::MoleculeIterator mi;
843      Molecule* mol;
844      Molecule::CutoffGroupIterator ci;
# Line 922 | Line 864 | namespace OpenMD {
864        }      
865      }
866  
867 <    //fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
926 <    std::vector<int> identArray;
867 >    // Build the identArray_
868  
869 <    //to avoid memory reallocation, reserve enough space identArray
870 <    identArray.reserve(getNAtoms());
930 <    
869 >    identArray_.clear();
870 >    identArray_.reserve(getNAtoms());    
871      for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {        
872        for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
873 <        identArray.push_back(atom->getIdent());
873 >        identArray_.push_back(atom->getIdent());
874        }
875      }    
876  
877      //fill molMembershipArray
878      //molMembershipArray is filled by SimCreator    
879 <    std::vector<int> molMembershipArray(nGlobalAtoms_);
879 >    vector<int> molMembershipArray(nGlobalAtoms_);
880      for (int i = 0; i < nGlobalAtoms_; i++) {
881        molMembershipArray[i] = globalMolMembership_[i] + 1;
882      }
# Line 953 | Line 893 | namespace OpenMD {
893      int* oneThreeList = oneThreeInteractions_.getPairList();
894      int* oneFourList = oneFourInteractions_.getPairList();
895  
896 <    setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
896 >    setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray_[0],
897                     &nExclude, excludeList,
898                     &nOneTwo, oneTwoList,
899                     &nOneThree, oneThreeList,
# Line 982 | Line 922 | namespace OpenMD {
922        setNeighbors(&nlistNeighbors);
923      }
924    
985 –
986 –  }
987 –
988 –
989 –  void SimInfo::setupFortranParallel() {
925   #ifdef IS_MPI    
991 –    //SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
992 –    std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
993 –    std::vector<int> localToGlobalCutoffGroupIndex;
994 –    SimInfo::MoleculeIterator mi;
995 –    Molecule::AtomIterator ai;
996 –    Molecule::CutoffGroupIterator ci;
997 –    Molecule* mol;
998 –    Atom* atom;
999 –    CutoffGroup* cg;
926      mpiSimData parallelData;
1001 –    int isError;
927  
1003 –    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
1004 –
1005 –      //local index(index in DataStorge) of atom is important
1006 –      for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
1007 –        localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
1008 –      }
1009 –
1010 –      //local index of cutoff group is trivial, it only depends on the order of travesing
1011 –      for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
1012 –        localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
1013 –      }        
1014 –        
1015 –    }
1016 –
928      //fill up mpiSimData struct
929      parallelData.nMolGlobal = getNGlobalMolecules();
930      parallelData.nMolLocal = getNMolecules();
# Line 1025 | Line 936 | namespace OpenMD {
936      MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
937  
938      //pass mpiSimData struct and index arrays to fortran
939 <    setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
940 <                    &localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
941 <                    &localToGlobalCutoffGroupIndex[0], &isError);
939 >    //setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
940 >    //                &localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
941 >    //                &localToGlobalCutoffGroupIndex[0], &isError);
942  
943      if (isError) {
944        sprintf(painCave.errMsg,
# Line 1038 | Line 949 | namespace OpenMD {
949  
950      sprintf(checkPointMsg, " mpiRefresh successful.\n");
951      errorCheckPoint();
1041 –
952   #endif
1043 –  }
953  
954 <  void SimInfo::setupCutoff() {          
955 <    
956 <    ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
957 <
958 <    // Check the cutoff policy
959 <    int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
1051 <
1052 <    // Set LJ shifting bools to false
1053 <    ljsp_ = 0;
1054 <    ljsf_ = 0;
1055 <
1056 <    std::string myPolicy;
1057 <    if (forceFieldOptions_.haveCutoffPolicy()){
1058 <      myPolicy = forceFieldOptions_.getCutoffPolicy();
1059 <    }else if (simParams_->haveCutoffPolicy()) {
1060 <      myPolicy = simParams_->getCutoffPolicy();
954 >    initFortranFF(&isError);
955 >    if (isError) {
956 >      sprintf(painCave.errMsg,
957 >              "initFortranFF errror: fortran didn't like something we gave it.\n");
958 >      painCave.isFatal = 1;
959 >      simError();
960      }
961 <
1063 <    if (!myPolicy.empty()){
1064 <      toUpper(myPolicy);
1065 <      if (myPolicy == "MIX") {
1066 <        cp = MIX_CUTOFF_POLICY;
1067 <      } else {
1068 <        if (myPolicy == "MAX") {
1069 <          cp = MAX_CUTOFF_POLICY;
1070 <        } else {
1071 <          if (myPolicy == "TRADITIONAL") {            
1072 <            cp = TRADITIONAL_CUTOFF_POLICY;
1073 <          } else {
1074 <            // throw error        
1075 <            sprintf( painCave.errMsg,
1076 <                     "SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
1077 <            painCave.isFatal = 1;
1078 <            simError();
1079 <          }    
1080 <        }          
1081 <      }
1082 <    }          
1083 <    notifyFortranCutoffPolicy(&cp);
1084 <
1085 <    // Check the Skin Thickness for neighborlists
1086 <    RealType skin;
1087 <    if (simParams_->haveSkinThickness()) {
1088 <      skin = simParams_->getSkinThickness();
1089 <      notifyFortranSkinThickness(&skin);
1090 <    }            
1091 <        
1092 <    // Check if the cutoff was set explicitly:
1093 <    if (simParams_->haveCutoffRadius()) {
1094 <      rcut_ = simParams_->getCutoffRadius();
1095 <      if (simParams_->haveSwitchingRadius()) {
1096 <        rsw_  = simParams_->getSwitchingRadius();
1097 <      } else {
1098 <        if (fInfo_.SIM_uses_Charges |
1099 <            fInfo_.SIM_uses_Dipoles |
1100 <            fInfo_.SIM_uses_RF) {
1101 <          
1102 <          rsw_ = 0.85 * rcut_;
1103 <          sprintf(painCave.errMsg,
1104 <                  "SimCreator Warning: No value was set for the switchingRadius.\n"
1105 <                  "\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
1106 <                  "\tswitchingRadius = %f. for this simulation\n", rsw_);
1107 <        painCave.isFatal = 0;
1108 <        simError();
1109 <        } else {
1110 <          rsw_ = rcut_;
1111 <          sprintf(painCave.errMsg,
1112 <                  "SimCreator Warning: No value was set for the switchingRadius.\n"
1113 <                  "\tOpenMD will use the same value as the cutoffRadius.\n"
1114 <                  "\tswitchingRadius = %f. for this simulation\n", rsw_);
1115 <          painCave.isFatal = 0;
1116 <          simError();
1117 <        }
1118 <      }
1119 <
1120 <      if (simParams_->haveElectrostaticSummationMethod()) {
1121 <        std::string myMethod = simParams_->getElectrostaticSummationMethod();
1122 <        toUpper(myMethod);
1123 <        
1124 <        if (myMethod == "SHIFTED_POTENTIAL") {
1125 <          ljsp_ = 1;
1126 <        } else if (myMethod == "SHIFTED_FORCE") {
1127 <          ljsf_ = 1;
1128 <        }
1129 <      }
1130 <
1131 <      notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1132 <      
1133 <    } else {
1134 <      
1135 <      // For electrostatic atoms, we'll assume a large safe value:
1136 <      if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
1137 <        sprintf(painCave.errMsg,
1138 <                "SimCreator Warning: No value was set for the cutoffRadius.\n"
1139 <                "\tOpenMD will use a default value of 15.0 angstroms"
1140 <                "\tfor the cutoffRadius.\n");
1141 <        painCave.isFatal = 0;
1142 <        simError();
1143 <        rcut_ = 15.0;
1144 <      
1145 <        if (simParams_->haveElectrostaticSummationMethod()) {
1146 <          std::string myMethod = simParams_->getElectrostaticSummationMethod();
1147 <          toUpper(myMethod);
1148 <          
1149 <          // For the time being, we're tethering the LJ shifted behavior to the
1150 <          // electrostaticSummationMethod keyword options
1151 <          if (myMethod == "SHIFTED_POTENTIAL") {
1152 <            ljsp_ = 1;
1153 <          } else if (myMethod == "SHIFTED_FORCE") {
1154 <            ljsf_ = 1;
1155 <          }
1156 <          if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1157 <            if (simParams_->haveSwitchingRadius()){
1158 <              sprintf(painCave.errMsg,
1159 <                      "SimInfo Warning: A value was set for the switchingRadius\n"
1160 <                      "\teven though the electrostaticSummationMethod was\n"
1161 <                      "\tset to %s\n", myMethod.c_str());
1162 <              painCave.isFatal = 1;
1163 <              simError();            
1164 <            }
1165 <          }
1166 <        }
1167 <      
1168 <        if (simParams_->haveSwitchingRadius()){
1169 <          rsw_ = simParams_->getSwitchingRadius();
1170 <        } else {        
1171 <          sprintf(painCave.errMsg,
1172 <                  "SimCreator Warning: No value was set for switchingRadius.\n"
1173 <                  "\tOpenMD will use a default value of\n"
1174 <                  "\t0.85 * cutoffRadius for the switchingRadius\n");
1175 <          painCave.isFatal = 0;
1176 <          simError();
1177 <          rsw_ = 0.85 * rcut_;
1178 <        }
1179 <
1180 <        Electrostatic::setElectrostaticCutoffRadius(rcut_, rsw_);
1181 <        notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1182 <
1183 <      } else {
1184 <        // We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1185 <        // We'll punt and let fortran figure out the cutoffs later.
1186 <        
1187 <        notifyFortranYouAreOnYourOwn();
1188 <
1189 <      }
1190 <    }
961 >    fortranInitialized_ = true;
962    }
963  
1193 –  void SimInfo::setupElectrostaticSummationMethod( int isError ) {    
1194 –    
1195 –    int errorOut;
1196 –    ElectrostaticSummationMethod esm = NONE;
1197 –    ElectrostaticScreeningMethod sm = UNDAMPED;
1198 –    RealType alphaVal;
1199 –    RealType dielectric;
1200 –    
1201 –    errorOut = isError;
1202 –
1203 –    if (simParams_->haveElectrostaticSummationMethod()) {
1204 –      std::string myMethod = simParams_->getElectrostaticSummationMethod();
1205 –      toUpper(myMethod);
1206 –      if (myMethod == "NONE") {
1207 –        esm = NONE;
1208 –      } else {
1209 –        if (myMethod == "SWITCHING_FUNCTION") {
1210 –          esm = SWITCHING_FUNCTION;
1211 –        } else {
1212 –          if (myMethod == "SHIFTED_POTENTIAL") {
1213 –            esm = SHIFTED_POTENTIAL;
1214 –          } else {
1215 –            if (myMethod == "SHIFTED_FORCE") {            
1216 –              esm = SHIFTED_FORCE;
1217 –            } else {
1218 –              if (myMethod == "REACTION_FIELD") {
1219 –                esm = REACTION_FIELD;
1220 –                dielectric = simParams_->getDielectric();
1221 –                if (!simParams_->haveDielectric()) {
1222 –                  // throw warning
1223 –                  sprintf( painCave.errMsg,
1224 –                           "SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
1225 –                           "\tA default value of %f will be used for the dielectric.\n", dielectric);
1226 –                  painCave.isFatal = 0;
1227 –                  simError();
1228 –                }
1229 –              } else {
1230 –                // throw error        
1231 –                sprintf( painCave.errMsg,
1232 –                         "SimInfo error: Unknown electrostaticSummationMethod.\n"
1233 –                         "\t(Input file specified %s .)\n"
1234 –                         "\telectrostaticSummationMethod must be one of: \"none\",\n"
1235 –                         "\t\"shifted_potential\", \"shifted_force\", or \n"
1236 –                         "\t\"reaction_field\".\n", myMethod.c_str() );
1237 –                painCave.isFatal = 1;
1238 –                simError();
1239 –              }    
1240 –            }          
1241 –          }
1242 –        }
1243 –      }
1244 –    }
1245 –    
1246 –    if (simParams_->haveElectrostaticScreeningMethod()) {
1247 –      std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1248 –      toUpper(myScreen);
1249 –      if (myScreen == "UNDAMPED") {
1250 –        sm = UNDAMPED;
1251 –      } else {
1252 –        if (myScreen == "DAMPED") {
1253 –          sm = DAMPED;
1254 –          if (!simParams_->haveDampingAlpha()) {
1255 –            // first set a cutoff dependent alpha value
1256 –            // we assume alpha depends linearly with rcut from 0 to 20.5 ang
1257 –            alphaVal = 0.5125 - rcut_* 0.025;
1258 –            // for values rcut > 20.5, alpha is zero
1259 –            if (alphaVal < 0) alphaVal = 0;
1260 –
1261 –            // throw warning
1262 –            sprintf( painCave.errMsg,
1263 –                     "SimInfo warning: dampingAlpha was not specified in the input file.\n"
1264 –                     "\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1265 –            painCave.isFatal = 0;
1266 –            simError();
1267 –          } else {
1268 –            alphaVal = simParams_->getDampingAlpha();
1269 –          }
1270 –          
1271 –        } else {
1272 –          // throw error        
1273 –          sprintf( painCave.errMsg,
1274 –                   "SimInfo error: Unknown electrostaticScreeningMethod.\n"
1275 –                   "\t(Input file specified %s .)\n"
1276 –                   "\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1277 –                   "or \"damped\".\n", myScreen.c_str() );
1278 –          painCave.isFatal = 1;
1279 –          simError();
1280 –        }
1281 –      }
1282 –    }
1283 –    
1284 –
1285 –    Electrostatic::setElectrostaticSummationMethod( esm );
1286 –    Electrostatic::setElectrostaticScreeningMethod( sm );
1287 –    Electrostatic::setDampingAlpha( alphaVal );
1288 –    Electrostatic::setReactionFieldDielectric( dielectric );
1289 –    initFortranFF( &errorOut );
1290 –  }
1291 –
1292 –  void SimInfo::setupSwitchingFunction() {    
1293 –    int ft = CUBIC;
1294 –
1295 –    if (simParams_->haveSwitchingFunctionType()) {
1296 –      std::string funcType = simParams_->getSwitchingFunctionType();
1297 –      toUpper(funcType);
1298 –      if (funcType == "CUBIC") {
1299 –        ft = CUBIC;
1300 –      } else {
1301 –        if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1302 –          ft = FIFTH_ORDER_POLY;
1303 –        } else {
1304 –          // throw error        
1305 –          sprintf( painCave.errMsg,
1306 –                   "SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1307 –          painCave.isFatal = 1;
1308 –          simError();
1309 –        }          
1310 –      }
1311 –    }
1312 –
1313 –    // send switching function notification to switcheroo
1314 –    setFunctionType(&ft);
1315 –
1316 –  }
1317 –
1318 –  void SimInfo::setupAccumulateBoxDipole() {    
1319 –
1320 –    // we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1321 –    if ( simParams_->haveAccumulateBoxDipole() )
1322 –      if ( simParams_->getAccumulateBoxDipole() ) {
1323 –        setAccumulateBoxDipole();
1324 –        calcBoxDipole_ = true;
1325 –      }
1326 –
1327 –  }
1328 –
964    void SimInfo::addProperty(GenericData* genData) {
965      properties_.addProperty(genData);  
966    }
967  
968 <  void SimInfo::removeProperty(const std::string& propName) {
968 >  void SimInfo::removeProperty(const string& propName) {
969      properties_.removeProperty(propName);  
970    }
971  
# Line 1338 | Line 973 | namespace OpenMD {
973      properties_.clearProperties();
974    }
975  
976 <  std::vector<std::string> SimInfo::getPropertyNames() {
976 >  vector<string> SimInfo::getPropertyNames() {
977      return properties_.getPropertyNames();  
978    }
979        
980 <  std::vector<GenericData*> SimInfo::getProperties() {
980 >  vector<GenericData*> SimInfo::getProperties() {
981      return properties_.getProperties();
982    }
983  
984 <  GenericData* SimInfo::getPropertyByName(const std::string& propName) {
984 >  GenericData* SimInfo::getPropertyByName(const string& propName) {
985      return properties_.getPropertyByName(propName);
986    }
987  
# Line 1360 | Line 995 | namespace OpenMD {
995      Molecule* mol;
996      RigidBody* rb;
997      Atom* atom;
998 +    CutoffGroup* cg;
999      SimInfo::MoleculeIterator mi;
1000      Molecule::RigidBodyIterator rbIter;
1001 <    Molecule::AtomIterator atomIter;;
1001 >    Molecule::AtomIterator atomIter;
1002 >    Molecule::CutoffGroupIterator cgIter;
1003  
1004      for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
1005          
# Line 1373 | Line 1010 | namespace OpenMD {
1010        for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1011          rb->setSnapshotManager(sman_);
1012        }
1013 +
1014 +      for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
1015 +        cg->setSnapshotManager(sman_);
1016 +      }
1017      }    
1018      
1019    }
# Line 1429 | Line 1070 | namespace OpenMD {
1070  
1071    }        
1072  
1073 <  std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1073 >  ostream& operator <<(ostream& o, SimInfo& info) {
1074  
1075      return o;
1076    }
# Line 1472 | Line 1113 | namespace OpenMD {
1113  
1114  
1115         [  Ixx -Ixy  -Ixz ]
1116 <  J =| -Iyx  Iyy  -Iyz |
1116 >    J =| -Iyx  Iyy  -Iyz |
1117         [ -Izx -Iyz   Izz ]
1118      */
1119  
# Line 1579 | Line 1220 | namespace OpenMD {
1220      return IOIndexToIntegrableObject.at(index);
1221    }
1222    
1223 <  void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1223 >  void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1224      IOIndexToIntegrableObject= v;
1225    }
1226  
# Line 1621 | Line 1262 | namespace OpenMD {
1262      return;
1263    }
1264   /*
1265 <   void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1265 >   void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1266        assert( v.size() == nAtoms_ + nRigidBodies_);
1267        sdByGlobalIndex_ = v;
1268      }
# Line 1631 | Line 1272 | namespace OpenMD {
1272        return sdByGlobalIndex_.at(index);
1273      }  
1274   */  
1275 +  int SimInfo::getNGlobalConstraints() {
1276 +    int nGlobalConstraints;
1277 + #ifdef IS_MPI
1278 +    MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1279 +                  MPI_COMM_WORLD);    
1280 + #else
1281 +    nGlobalConstraints =  nConstraints_;
1282 + #endif
1283 +    return nGlobalConstraints;
1284 +  }
1285 +
1286   }//end namespace OpenMD
1287  

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