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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 1597 by gezelter, Tue Jul 26 15:49:24 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"
60 – #include "UseTheForce/DarkSide/neighborLists_interface.h"
61 – #include "UseTheForce/DarkSide/switcheroo_interface.h"
57   #include "utils/MemoryUtils.hpp"
58   #include "utils/simError.h"
59   #include "selection/SelectionManager.hpp"
60   #include "io/ForceFieldOptions.hpp"
61   #include "UseTheForce/ForceField.hpp"
62 + #include "nonbonded/SwitchingFunction.hpp"
63  
64 <
69 < #ifdef IS_MPI
70 < #include "UseTheForce/mpiComponentPlan.h"
71 < #include "UseTheForce/DarkSide/simParallel_interface.h"
72 < #endif
73 <
64 > using namespace std;
65   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 –  }
66    
67    SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
68      forceField_(ff), simParams_(simParams),
# Line 89 | Line 71 | namespace OpenMD {
71      nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
72      nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
73      nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
74 <    nConstraints_(0), sman_(NULL), fortranInitialized_(false),
75 <    calcBoxDipole_(false), useAtomicVirial_(true) {
76 <
77 <
78 <      MoleculeStamp* molStamp;
79 <      int nMolWithSameStamp;
80 <      int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
81 <      int nGroups = 0;      //total cutoff groups defined in meta-data file
82 <      CutoffGroupStamp* cgStamp;    
83 <      RigidBodyStamp* rbStamp;
84 <      int nRigidAtoms = 0;
85 <
86 <      std::vector<Component*> components = simParams->getComponents();
74 >    nConstraints_(0), sman_(NULL), topologyDone_(false),
75 >    calcBoxDipole_(false), useAtomicVirial_(true) {    
76 >    
77 >    MoleculeStamp* molStamp;
78 >    int nMolWithSameStamp;
79 >    int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
80 >    int nGroups = 0;       //total cutoff groups defined in meta-data file
81 >    CutoffGroupStamp* cgStamp;    
82 >    RigidBodyStamp* rbStamp;
83 >    int nRigidAtoms = 0;
84 >    
85 >    vector<Component*> components = simParams->getComponents();
86 >    
87 >    for (vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
88 >      molStamp = (*i)->getMoleculeStamp();
89 >      nMolWithSameStamp = (*i)->getNMol();
90        
91 <      for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
92 <        molStamp = (*i)->getMoleculeStamp();
93 <        nMolWithSameStamp = (*i)->getNMol();
94 <        
95 <        addMoleculeStamp(molStamp, nMolWithSameStamp);
96 <
97 <        //calculate atoms in molecules
98 <        nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;  
99 <
100 <        //calculate atoms in cutoff groups
101 <        int nAtomsInGroups = 0;
102 <        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 <        
91 >      addMoleculeStamp(molStamp, nMolWithSameStamp);
92 >      
93 >      //calculate atoms in molecules
94 >      nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;  
95 >      
96 >      //calculate atoms in cutoff groups
97 >      int nAtomsInGroups = 0;
98 >      int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
99 >      
100 >      for (int j=0; j < nCutoffGroupsInStamp; j++) {
101 >        cgStamp = molStamp->getCutoffGroupStamp(j);
102 >        nAtomsInGroups += cgStamp->getNMembers();
103        }
104 <
105 <      //every free atom (atom does not belong to cutoff groups) is a cutoff
106 <      //group therefore the total number of cutoff groups in the system is
107 <      //equal to the total number of atoms minus number of atoms belong to
108 <      //cutoff group defined in meta-data file plus the number of cutoff
109 <      //groups defined in meta-data file
110 <      nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
111 <
112 <      //every free atom (atom does not belong to rigid bodies) is an
113 <      //integrable object therefore the total number of integrable objects
114 <      //in the system is equal to the total number of atoms minus number of
115 <      //atoms belong to rigid body defined in meta-data file plus the number
116 <      //of rigid bodies defined in meta-data file
117 <      nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
118 <                                                + nGlobalRigidBodies_;
119 <  
120 <      nGlobalMols_ = molStampIds_.size();
158 <      molToProcMap_.resize(nGlobalMols_);
104 >      
105 >      nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
106 >      
107 >      nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;            
108 >      
109 >      //calculate atoms in rigid bodies
110 >      int nAtomsInRigidBodies = 0;
111 >      int nRigidBodiesInStamp = molStamp->getNRigidBodies();
112 >      
113 >      for (int j=0; j < nRigidBodiesInStamp; j++) {
114 >        rbStamp = molStamp->getRigidBodyStamp(j);
115 >        nAtomsInRigidBodies += rbStamp->getNMembers();
116 >      }
117 >      
118 >      nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
119 >      nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;            
120 >      
121      }
122 +    
123 +    //every free atom (atom does not belong to cutoff groups) is a cutoff
124 +    //group therefore the total number of cutoff groups in the system is
125 +    //equal to the total number of atoms minus number of atoms belong to
126 +    //cutoff group defined in meta-data file plus the number of cutoff
127 +    //groups defined in meta-data file
128  
129 +    nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
130 +    
131 +    //every free atom (atom does not belong to rigid bodies) is an
132 +    //integrable object therefore the total number of integrable objects
133 +    //in the system is equal to the total number of atoms minus number of
134 +    //atoms belong to rigid body defined in meta-data file plus the number
135 +    //of rigid bodies defined in meta-data file
136 +    nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
137 +      + nGlobalRigidBodies_;
138 +    
139 +    nGlobalMols_ = molStampIds_.size();
140 +    molToProcMap_.resize(nGlobalMols_);
141 +  }
142 +  
143    SimInfo::~SimInfo() {
144 <    std::map<int, Molecule*>::iterator i;
144 >    map<int, Molecule*>::iterator i;
145      for (i = molecules_.begin(); i != molecules_.end(); ++i) {
146        delete i->second;
147      }
# Line 170 | Line 152 | namespace OpenMD {
152      delete forceField_;
153    }
154  
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 –  }
155  
156    bool SimInfo::addMolecule(Molecule* mol) {
157      MoleculeIterator i;
158 <
158 >    
159      i = molecules_.find(mol->getGlobalIndex());
160      if (i == molecules_.end() ) {
161 <
162 <      molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
163 <        
161 >      
162 >      molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
163 >      
164        nAtoms_ += mol->getNAtoms();
165        nBonds_ += mol->getNBonds();
166        nBends_ += mol->getNBends();
# Line 198 | Line 170 | namespace OpenMD {
170        nIntegrableObjects_ += mol->getNIntegrableObjects();
171        nCutoffGroups_ += mol->getNCutoffGroups();
172        nConstraints_ += mol->getNConstraintPairs();
173 <
173 >      
174        addInteractionPairs(mol);
175 <  
175 >      
176        return true;
177      } else {
178        return false;
179      }
180    }
181 <
181 >  
182    bool SimInfo::removeMolecule(Molecule* mol) {
183      MoleculeIterator i;
184      i = molecules_.find(mol->getGlobalIndex());
# Line 234 | Line 206 | namespace OpenMD {
206      } else {
207        return false;
208      }
237 –
238 –
209    }    
210  
211          
# Line 253 | Line 223 | namespace OpenMD {
223    void SimInfo::calcNdf() {
224      int ndf_local;
225      MoleculeIterator i;
226 <    std::vector<StuntDouble*>::iterator j;
226 >    vector<StuntDouble*>::iterator j;
227      Molecule* mol;
228      StuntDouble* integrableObject;
229  
# Line 299 | Line 269 | namespace OpenMD {
269   #endif
270      return fdf_;
271    }
272 +  
273 +  unsigned int SimInfo::getNLocalCutoffGroups(){
274 +    int nLocalCutoffAtoms = 0;
275 +    Molecule* mol;
276 +    MoleculeIterator mi;
277 +    CutoffGroup* cg;
278 +    Molecule::CutoffGroupIterator ci;
279      
280 +    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
281 +      
282 +      for (cg = mol->beginCutoffGroup(ci); cg != NULL;
283 +           cg = mol->nextCutoffGroup(ci)) {
284 +        nLocalCutoffAtoms += cg->getNumAtom();
285 +        
286 +      }        
287 +    }
288 +    
289 +    return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_;
290 +  }
291 +    
292    void SimInfo::calcNdfRaw() {
293      int ndfRaw_local;
294  
295      MoleculeIterator i;
296 <    std::vector<StuntDouble*>::iterator j;
296 >    vector<StuntDouble*>::iterator j;
297      Molecule* mol;
298      StuntDouble* integrableObject;
299  
# Line 353 | Line 342 | namespace OpenMD {
342  
343    void SimInfo::addInteractionPairs(Molecule* mol) {
344      ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
345 <    std::vector<Bond*>::iterator bondIter;
346 <    std::vector<Bend*>::iterator bendIter;
347 <    std::vector<Torsion*>::iterator torsionIter;
348 <    std::vector<Inversion*>::iterator inversionIter;
345 >    vector<Bond*>::iterator bondIter;
346 >    vector<Bend*>::iterator bendIter;
347 >    vector<Torsion*>::iterator torsionIter;
348 >    vector<Inversion*>::iterator inversionIter;
349      Bond* bond;
350      Bend* bend;
351      Torsion* torsion;
# Line 374 | Line 363 | namespace OpenMD {
363      // always be excluded.  These are done at the bottom of this
364      // function.
365  
366 <    std::map<int, std::set<int> > atomGroups;
366 >    map<int, set<int> > atomGroups;
367      Molecule::RigidBodyIterator rbIter;
368      RigidBody* rb;
369      Molecule::IntegrableObjectIterator ii;
# Line 386 | Line 375 | namespace OpenMD {
375        
376        if (integrableObject->isRigidBody()) {
377          rb = static_cast<RigidBody*>(integrableObject);
378 <        std::vector<Atom*> atoms = rb->getAtoms();
379 <        std::set<int> rigidAtoms;
378 >        vector<Atom*> atoms = rb->getAtoms();
379 >        set<int> rigidAtoms;
380          for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
381            rigidAtoms.insert(atoms[i]->getGlobalIndex());
382          }
383          for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
384 <          atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
384 >          atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
385          }      
386        } else {
387 <        std::set<int> oneAtomSet;
387 >        set<int> oneAtomSet;
388          oneAtomSet.insert(integrableObject->getGlobalIndex());
389 <        atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));        
389 >        atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));        
390        }
391      }  
392            
# Line 500 | Line 489 | namespace OpenMD {
489  
490      for (rb = mol->beginRigidBody(rbIter); rb != NULL;
491           rb = mol->nextRigidBody(rbIter)) {
492 <      std::vector<Atom*> atoms = rb->getAtoms();
492 >      vector<Atom*> atoms = rb->getAtoms();
493        for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
494          for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
495            a = atoms[i]->getGlobalIndex();
# Line 514 | Line 503 | namespace OpenMD {
503  
504    void SimInfo::removeInteractionPairs(Molecule* mol) {
505      ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
506 <    std::vector<Bond*>::iterator bondIter;
507 <    std::vector<Bend*>::iterator bendIter;
508 <    std::vector<Torsion*>::iterator torsionIter;
509 <    std::vector<Inversion*>::iterator inversionIter;
506 >    vector<Bond*>::iterator bondIter;
507 >    vector<Bend*>::iterator bendIter;
508 >    vector<Torsion*>::iterator torsionIter;
509 >    vector<Inversion*>::iterator inversionIter;
510      Bond* bond;
511      Bend* bend;
512      Torsion* torsion;
# Line 527 | Line 516 | namespace OpenMD {
516      int c;
517      int d;
518  
519 <    std::map<int, std::set<int> > atomGroups;
519 >    map<int, set<int> > atomGroups;
520      Molecule::RigidBodyIterator rbIter;
521      RigidBody* rb;
522      Molecule::IntegrableObjectIterator ii;
# Line 539 | Line 528 | namespace OpenMD {
528        
529        if (integrableObject->isRigidBody()) {
530          rb = static_cast<RigidBody*>(integrableObject);
531 <        std::vector<Atom*> atoms = rb->getAtoms();
532 <        std::set<int> rigidAtoms;
531 >        vector<Atom*> atoms = rb->getAtoms();
532 >        set<int> rigidAtoms;
533          for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
534            rigidAtoms.insert(atoms[i]->getGlobalIndex());
535          }
536          for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
537 <          atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
537 >          atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
538          }      
539        } else {
540 <        std::set<int> oneAtomSet;
540 >        set<int> oneAtomSet;
541          oneAtomSet.insert(integrableObject->getGlobalIndex());
542 <        atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));        
542 >        atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));        
543        }
544      }  
545  
# Line 653 | Line 642 | namespace OpenMD {
642  
643      for (rb = mol->beginRigidBody(rbIter); rb != NULL;
644           rb = mol->nextRigidBody(rbIter)) {
645 <      std::vector<Atom*> atoms = rb->getAtoms();
645 >      vector<Atom*> atoms = rb->getAtoms();
646        for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
647          for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
648            a = atoms[i]->getGlobalIndex();
# Line 676 | Line 665 | namespace OpenMD {
665      molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
666    }
667  
679 –  void SimInfo::update() {
668  
669 <    setupSimType();
670 <
671 < #ifdef IS_MPI
672 <    setupFortranParallel();
673 < #endif
674 <
675 <    setupFortranSim();
676 <
677 <    //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 <
669 >  /**
670 >   * update
671 >   *
672 >   *  Performs the global checks and variable settings after the
673 >   *  objects have been created.
674 >   *
675 >   */
676 >  void SimInfo::update() {  
677 >    setupSimVariables();
678      calcNdf();
679      calcNdfRaw();
680      calcNdfTrans();
709 –
710 –    fortranInitialized_ = true;
681    }
682 <
683 <  std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
682 >  
683 >  /**
684 >   * getSimulatedAtomTypes
685 >   *
686 >   * Returns an STL set of AtomType* that are actually present in this
687 >   * simulation.  Must query all processors to assemble this information.
688 >   *
689 >   */
690 >  set<AtomType*> SimInfo::getSimulatedAtomTypes() {
691      SimInfo::MoleculeIterator mi;
692      Molecule* mol;
693      Molecule::AtomIterator ai;
694      Atom* atom;
695 <    std::set<AtomType*> atomTypes;
696 <
695 >    set<AtomType*> atomTypes;
696 >    
697      for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
698 <
699 <      for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
698 >      for(atom = mol->beginAtom(ai); atom != NULL;
699 >          atom = mol->nextAtom(ai)) {
700          atomTypes.insert(atom->getAtomType());
701 <      }
702 <        
703 <    }
701 >      }      
702 >    }    
703 >    
704 > #ifdef IS_MPI
705  
706 <    return atomTypes;        
707 <  }
730 <
731 <  void SimInfo::setupSimType() {
732 <    std::set<AtomType*>::iterator i;
733 <    std::set<AtomType*> atomTypes;
734 <    atomTypes = getUniqueAtomTypes();
706 >    // loop over the found atom types on this processor, and add their
707 >    // numerical idents to a vector:
708      
709 <    int useLennardJones = 0;
710 <    int useElectrostatic = 0;
711 <    int useEAM = 0;
712 <    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;
709 >    vector<int> foundTypes;
710 >    set<AtomType*>::iterator i;
711 >    for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
712 >      foundTypes.push_back( (*i)->getIdent() );
713  
714 <    std::string myMethod;
714 >    // count_local holds the number of found types on this processor
715 >    int count_local = foundTypes.size();
716  
717 <    // set the useRF logical
760 <    useRF = 0;
761 <    useSF = 0;
762 <    useSP = 0;
763 <    useBoxDipole = 0;
717 >    int nproc = MPI::COMM_WORLD.Get_size();
718  
719 +    // we need arrays to hold the counts and displacement vectors for
720 +    // all processors
721 +    vector<int> counts(nproc, 0);
722 +    vector<int> disps(nproc, 0);
723  
724 <    if (simParams_->haveElectrostaticSummationMethod()) {
725 <      std::string myMethod = simParams_->getElectrostaticSummationMethod();
726 <      toUpper(myMethod);
727 <      if (myMethod == "REACTION_FIELD"){
728 <        useRF = 1;
729 <      } else if (myMethod == "SHIFTED_FORCE"){
730 <        useSF = 1;
731 <      } else if (myMethod == "SHIFTED_POTENTIAL"){
732 <        useSP = 1;
733 <      }
724 >    // fill the counts array
725 >    MPI::COMM_WORLD.Allgather(&count_local, 1, MPI::INT, &counts[0],
726 >                              1, MPI::INT);
727 >  
728 >    // use the processor counts to compute the displacement array
729 >    disps[0] = 0;    
730 >    int totalCount = counts[0];
731 >    for (int iproc = 1; iproc < nproc; iproc++) {
732 >      disps[iproc] = disps[iproc-1] + counts[iproc-1];
733 >      totalCount += counts[iproc];
734      }
735 +
736 +    // we need a (possibly redundant) set of all found types:
737 +    vector<int> ftGlobal(totalCount);
738      
739 <    if (simParams_->haveAccumulateBoxDipole())
740 <      if (simParams_->getAccumulateBoxDipole())
741 <        useBoxDipole = 1;
739 >    // now spray out the foundTypes to all the other processors:    
740 >    MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
741 >                               &ftGlobal[0], &counts[0], &disps[0],
742 >                               MPI::INT);
743  
744 <    useAtomicVirial_ = simParams_->getUseAtomicVirial();
744 >    vector<int>::iterator j;
745  
746 <    //loop over all of the atom types
747 <    for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
748 <      useLennardJones |= (*i)->isLennardJones();
787 <      useElectrostatic |= (*i)->isElectrostatic();
788 <      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();
797 <    }
746 >    // foundIdents is a stl set, so inserting an already found ident
747 >    // will have no effect.
748 >    set<int> foundIdents;
749  
750 <    if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
751 <      useDirectionalAtom = 1;
752 <    }
750 >    for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
751 >      foundIdents.insert((*j));
752 >    
753 >    // now iterate over the foundIdents and get the actual atom types
754 >    // that correspond to these:
755 >    set<int>::iterator it;
756 >    for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
757 >      atomTypes.insert( forceField_->getAtomType((*it)) );
758 >
759 > #endif
760  
761 <    if (useCharge || useDipole) {
762 <      useElectrostatics = 1;
805 <    }
761 >    return atomTypes;        
762 >  }
763  
764 +  void SimInfo::setupSimVariables() {
765 +    useAtomicVirial_ = simParams_->getUseAtomicVirial();
766 +    // we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
767 +    calcBoxDipole_ = false;
768 +    if ( simParams_->haveAccumulateBoxDipole() )
769 +      if ( simParams_->getAccumulateBoxDipole() ) {
770 +        calcBoxDipole_ = true;      
771 +      }
772 +    
773 +    set<AtomType*>::iterator i;
774 +    set<AtomType*> atomTypes;
775 +    atomTypes = getSimulatedAtomTypes();    
776 +    int usesElectrostatic = 0;
777 +    int usesMetallic = 0;
778 +    int usesDirectional = 0;
779 +    //loop over all of the atom types
780 +    for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
781 +      usesElectrostatic |= (*i)->isElectrostatic();
782 +      usesMetallic |= (*i)->isMetal();
783 +      usesDirectional |= (*i)->isDirectional();
784 +    }
785 +    
786   #ifdef IS_MPI    
787      int temp;
788 <
789 <    temp = usePBC;
811 <    MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
812 <
813 <    temp = useDirectionalAtom;
814 <    MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
815 <
816 <    temp = useLennardJones;
817 <    MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
818 <
819 <    temp = useElectrostatics;
820 <    MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
821 <
822 <    temp = useCharge;
823 <    MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
824 <
825 <    temp = useDipole;
826 <    MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
827 <
828 <    temp = useSticky;
829 <    MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
830 <
831 <    temp = useStickyPower;
832 <    MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
788 >    temp = usesDirectional;
789 >    MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
790      
791 <    temp = useGayBerne;
792 <    MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
791 >    temp = usesMetallic;
792 >    MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
793 >    
794 >    temp = usesElectrostatic;
795 >    MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
796 > #else
797  
798 <    temp = useEAM;
799 <    MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
798 >    usesDirectionalAtoms_ = usesDirectional;
799 >    usesMetallicAtoms_ = usesMetallic;
800 >    usesElectrostaticAtoms_ = usesElectrostatic;
801  
802 <    temp = useSC;
841 <    MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
802 > #endif
803      
804 <    temp = useShape;
805 <    MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);  
804 >    requiresPrepair_ = usesMetallicAtoms_ ? true : false;
805 >    requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
806 >    requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;    
807 >  }
808  
846 –    temp = useFLARB;
847 –    MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
809  
810 <    temp = useRF;
811 <    MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
810 >  vector<int> SimInfo::getGlobalAtomIndices() {
811 >    SimInfo::MoleculeIterator mi;
812 >    Molecule* mol;
813 >    Molecule::AtomIterator ai;
814 >    Atom* atom;
815  
816 <    temp = useSF;
817 <    MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);  
818 <
819 <    temp = useSP;
820 <    MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
821 <
822 <    temp = useBoxDipole;
823 <    MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
824 <
825 <    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_;
816 >    vector<int> GlobalAtomIndices(getNAtoms(), 0);
817 >    
818 >    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
819 >      
820 >      for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
821 >        GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
822 >        cerr << "LI = " << atom->getLocalIndex() << "GAI = " << GlobalAtomIndices[atom->getLocalIndex()] << "\n";
823 >      }
824 >    }
825 >    return GlobalAtomIndices;
826    }
827  
886 –  void SimInfo::setupFortranSim() {
887 –    int isError;
888 –    int nExclude, nOneTwo, nOneThree, nOneFour;
889 –    std::vector<int> fortranGlobalGroupMembership;
890 –    
891 –    isError = 0;
828  
829 <    //globalGroupMembership_ is filled by SimCreator    
830 <    for (int i = 0; i < nGlobalAtoms_; i++) {
831 <      fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
829 >  vector<int> SimInfo::getGlobalGroupIndices() {
830 >    SimInfo::MoleculeIterator mi;
831 >    Molecule* mol;
832 >    Molecule::CutoffGroupIterator ci;
833 >    CutoffGroup* cg;
834 >
835 >    vector<int> GlobalGroupIndices;
836 >    
837 >    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
838 >      
839 >      //local index of cutoff group is trivial, it only depends on the
840 >      //order of travesing
841 >      for (cg = mol->beginCutoffGroup(ci); cg != NULL;
842 >           cg = mol->nextCutoffGroup(ci)) {
843 >        GlobalGroupIndices.push_back(cg->getGlobalIndex());
844 >        cerr << "LI, GGI = " << GlobalGroupIndices.size() << " " << cg->getGlobalIndex() << "\n";
845 >      }        
846      }
847 +    return GlobalGroupIndices;
848 +  }
849  
850 +
851 +  void SimInfo::prepareTopology() {
852 +    int nExclude, nOneTwo, nOneThree, nOneFour;
853 +
854      //calculate mass ratio of cutoff group
899 –    std::vector<RealType> mfact;
855      SimInfo::MoleculeIterator mi;
856      Molecule* mol;
857      Molecule::CutoffGroupIterator ci;
# Line 905 | Line 860 | namespace OpenMD {
860      Atom* atom;
861      RealType totalMass;
862  
863 <    //to avoid memory reallocation, reserve enough space for mfact
864 <    mfact.reserve(getNCutoffGroups());
863 >    /**
864 >     * The mass factor is the relative mass of an atom to the total
865 >     * mass of the cutoff group it belongs to.  By default, all atoms
866 >     * are their own cutoff groups, and therefore have mass factors of
867 >     * 1.  We need some special handling for massless atoms, which
868 >     * will be treated as carrying the entire mass of the cutoff
869 >     * group.
870 >     */
871 >    massFactors_.clear();
872 >    massFactors_.resize(getNAtoms(), 1.0);
873      
874      for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {        
875 <      for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
875 >      for (cg = mol->beginCutoffGroup(ci); cg != NULL;
876 >           cg = mol->nextCutoffGroup(ci)) {
877  
878          totalMass = cg->getMass();
879          for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
880            // Check for massless groups - set mfact to 1 if true
881 <          if (totalMass != 0)
882 <            mfact.push_back(atom->getMass()/totalMass);
881 >          if (totalMass != 0)
882 >            massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
883            else
884 <            mfact.push_back( 1.0 );
884 >            massFactors_[atom->getLocalIndex()] = 1.0;
885          }
886        }      
887      }
888  
889 <    //fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
926 <    std::vector<int> identArray;
889 >    // Build the identArray_
890  
891 <    //to avoid memory reallocation, reserve enough space identArray
892 <    identArray.reserve(getNAtoms());
930 <    
891 >    identArray_.clear();
892 >    identArray_.reserve(getNAtoms());    
893      for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {        
894        for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
895 <        identArray.push_back(atom->getIdent());
895 >        identArray_.push_back(atom->getIdent());
896        }
897      }    
936 –
937 –    //fill molMembershipArray
938 –    //molMembershipArray is filled by SimCreator    
939 –    std::vector<int> molMembershipArray(nGlobalAtoms_);
940 –    for (int i = 0; i < nGlobalAtoms_; i++) {
941 –      molMembershipArray[i] = globalMolMembership_[i] + 1;
942 –    }
898      
899 <    //setup fortran simulation
899 >    //scan topology
900  
901      nExclude = excludedInteractions_.getSize();
902      nOneTwo = oneTwoInteractions_.getSize();
# Line 953 | Line 908 | namespace OpenMD {
908      int* oneThreeList = oneThreeInteractions_.getPairList();
909      int* oneFourList = oneFourInteractions_.getPairList();
910  
911 <    setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
957 <                   &nExclude, excludeList,
958 <                   &nOneTwo, oneTwoList,
959 <                   &nOneThree, oneThreeList,
960 <                   &nOneFour, oneFourList,
961 <                   &molMembershipArray[0], &mfact[0], &nCutoffGroups_,
962 <                   &fortranGlobalGroupMembership[0], &isError);
963 <    
964 <    if( isError ){
965 <      
966 <      sprintf( painCave.errMsg,
967 <               "There was an error setting the simulation information in fortran.\n" );
968 <      painCave.isFatal = 1;
969 <      painCave.severity = OPENMD_ERROR;
970 <      simError();
971 <    }
972 <    
973 <    
974 <    sprintf( checkPointMsg,
975 <             "succesfully sent the simulation information to fortran.\n");
976 <    
977 <    errorCheckPoint();
978 <    
979 <    // Setup number of neighbors in neighbor list if present
980 <    if (simParams_->haveNeighborListNeighbors()) {
981 <      int nlistNeighbors = simParams_->getNeighborListNeighbors();
982 <      setNeighbors(&nlistNeighbors);
983 <    }
984 <  
985 <
986 <  }
987 <
988 <
989 <  void SimInfo::setupFortranParallel() {
990 < #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;
1000 <    mpiSimData parallelData;
1001 <    int isError;
1002 <
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 <
1017 <    //fill up mpiSimData struct
1018 <    parallelData.nMolGlobal = getNGlobalMolecules();
1019 <    parallelData.nMolLocal = getNMolecules();
1020 <    parallelData.nAtomsGlobal = getNGlobalAtoms();
1021 <    parallelData.nAtomsLocal = getNAtoms();
1022 <    parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
1023 <    parallelData.nGroupsLocal = getNCutoffGroups();
1024 <    parallelData.myNode = worldRank;
1025 <    MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
1026 <
1027 <    //pass mpiSimData struct and index arrays to fortran
1028 <    setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
1029 <                    &localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
1030 <                    &localToGlobalCutoffGroupIndex[0], &isError);
1031 <
1032 <    if (isError) {
1033 <      sprintf(painCave.errMsg,
1034 <              "mpiRefresh errror: fortran didn't like something we gave it.\n");
1035 <      painCave.isFatal = 1;
1036 <      simError();
1037 <    }
1038 <
1039 <    sprintf(checkPointMsg, " mpiRefresh successful.\n");
1040 <    errorCheckPoint();
1041 <
1042 < #endif
1043 <  }
1044 <
1045 <  void SimInfo::setupCutoff() {          
1046 <    
1047 <    ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
1048 <
1049 <    // Check the cutoff policy
1050 <    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();
1061 <    }
1062 <
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 <    }
911 >    topologyDone_ = true;
912    }
913  
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 –
914    void SimInfo::addProperty(GenericData* genData) {
915      properties_.addProperty(genData);  
916    }
917  
918 <  void SimInfo::removeProperty(const std::string& propName) {
918 >  void SimInfo::removeProperty(const string& propName) {
919      properties_.removeProperty(propName);  
920    }
921  
# Line 1338 | Line 923 | namespace OpenMD {
923      properties_.clearProperties();
924    }
925  
926 <  std::vector<std::string> SimInfo::getPropertyNames() {
926 >  vector<string> SimInfo::getPropertyNames() {
927      return properties_.getPropertyNames();  
928    }
929        
930 <  std::vector<GenericData*> SimInfo::getProperties() {
930 >  vector<GenericData*> SimInfo::getProperties() {
931      return properties_.getProperties();
932    }
933  
934 <  GenericData* SimInfo::getPropertyByName(const std::string& propName) {
934 >  GenericData* SimInfo::getPropertyByName(const string& propName) {
935      return properties_.getPropertyByName(propName);
936    }
937  
# Line 1360 | Line 945 | namespace OpenMD {
945      Molecule* mol;
946      RigidBody* rb;
947      Atom* atom;
948 +    CutoffGroup* cg;
949      SimInfo::MoleculeIterator mi;
950      Molecule::RigidBodyIterator rbIter;
951 <    Molecule::AtomIterator atomIter;;
951 >    Molecule::AtomIterator atomIter;
952 >    Molecule::CutoffGroupIterator cgIter;
953  
954      for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
955          
# Line 1373 | Line 960 | namespace OpenMD {
960        for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
961          rb->setSnapshotManager(sman_);
962        }
963 +
964 +      for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
965 +        cg->setSnapshotManager(sman_);
966 +      }
967      }    
968      
969    }
# Line 1429 | Line 1020 | namespace OpenMD {
1020  
1021    }        
1022  
1023 <  std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1023 >  ostream& operator <<(ostream& o, SimInfo& info) {
1024  
1025      return o;
1026    }
# Line 1472 | Line 1063 | namespace OpenMD {
1063  
1064  
1065         [  Ixx -Ixy  -Ixz ]
1066 <  J =| -Iyx  Iyy  -Iyz |
1066 >    J =| -Iyx  Iyy  -Iyz |
1067         [ -Izx -Iyz   Izz ]
1068      */
1069  
# Line 1579 | Line 1170 | namespace OpenMD {
1170      return IOIndexToIntegrableObject.at(index);
1171    }
1172    
1173 <  void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1173 >  void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1174      IOIndexToIntegrableObject= v;
1175    }
1176  
# Line 1621 | Line 1212 | namespace OpenMD {
1212      return;
1213    }
1214   /*
1215 <   void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1215 >   void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1216        assert( v.size() == nAtoms_ + nRigidBodies_);
1217        sdByGlobalIndex_ = v;
1218      }
# Line 1631 | Line 1222 | namespace OpenMD {
1222        return sdByGlobalIndex_.at(index);
1223      }  
1224   */  
1225 +  int SimInfo::getNGlobalConstraints() {
1226 +    int nGlobalConstraints;
1227 + #ifdef IS_MPI
1228 +    MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1229 +                  MPI_COMM_WORLD);    
1230 + #else
1231 +    nGlobalConstraints =  nConstraints_;
1232 + #endif
1233 +    return nGlobalConstraints;
1234 +  }
1235 +
1236   }//end namespace OpenMD
1237  

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