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root/OpenMD/branches/development/src/brains/SimInfo.cpp
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Comparing branches/development/src/brains/SimInfo.cpp (file contents):
Revision 1465 by chuckv, Fri Jul 9 23:08:25 2010 UTC vs.
Revision 1627 by gezelter, Tue Sep 13 22:05:04 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/fElectrostaticSummationMethod.h"
59 – #include "UseTheForce/DarkSide/fElectrostaticScreeningMethod.h"
60 – #include "UseTheForce/DarkSide/fSwitchingFunctionType.h"
61 – #include "UseTheForce/doForces_interface.h"
62 – #include "UseTheForce/DarkSide/neighborLists_interface.h"
63 – #include "UseTheForce/DarkSide/electrostatic_interface.h"
64 – #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 <
71 <
62 > #include "nonbonded/SwitchingFunction.hpp"
63   #ifdef IS_MPI
64 < #include "UseTheForce/mpiComponentPlan.h"
65 < #include "UseTheForce/DarkSide/simParallel_interface.h"
75 < #endif
64 > #include <mpi.h>
65 > #endif
66  
67 + using namespace std;
68   namespace OpenMD {
78 –  std::set<int> getRigidSet(int index, std::map<int, std::set<int> >& container) {
79 –    std::map<int, std::set<int> >::iterator i = container.find(index);
80 –    std::set<int> result;
81 –    if (i != container.end()) {
82 –        result = i->second;
83 –    }
84 –
85 –    return result;
86 –  }
69    
70    SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
71      forceField_(ff), simParams_(simParams),
# Line 92 | Line 74 | namespace OpenMD {
74      nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
75      nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
76      nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
77 <    nConstraints_(0), sman_(NULL), fortranInitialized_(false),
78 <    calcBoxDipole_(false), useAtomicVirial_(true) {
79 <
80 <
81 <      MoleculeStamp* molStamp;
82 <      int nMolWithSameStamp;
83 <      int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
84 <      int nGroups = 0;      //total cutoff groups defined in meta-data file
85 <      CutoffGroupStamp* cgStamp;    
86 <      RigidBodyStamp* rbStamp;
87 <      int nRigidAtoms = 0;
88 <
89 <      std::vector<Component*> components = simParams->getComponents();
77 >    nConstraints_(0), sman_(NULL), topologyDone_(false),
78 >    calcBoxDipole_(false), useAtomicVirial_(true) {    
79 >    
80 >    MoleculeStamp* molStamp;
81 >    int nMolWithSameStamp;
82 >    int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
83 >    int nGroups = 0;       //total cutoff groups defined in meta-data file
84 >    CutoffGroupStamp* cgStamp;    
85 >    RigidBodyStamp* rbStamp;
86 >    int nRigidAtoms = 0;
87 >    
88 >    vector<Component*> components = simParams->getComponents();
89 >    
90 >    for (vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
91 >      molStamp = (*i)->getMoleculeStamp();
92 >      nMolWithSameStamp = (*i)->getNMol();
93        
94 <      for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
95 <        molStamp = (*i)->getMoleculeStamp();
96 <        nMolWithSameStamp = (*i)->getNMol();
97 <        
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();
121 <        
122 <        for (int j=0; j < nCutoffGroupsInStamp; j++) {
123 <          cgStamp = molStamp->getCutoffGroupStamp(j);
124 <          nAtomsInGroups += cgStamp->getNMembers();
125 <        }
126 <
127 <        nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
128 <
129 <        nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;            
130 <
131 <        //calculate atoms in rigid bodies
132 <        int nAtomsInRigidBodies = 0;
133 <        int nRigidBodiesInStamp = molStamp->getNRigidBodies();
134 <        
135 <        for (int j=0; j < nRigidBodiesInStamp; j++) {
136 <          rbStamp = molStamp->getRigidBodyStamp(j);
137 <          nAtomsInRigidBodies += rbStamp->getNMembers();
138 <        }
139 <
140 <        nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
141 <        nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;            
142 <        
94 >      addMoleculeStamp(molStamp, nMolWithSameStamp);
95 >      
96 >      //calculate atoms in molecules
97 >      nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;  
98 >      
99 >      //calculate atoms in cutoff groups
100 >      int nAtomsInGroups = 0;
101 >      int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
102 >      
103 >      for (int j=0; j < nCutoffGroupsInStamp; j++) {
104 >        cgStamp = molStamp->getCutoffGroupStamp(j);
105 >        nAtomsInGroups += cgStamp->getNMembers();
106        }
107 <
108 <      //every free atom (atom does not belong to cutoff groups) is a cutoff
109 <      //group therefore the total number of cutoff groups in the system is
110 <      //equal to the total number of atoms minus number of atoms belong to
111 <      //cutoff group defined in meta-data file plus the number of cutoff
112 <      //groups defined in meta-data file
113 <      nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
114 <
115 <      //every free atom (atom does not belong to rigid bodies) is an
116 <      //integrable object therefore the total number of integrable objects
117 <      //in the system is equal to the total number of atoms minus number of
118 <      //atoms belong to rigid body defined in meta-data file plus the number
119 <      //of rigid bodies defined in meta-data file
120 <      nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
121 <                                                + nGlobalRigidBodies_;
122 <  
123 <      nGlobalMols_ = molStampIds_.size();
161 <      molToProcMap_.resize(nGlobalMols_);
107 >      
108 >      nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
109 >      
110 >      nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;            
111 >      
112 >      //calculate atoms in rigid bodies
113 >      int nAtomsInRigidBodies = 0;
114 >      int nRigidBodiesInStamp = molStamp->getNRigidBodies();
115 >      
116 >      for (int j=0; j < nRigidBodiesInStamp; j++) {
117 >        rbStamp = molStamp->getRigidBodyStamp(j);
118 >        nAtomsInRigidBodies += rbStamp->getNMembers();
119 >      }
120 >      
121 >      nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
122 >      nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;            
123 >      
124      }
125 +    
126 +    //every free atom (atom does not belong to cutoff groups) is a cutoff
127 +    //group therefore the total number of cutoff groups in the system is
128 +    //equal to the total number of atoms minus number of atoms belong to
129 +    //cutoff group defined in meta-data file plus the number of cutoff
130 +    //groups defined in meta-data file
131  
132 +    nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
133 +    
134 +    //every free atom (atom does not belong to rigid bodies) is an
135 +    //integrable object therefore the total number of integrable objects
136 +    //in the system is equal to the total number of atoms minus number of
137 +    //atoms belong to rigid body defined in meta-data file plus the number
138 +    //of rigid bodies defined in meta-data file
139 +    nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
140 +      + nGlobalRigidBodies_;
141 +    
142 +    nGlobalMols_ = molStampIds_.size();
143 +    molToProcMap_.resize(nGlobalMols_);
144 +  }
145 +  
146    SimInfo::~SimInfo() {
147 <    std::map<int, Molecule*>::iterator i;
147 >    map<int, Molecule*>::iterator i;
148      for (i = molecules_.begin(); i != molecules_.end(); ++i) {
149        delete i->second;
150      }
# Line 173 | Line 155 | namespace OpenMD {
155      delete forceField_;
156    }
157  
176 –  int SimInfo::getNGlobalConstraints() {
177 –    int nGlobalConstraints;
178 – #ifdef IS_MPI
179 –    MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
180 –                  MPI_COMM_WORLD);    
181 – #else
182 –    nGlobalConstraints =  nConstraints_;
183 – #endif
184 –    return nGlobalConstraints;
185 –  }
158  
159    bool SimInfo::addMolecule(Molecule* mol) {
160      MoleculeIterator i;
161 <
161 >    
162      i = molecules_.find(mol->getGlobalIndex());
163      if (i == molecules_.end() ) {
164 <
165 <      molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
166 <        
164 >      
165 >      molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
166 >      
167        nAtoms_ += mol->getNAtoms();
168        nBonds_ += mol->getNBonds();
169        nBends_ += mol->getNBends();
# Line 201 | Line 173 | namespace OpenMD {
173        nIntegrableObjects_ += mol->getNIntegrableObjects();
174        nCutoffGroups_ += mol->getNCutoffGroups();
175        nConstraints_ += mol->getNConstraintPairs();
176 <
176 >      
177        addInteractionPairs(mol);
178 <  
178 >      
179        return true;
180      } else {
181        return false;
182      }
183    }
184 <
184 >  
185    bool SimInfo::removeMolecule(Molecule* mol) {
186      MoleculeIterator i;
187      i = molecules_.find(mol->getGlobalIndex());
# Line 237 | Line 209 | namespace OpenMD {
209      } else {
210        return false;
211      }
240 –
241 –
212    }    
213  
214          
# Line 256 | Line 226 | namespace OpenMD {
226    void SimInfo::calcNdf() {
227      int ndf_local;
228      MoleculeIterator i;
229 <    std::vector<StuntDouble*>::iterator j;
229 >    vector<StuntDouble*>::iterator j;
230      Molecule* mol;
231      StuntDouble* integrableObject;
232  
# Line 302 | Line 272 | namespace OpenMD {
272   #endif
273      return fdf_;
274    }
275 +  
276 +  unsigned int SimInfo::getNLocalCutoffGroups(){
277 +    int nLocalCutoffAtoms = 0;
278 +    Molecule* mol;
279 +    MoleculeIterator mi;
280 +    CutoffGroup* cg;
281 +    Molecule::CutoffGroupIterator ci;
282      
283 +    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
284 +      
285 +      for (cg = mol->beginCutoffGroup(ci); cg != NULL;
286 +           cg = mol->nextCutoffGroup(ci)) {
287 +        nLocalCutoffAtoms += cg->getNumAtom();
288 +        
289 +      }        
290 +    }
291 +    
292 +    return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_;
293 +  }
294 +    
295    void SimInfo::calcNdfRaw() {
296      int ndfRaw_local;
297  
298      MoleculeIterator i;
299 <    std::vector<StuntDouble*>::iterator j;
299 >    vector<StuntDouble*>::iterator j;
300      Molecule* mol;
301      StuntDouble* integrableObject;
302  
# Line 356 | Line 345 | namespace OpenMD {
345  
346    void SimInfo::addInteractionPairs(Molecule* mol) {
347      ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
348 <    std::vector<Bond*>::iterator bondIter;
349 <    std::vector<Bend*>::iterator bendIter;
350 <    std::vector<Torsion*>::iterator torsionIter;
351 <    std::vector<Inversion*>::iterator inversionIter;
348 >    vector<Bond*>::iterator bondIter;
349 >    vector<Bend*>::iterator bendIter;
350 >    vector<Torsion*>::iterator torsionIter;
351 >    vector<Inversion*>::iterator inversionIter;
352      Bond* bond;
353      Bend* bend;
354      Torsion* torsion;
# Line 377 | Line 366 | namespace OpenMD {
366      // always be excluded.  These are done at the bottom of this
367      // function.
368  
369 <    std::map<int, std::set<int> > atomGroups;
369 >    map<int, set<int> > atomGroups;
370      Molecule::RigidBodyIterator rbIter;
371      RigidBody* rb;
372      Molecule::IntegrableObjectIterator ii;
# Line 389 | Line 378 | namespace OpenMD {
378        
379        if (integrableObject->isRigidBody()) {
380          rb = static_cast<RigidBody*>(integrableObject);
381 <        std::vector<Atom*> atoms = rb->getAtoms();
382 <        std::set<int> rigidAtoms;
381 >        vector<Atom*> atoms = rb->getAtoms();
382 >        set<int> rigidAtoms;
383          for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
384            rigidAtoms.insert(atoms[i]->getGlobalIndex());
385          }
386          for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
387 <          atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
387 >          atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
388          }      
389        } else {
390 <        std::set<int> oneAtomSet;
390 >        set<int> oneAtomSet;
391          oneAtomSet.insert(integrableObject->getGlobalIndex());
392 <        atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));        
392 >        atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));        
393        }
394      }  
395            
# Line 503 | Line 492 | namespace OpenMD {
492  
493      for (rb = mol->beginRigidBody(rbIter); rb != NULL;
494           rb = mol->nextRigidBody(rbIter)) {
495 <      std::vector<Atom*> atoms = rb->getAtoms();
495 >      vector<Atom*> atoms = rb->getAtoms();
496        for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
497          for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
498            a = atoms[i]->getGlobalIndex();
# Line 517 | Line 506 | namespace OpenMD {
506  
507    void SimInfo::removeInteractionPairs(Molecule* mol) {
508      ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
509 <    std::vector<Bond*>::iterator bondIter;
510 <    std::vector<Bend*>::iterator bendIter;
511 <    std::vector<Torsion*>::iterator torsionIter;
512 <    std::vector<Inversion*>::iterator inversionIter;
509 >    vector<Bond*>::iterator bondIter;
510 >    vector<Bend*>::iterator bendIter;
511 >    vector<Torsion*>::iterator torsionIter;
512 >    vector<Inversion*>::iterator inversionIter;
513      Bond* bond;
514      Bend* bend;
515      Torsion* torsion;
# Line 530 | Line 519 | namespace OpenMD {
519      int c;
520      int d;
521  
522 <    std::map<int, std::set<int> > atomGroups;
522 >    map<int, set<int> > atomGroups;
523      Molecule::RigidBodyIterator rbIter;
524      RigidBody* rb;
525      Molecule::IntegrableObjectIterator ii;
# Line 542 | Line 531 | namespace OpenMD {
531        
532        if (integrableObject->isRigidBody()) {
533          rb = static_cast<RigidBody*>(integrableObject);
534 <        std::vector<Atom*> atoms = rb->getAtoms();
535 <        std::set<int> rigidAtoms;
534 >        vector<Atom*> atoms = rb->getAtoms();
535 >        set<int> rigidAtoms;
536          for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
537            rigidAtoms.insert(atoms[i]->getGlobalIndex());
538          }
539          for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
540 <          atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
540 >          atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
541          }      
542        } else {
543 <        std::set<int> oneAtomSet;
543 >        set<int> oneAtomSet;
544          oneAtomSet.insert(integrableObject->getGlobalIndex());
545 <        atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));        
545 >        atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));        
546        }
547      }  
548  
# Line 656 | Line 645 | namespace OpenMD {
645  
646      for (rb = mol->beginRigidBody(rbIter); rb != NULL;
647           rb = mol->nextRigidBody(rbIter)) {
648 <      std::vector<Atom*> atoms = rb->getAtoms();
648 >      vector<Atom*> atoms = rb->getAtoms();
649        for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
650          for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
651            a = atoms[i]->getGlobalIndex();
# Line 679 | Line 668 | namespace OpenMD {
668      molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
669    }
670  
682 –  void SimInfo::update() {
671  
672 <    setupSimType();
673 <
674 < #ifdef IS_MPI
675 <    setupFortranParallel();
676 < #endif
677 <
678 <    setupFortranSim();
679 <
680 <    //setup fortran force field
693 <    /** @deprecate */    
694 <    int isError = 0;
695 <    
696 <    setupCutoff();
697 <    
698 <    setupElectrostaticSummationMethod( isError );
699 <    setupSwitchingFunction();
700 <    setupAccumulateBoxDipole();
701 <
702 <    if(isError){
703 <      sprintf( painCave.errMsg,
704 <               "ForceField error: There was an error initializing the forceField in fortran.\n" );
705 <      painCave.isFatal = 1;
706 <      simError();
707 <    }
708 <
672 >  /**
673 >   * update
674 >   *
675 >   *  Performs the global checks and variable settings after the
676 >   *  objects have been created.
677 >   *
678 >   */
679 >  void SimInfo::update() {  
680 >    setupSimVariables();
681      calcNdf();
682      calcNdfRaw();
683      calcNdfTrans();
712 –
713 –    fortranInitialized_ = true;
684    }
685 <
686 <  std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
685 >  
686 >  /**
687 >   * getSimulatedAtomTypes
688 >   *
689 >   * Returns an STL set of AtomType* that are actually present in this
690 >   * simulation.  Must query all processors to assemble this information.
691 >   *
692 >   */
693 >  set<AtomType*> SimInfo::getSimulatedAtomTypes() {
694      SimInfo::MoleculeIterator mi;
695      Molecule* mol;
696      Molecule::AtomIterator ai;
697      Atom* atom;
698 <    std::set<AtomType*> atomTypes;
699 <
698 >    set<AtomType*> atomTypes;
699 >    
700      for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
701 <
702 <      for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
701 >      for(atom = mol->beginAtom(ai); atom != NULL;
702 >          atom = mol->nextAtom(ai)) {
703          atomTypes.insert(atom->getAtomType());
704 <      }
705 <        
706 <    }
704 >      }      
705 >    }    
706 >    
707 > #ifdef IS_MPI
708  
709 <    return atomTypes;        
710 <  }
733 <
734 <  void SimInfo::setupSimType() {
735 <    std::set<AtomType*>::iterator i;
736 <    std::set<AtomType*> atomTypes;
737 <    atomTypes = getUniqueAtomTypes();
709 >    // loop over the found atom types on this processor, and add their
710 >    // numerical idents to a vector:
711      
712 <    int useLennardJones = 0;
713 <    int useElectrostatic = 0;
714 <    int useEAM = 0;
715 <    int useSC = 0;
743 <    int useCharge = 0;
744 <    int useDirectional = 0;
745 <    int useDipole = 0;
746 <    int useGayBerne = 0;
747 <    int useSticky = 0;
748 <    int useStickyPower = 0;
749 <    int useShape = 0;
750 <    int useFLARB = 0; //it is not in AtomType yet
751 <    int useDirectionalAtom = 0;    
752 <    int useElectrostatics = 0;
753 <    //usePBC and useRF are from simParams
754 <    int usePBC = simParams_->getUsePeriodicBoundaryConditions();
755 <    int useRF;
756 <    int useSF;
757 <    int useSP;
758 <    int useBoxDipole;
712 >    vector<int> foundTypes;
713 >    set<AtomType*>::iterator i;
714 >    for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
715 >      foundTypes.push_back( (*i)->getIdent() );
716  
717 <    std::string myMethod;
717 >    // count_local holds the number of found types on this processor
718 >    int count_local = foundTypes.size();
719  
720 <    // set the useRF logical
763 <    useRF = 0;
764 <    useSF = 0;
765 <    useSP = 0;
766 <    useBoxDipole = 0;
720 >    int nproc = MPI::COMM_WORLD.Get_size();
721  
722 +    // we need arrays to hold the counts and displacement vectors for
723 +    // all processors
724 +    vector<int> counts(nproc, 0);
725 +    vector<int> disps(nproc, 0);
726  
727 <    if (simParams_->haveElectrostaticSummationMethod()) {
728 <      std::string myMethod = simParams_->getElectrostaticSummationMethod();
729 <      toUpper(myMethod);
730 <      if (myMethod == "REACTION_FIELD"){
731 <        useRF = 1;
732 <      } else if (myMethod == "SHIFTED_FORCE"){
733 <        useSF = 1;
734 <      } else if (myMethod == "SHIFTED_POTENTIAL"){
735 <        useSP = 1;
736 <      }
727 >    // fill the counts array
728 >    MPI::COMM_WORLD.Allgather(&count_local, 1, MPI::INT, &counts[0],
729 >                              1, MPI::INT);
730 >  
731 >    // use the processor counts to compute the displacement array
732 >    disps[0] = 0;    
733 >    int totalCount = counts[0];
734 >    for (int iproc = 1; iproc < nproc; iproc++) {
735 >      disps[iproc] = disps[iproc-1] + counts[iproc-1];
736 >      totalCount += counts[iproc];
737      }
738 +
739 +    // we need a (possibly redundant) set of all found types:
740 +    vector<int> ftGlobal(totalCount);
741      
742 <    if (simParams_->haveAccumulateBoxDipole())
743 <      if (simParams_->getAccumulateBoxDipole())
744 <        useBoxDipole = 1;
742 >    // now spray out the foundTypes to all the other processors:    
743 >    MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
744 >                               &ftGlobal[0], &counts[0], &disps[0],
745 >                               MPI::INT);
746  
747 <    useAtomicVirial_ = simParams_->getUseAtomicVirial();
747 >    vector<int>::iterator j;
748  
749 <    //loop over all of the atom types
750 <    for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
751 <      useLennardJones |= (*i)->isLennardJones();
790 <      useElectrostatic |= (*i)->isElectrostatic();
791 <      useEAM |= (*i)->isEAM();
792 <      useSC |= (*i)->isSC();
793 <      useCharge |= (*i)->isCharge();
794 <      useDirectional |= (*i)->isDirectional();
795 <      useDipole |= (*i)->isDipole();
796 <      useGayBerne |= (*i)->isGayBerne();
797 <      useSticky |= (*i)->isSticky();
798 <      useStickyPower |= (*i)->isStickyPower();
799 <      useShape |= (*i)->isShape();
800 <    }
749 >    // foundIdents is a stl set, so inserting an already found ident
750 >    // will have no effect.
751 >    set<int> foundIdents;
752  
753 <    if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
754 <      useDirectionalAtom = 1;
755 <    }
753 >    for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
754 >      foundIdents.insert((*j));
755 >    
756 >    // now iterate over the foundIdents and get the actual atom types
757 >    // that correspond to these:
758 >    set<int>::iterator it;
759 >    for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
760 >      atomTypes.insert( forceField_->getAtomType((*it)) );
761 >
762 > #endif
763  
764 <    if (useCharge || useDipole) {
765 <      useElectrostatics = 1;
808 <    }
764 >    return atomTypes;        
765 >  }
766  
767 +  void SimInfo::setupSimVariables() {
768 +    useAtomicVirial_ = simParams_->getUseAtomicVirial();
769 +    // we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
770 +    calcBoxDipole_ = false;
771 +    if ( simParams_->haveAccumulateBoxDipole() )
772 +      if ( simParams_->getAccumulateBoxDipole() ) {
773 +        calcBoxDipole_ = true;      
774 +      }
775 +    
776 +    set<AtomType*>::iterator i;
777 +    set<AtomType*> atomTypes;
778 +    atomTypes = getSimulatedAtomTypes();    
779 +    int usesElectrostatic = 0;
780 +    int usesMetallic = 0;
781 +    int usesDirectional = 0;
782 +    //loop over all of the atom types
783 +    for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
784 +      usesElectrostatic |= (*i)->isElectrostatic();
785 +      usesMetallic |= (*i)->isMetal();
786 +      usesDirectional |= (*i)->isDirectional();
787 +    }
788 +    
789   #ifdef IS_MPI    
790      int temp;
791 +    temp = usesDirectional;
792 +    MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
793 +    
794 +    temp = usesMetallic;
795 +    MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
796 +    
797 +    temp = usesElectrostatic;
798 +    MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
799 + #else
800  
801 <    temp = usePBC;
802 <    MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
801 >    usesDirectionalAtoms_ = usesDirectional;
802 >    usesMetallicAtoms_ = usesMetallic;
803 >    usesElectrostaticAtoms_ = usesElectrostatic;
804  
805 <    temp = useDirectionalAtom;
806 <    MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
805 > #endif
806 >    
807 >    requiresPrepair_ = usesMetallicAtoms_ ? true : false;
808 >    requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
809 >    requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;    
810 >  }
811  
819 –    temp = useLennardJones;
820 –    MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
812  
813 <    temp = useElectrostatics;
814 <    MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
813 >  vector<int> SimInfo::getGlobalAtomIndices() {
814 >    SimInfo::MoleculeIterator mi;
815 >    Molecule* mol;
816 >    Molecule::AtomIterator ai;
817 >    Atom* atom;
818  
819 <    temp = useCharge;
826 <    MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
827 <
828 <    temp = useDipole;
829 <    MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
830 <
831 <    temp = useSticky;
832 <    MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
833 <
834 <    temp = useStickyPower;
835 <    MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
819 >    vector<int> GlobalAtomIndices(getNAtoms(), 0);
820      
821 <    temp = useGayBerne;
822 <    MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
821 >    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
822 >      
823 >      for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
824 >        GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
825 >      }
826 >    }
827 >    return GlobalAtomIndices;
828 >  }
829  
840 –    temp = useEAM;
841 –    MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
830  
831 <    temp = useSC;
832 <    MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
833 <    
834 <    temp = useShape;
835 <    MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);  
831 >  vector<int> SimInfo::getGlobalGroupIndices() {
832 >    SimInfo::MoleculeIterator mi;
833 >    Molecule* mol;
834 >    Molecule::CutoffGroupIterator ci;
835 >    CutoffGroup* cg;
836  
837 <    temp = useFLARB;
838 <    MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
839 <
840 <    temp = useRF;
841 <    MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
842 <
843 <    temp = useSF;
844 <    MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);  
845 <
846 <    temp = useSP;
847 <    MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
848 <
861 <    temp = useBoxDipole;
862 <    MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
863 <
864 <    temp = useAtomicVirial_;
865 <    MPI_Allreduce(&temp, &useAtomicVirial_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
866 <
867 < #endif
868 <
869 <    fInfo_.SIM_uses_PBC = usePBC;    
870 <    fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
871 <    fInfo_.SIM_uses_LennardJones = useLennardJones;
872 <    fInfo_.SIM_uses_Electrostatics = useElectrostatics;    
873 <    fInfo_.SIM_uses_Charges = useCharge;
874 <    fInfo_.SIM_uses_Dipoles = useDipole;
875 <    fInfo_.SIM_uses_Sticky = useSticky;
876 <    fInfo_.SIM_uses_StickyPower = useStickyPower;
877 <    fInfo_.SIM_uses_GayBerne = useGayBerne;
878 <    fInfo_.SIM_uses_EAM = useEAM;
879 <    fInfo_.SIM_uses_SC = useSC;
880 <    fInfo_.SIM_uses_Shapes = useShape;
881 <    fInfo_.SIM_uses_FLARB = useFLARB;
882 <    fInfo_.SIM_uses_RF = useRF;
883 <    fInfo_.SIM_uses_SF = useSF;
884 <    fInfo_.SIM_uses_SP = useSP;
885 <    fInfo_.SIM_uses_BoxDipole = useBoxDipole;
886 <    fInfo_.SIM_uses_AtomicVirial = useAtomicVirial_;
837 >    vector<int> GlobalGroupIndices;
838 >    
839 >    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
840 >      
841 >      //local index of cutoff group is trivial, it only depends on the
842 >      //order of travesing
843 >      for (cg = mol->beginCutoffGroup(ci); cg != NULL;
844 >           cg = mol->nextCutoffGroup(ci)) {
845 >        GlobalGroupIndices.push_back(cg->getGlobalIndex());
846 >      }        
847 >    }
848 >    return GlobalGroupIndices;
849    }
850  
851 <  void SimInfo::setupFortranSim() {
852 <    int isError;
851 >
852 >  void SimInfo::prepareTopology() {
853      int nExclude, nOneTwo, nOneThree, nOneFour;
892 –    std::vector<int> fortranGlobalGroupMembership;
893 –    
894 –    isError = 0;
854  
896 –    //globalGroupMembership_ is filled by SimCreator    
897 –    for (int i = 0; i < nGlobalAtoms_; i++) {
898 –      fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
899 –    }
900 –
855      //calculate mass ratio of cutoff group
902 –    std::vector<RealType> mfact;
856      SimInfo::MoleculeIterator mi;
857      Molecule* mol;
858      Molecule::CutoffGroupIterator ci;
# Line 908 | Line 861 | namespace OpenMD {
861      Atom* atom;
862      RealType totalMass;
863  
864 <    //to avoid memory reallocation, reserve enough space for mfact
865 <    mfact.reserve(getNCutoffGroups());
864 >    /**
865 >     * The mass factor is the relative mass of an atom to the total
866 >     * mass of the cutoff group it belongs to.  By default, all atoms
867 >     * are their own cutoff groups, and therefore have mass factors of
868 >     * 1.  We need some special handling for massless atoms, which
869 >     * will be treated as carrying the entire mass of the cutoff
870 >     * group.
871 >     */
872 >    massFactors_.clear();
873 >    massFactors_.resize(getNAtoms(), 1.0);
874      
875      for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {        
876 <      for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
876 >      for (cg = mol->beginCutoffGroup(ci); cg != NULL;
877 >           cg = mol->nextCutoffGroup(ci)) {
878  
879          totalMass = cg->getMass();
880          for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
881            // Check for massless groups - set mfact to 1 if true
882 <          if (totalMass != 0)
883 <            mfact.push_back(atom->getMass()/totalMass);
882 >          if (totalMass != 0)
883 >            massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
884            else
885 <            mfact.push_back( 1.0 );
885 >            massFactors_[atom->getLocalIndex()] = 1.0;
886          }
887        }      
888      }
889  
890 <    //fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
929 <    std::vector<int> identArray;
890 >    // Build the identArray_
891  
892 <    //to avoid memory reallocation, reserve enough space identArray
893 <    identArray.reserve(getNAtoms());
933 <    
892 >    identArray_.clear();
893 >    identArray_.reserve(getNAtoms());    
894      for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {        
895        for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
896 <        identArray.push_back(atom->getIdent());
896 >        identArray_.push_back(atom->getIdent());
897        }
898      }    
939 –
940 –    //fill molMembershipArray
941 –    //molMembershipArray is filled by SimCreator    
942 –    std::vector<int> molMembershipArray(nGlobalAtoms_);
943 –    for (int i = 0; i < nGlobalAtoms_; i++) {
944 –      molMembershipArray[i] = globalMolMembership_[i] + 1;
945 –    }
899      
900 <    //setup fortran simulation
900 >    //scan topology
901  
902      nExclude = excludedInteractions_.getSize();
903      nOneTwo = oneTwoInteractions_.getSize();
# Line 956 | Line 909 | namespace OpenMD {
909      int* oneThreeList = oneThreeInteractions_.getPairList();
910      int* oneFourList = oneFourInteractions_.getPairList();
911  
912 <    setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
960 <                   &nExclude, excludeList,
961 <                   &nOneTwo, oneTwoList,
962 <                   &nOneThree, oneThreeList,
963 <                   &nOneFour, oneFourList,
964 <                   &molMembershipArray[0], &mfact[0], &nCutoffGroups_,
965 <                   &fortranGlobalGroupMembership[0], &isError);
966 <    
967 <    if( isError ){
968 <      
969 <      sprintf( painCave.errMsg,
970 <               "There was an error setting the simulation information in fortran.\n" );
971 <      painCave.isFatal = 1;
972 <      painCave.severity = OPENMD_ERROR;
973 <      simError();
974 <    }
975 <    
976 <    
977 <    sprintf( checkPointMsg,
978 <             "succesfully sent the simulation information to fortran.\n");
979 <    
980 <    errorCheckPoint();
981 <    
982 <    // Setup number of neighbors in neighbor list if present
983 <    if (simParams_->haveNeighborListNeighbors()) {
984 <      int nlistNeighbors = simParams_->getNeighborListNeighbors();
985 <      setNeighbors(&nlistNeighbors);
986 <    }
987 <  
988 <
989 <  }
990 <
991 <
992 <  void SimInfo::setupFortranParallel() {
993 < #ifdef IS_MPI    
994 <    //SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
995 <    std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
996 <    std::vector<int> localToGlobalCutoffGroupIndex;
997 <    SimInfo::MoleculeIterator mi;
998 <    Molecule::AtomIterator ai;
999 <    Molecule::CutoffGroupIterator ci;
1000 <    Molecule* mol;
1001 <    Atom* atom;
1002 <    CutoffGroup* cg;
1003 <    mpiSimData parallelData;
1004 <    int isError;
1005 <
1006 <    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
1007 <
1008 <      //local index(index in DataStorge) of atom is important
1009 <      for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
1010 <        localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
1011 <      }
1012 <
1013 <      //local index of cutoff group is trivial, it only depends on the order of travesing
1014 <      for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
1015 <        localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
1016 <      }        
1017 <        
1018 <    }
1019 <
1020 <    //fill up mpiSimData struct
1021 <    parallelData.nMolGlobal = getNGlobalMolecules();
1022 <    parallelData.nMolLocal = getNMolecules();
1023 <    parallelData.nAtomsGlobal = getNGlobalAtoms();
1024 <    parallelData.nAtomsLocal = getNAtoms();
1025 <    parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
1026 <    parallelData.nGroupsLocal = getNCutoffGroups();
1027 <    parallelData.myNode = worldRank;
1028 <    MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
1029 <
1030 <    //pass mpiSimData struct and index arrays to fortran
1031 <    setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
1032 <                    &localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
1033 <                    &localToGlobalCutoffGroupIndex[0], &isError);
1034 <
1035 <    if (isError) {
1036 <      sprintf(painCave.errMsg,
1037 <              "mpiRefresh errror: fortran didn't like something we gave it.\n");
1038 <      painCave.isFatal = 1;
1039 <      simError();
1040 <    }
1041 <
1042 <    sprintf(checkPointMsg, " mpiRefresh successful.\n");
1043 <    errorCheckPoint();
1044 <
1045 < #endif
1046 <  }
1047 <
1048 <  void SimInfo::setupCutoff() {          
1049 <    
1050 <    ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
1051 <
1052 <    // Check the cutoff policy
1053 <    int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
1054 <
1055 <    // Set LJ shifting bools to false
1056 <    ljsp_ = 0;
1057 <    ljsf_ = 0;
1058 <
1059 <    std::string myPolicy;
1060 <    if (forceFieldOptions_.haveCutoffPolicy()){
1061 <      myPolicy = forceFieldOptions_.getCutoffPolicy();
1062 <    }else if (simParams_->haveCutoffPolicy()) {
1063 <      myPolicy = simParams_->getCutoffPolicy();
1064 <    }
1065 <
1066 <    if (!myPolicy.empty()){
1067 <      toUpper(myPolicy);
1068 <      if (myPolicy == "MIX") {
1069 <        cp = MIX_CUTOFF_POLICY;
1070 <      } else {
1071 <        if (myPolicy == "MAX") {
1072 <          cp = MAX_CUTOFF_POLICY;
1073 <        } else {
1074 <          if (myPolicy == "TRADITIONAL") {            
1075 <            cp = TRADITIONAL_CUTOFF_POLICY;
1076 <          } else {
1077 <            // throw error        
1078 <            sprintf( painCave.errMsg,
1079 <                     "SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
1080 <            painCave.isFatal = 1;
1081 <            simError();
1082 <          }    
1083 <        }          
1084 <      }
1085 <    }          
1086 <    notifyFortranCutoffPolicy(&cp);
1087 <
1088 <    // Check the Skin Thickness for neighborlists
1089 <    RealType skin;
1090 <    if (simParams_->haveSkinThickness()) {
1091 <      skin = simParams_->getSkinThickness();
1092 <      notifyFortranSkinThickness(&skin);
1093 <    }            
1094 <        
1095 <    // Check if the cutoff was set explicitly:
1096 <    if (simParams_->haveCutoffRadius()) {
1097 <      rcut_ = simParams_->getCutoffRadius();
1098 <      if (simParams_->haveSwitchingRadius()) {
1099 <        rsw_  = simParams_->getSwitchingRadius();
1100 <      } else {
1101 <        if (fInfo_.SIM_uses_Charges |
1102 <            fInfo_.SIM_uses_Dipoles |
1103 <            fInfo_.SIM_uses_RF) {
1104 <          
1105 <          rsw_ = 0.85 * rcut_;
1106 <          sprintf(painCave.errMsg,
1107 <                  "SimCreator Warning: No value was set for the switchingRadius.\n"
1108 <                  "\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
1109 <                  "\tswitchingRadius = %f. for this simulation\n", rsw_);
1110 <        painCave.isFatal = 0;
1111 <        simError();
1112 <        } else {
1113 <          rsw_ = rcut_;
1114 <          sprintf(painCave.errMsg,
1115 <                  "SimCreator Warning: No value was set for the switchingRadius.\n"
1116 <                  "\tOpenMD will use the same value as the cutoffRadius.\n"
1117 <                  "\tswitchingRadius = %f. for this simulation\n", rsw_);
1118 <          painCave.isFatal = 0;
1119 <          simError();
1120 <        }
1121 <      }
1122 <
1123 <      if (simParams_->haveElectrostaticSummationMethod()) {
1124 <        std::string myMethod = simParams_->getElectrostaticSummationMethod();
1125 <        toUpper(myMethod);
1126 <        
1127 <        if (myMethod == "SHIFTED_POTENTIAL") {
1128 <          ljsp_ = 1;
1129 <        } else if (myMethod == "SHIFTED_FORCE") {
1130 <          ljsf_ = 1;
1131 <        }
1132 <      }
1133 <
1134 <      notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1135 <      
1136 <    } else {
1137 <      
1138 <      // For electrostatic atoms, we'll assume a large safe value:
1139 <      if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
1140 <        sprintf(painCave.errMsg,
1141 <                "SimCreator Warning: No value was set for the cutoffRadius.\n"
1142 <                "\tOpenMD will use a default value of 15.0 angstroms"
1143 <                "\tfor the cutoffRadius.\n");
1144 <        painCave.isFatal = 0;
1145 <        simError();
1146 <        rcut_ = 15.0;
1147 <      
1148 <        if (simParams_->haveElectrostaticSummationMethod()) {
1149 <          std::string myMethod = simParams_->getElectrostaticSummationMethod();
1150 <          toUpper(myMethod);
1151 <      
1152 <      // For the time being, we're tethering the LJ shifted behavior to the
1153 <      // electrostaticSummationMethod keyword options
1154 <          if (myMethod == "SHIFTED_POTENTIAL") {
1155 <            ljsp_ = 1;
1156 <          } else if (myMethod == "SHIFTED_FORCE") {
1157 <            ljsf_ = 1;
1158 <          }
1159 <          if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1160 <            if (simParams_->haveSwitchingRadius()){
1161 <              sprintf(painCave.errMsg,
1162 <                      "SimInfo Warning: A value was set for the switchingRadius\n"
1163 <                      "\teven though the electrostaticSummationMethod was\n"
1164 <                      "\tset to %s\n", myMethod.c_str());
1165 <              painCave.isFatal = 1;
1166 <              simError();            
1167 <            }
1168 <          }
1169 <        }
1170 <      
1171 <        if (simParams_->haveSwitchingRadius()){
1172 <          rsw_ = simParams_->getSwitchingRadius();
1173 <        } else {        
1174 <          sprintf(painCave.errMsg,
1175 <                  "SimCreator Warning: No value was set for switchingRadius.\n"
1176 <                  "\tOpenMD will use a default value of\n"
1177 <                  "\t0.85 * cutoffRadius for the switchingRadius\n");
1178 <          painCave.isFatal = 0;
1179 <          simError();
1180 <          rsw_ = 0.85 * rcut_;
1181 <        }
1182 <
1183 <        notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1184 <
1185 <      } else {
1186 <        // We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1187 <        // We'll punt and let fortran figure out the cutoffs later.
1188 <        
1189 <        notifyFortranYouAreOnYourOwn();
1190 <
1191 <      }
1192 <    }
1193 <  }
1194 <
1195 <  void SimInfo::setupElectrostaticSummationMethod( int isError ) {    
1196 <    
1197 <    int errorOut;
1198 <    int esm =  NONE;
1199 <    int sm = UNDAMPED;
1200 <    RealType alphaVal;
1201 <    RealType dielectric;
1202 <    
1203 <    errorOut = isError;
1204 <
1205 <    if (simParams_->haveElectrostaticSummationMethod()) {
1206 <      std::string myMethod = simParams_->getElectrostaticSummationMethod();
1207 <      toUpper(myMethod);
1208 <      if (myMethod == "NONE") {
1209 <        esm = NONE;
1210 <      } else {
1211 <        if (myMethod == "SWITCHING_FUNCTION") {
1212 <          esm = SWITCHING_FUNCTION;
1213 <        } else {
1214 <          if (myMethod == "SHIFTED_POTENTIAL") {
1215 <            esm = SHIFTED_POTENTIAL;
1216 <          } else {
1217 <            if (myMethod == "SHIFTED_FORCE") {            
1218 <              esm = SHIFTED_FORCE;
1219 <            } else {
1220 <              if (myMethod == "REACTION_FIELD") {
1221 <                esm = REACTION_FIELD;
1222 <                dielectric = simParams_->getDielectric();
1223 <                if (!simParams_->haveDielectric()) {
1224 <                  // throw warning
1225 <                  sprintf( painCave.errMsg,
1226 <                           "SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
1227 <                           "\tA default value of %f will be used for the dielectric.\n", dielectric);
1228 <                  painCave.isFatal = 0;
1229 <                  simError();
1230 <                }
1231 <              } else {
1232 <                // throw error        
1233 <                sprintf( painCave.errMsg,
1234 <                         "SimInfo error: Unknown electrostaticSummationMethod.\n"
1235 <                         "\t(Input file specified %s .)\n"
1236 <                         "\telectrostaticSummationMethod must be one of: \"none\",\n"
1237 <                         "\t\"shifted_potential\", \"shifted_force\", or \n"
1238 <                         "\t\"reaction_field\".\n", myMethod.c_str() );
1239 <                painCave.isFatal = 1;
1240 <                simError();
1241 <              }    
1242 <            }          
1243 <          }
1244 <        }
1245 <      }
1246 <    }
1247 <    
1248 <    if (simParams_->haveElectrostaticScreeningMethod()) {
1249 <      std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1250 <      toUpper(myScreen);
1251 <      if (myScreen == "UNDAMPED") {
1252 <        sm = UNDAMPED;
1253 <      } else {
1254 <        if (myScreen == "DAMPED") {
1255 <          sm = DAMPED;
1256 <          if (!simParams_->haveDampingAlpha()) {
1257 <            // first set a cutoff dependent alpha value
1258 <            // we assume alpha depends linearly with rcut from 0 to 20.5 ang
1259 <            alphaVal = 0.5125 - rcut_* 0.025;
1260 <            // for values rcut > 20.5, alpha is zero
1261 <            if (alphaVal < 0) alphaVal = 0;
1262 <
1263 <            // throw warning
1264 <            sprintf( painCave.errMsg,
1265 <                     "SimInfo warning: dampingAlpha was not specified in the input file.\n"
1266 <                     "\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1267 <            painCave.isFatal = 0;
1268 <            simError();
1269 <          } else {
1270 <            alphaVal = simParams_->getDampingAlpha();
1271 <          }
1272 <          
1273 <        } else {
1274 <          // throw error        
1275 <          sprintf( painCave.errMsg,
1276 <                   "SimInfo error: Unknown electrostaticScreeningMethod.\n"
1277 <                   "\t(Input file specified %s .)\n"
1278 <                   "\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1279 <                   "or \"damped\".\n", myScreen.c_str() );
1280 <          painCave.isFatal = 1;
1281 <          simError();
1282 <        }
1283 <      }
1284 <    }
1285 <    
1286 <    // let's pass some summation method variables to fortran
1287 <    setElectrostaticSummationMethod( &esm );
1288 <    setFortranElectrostaticMethod( &esm );
1289 <    setScreeningMethod( &sm );
1290 <    setDampingAlpha( &alphaVal );
1291 <    setReactionFieldDielectric( &dielectric );
1292 <    initFortranFF( &errorOut );
1293 <  }
1294 <
1295 <  void SimInfo::setupSwitchingFunction() {    
1296 <    int ft = CUBIC;
1297 <
1298 <    if (simParams_->haveSwitchingFunctionType()) {
1299 <      std::string funcType = simParams_->getSwitchingFunctionType();
1300 <      toUpper(funcType);
1301 <      if (funcType == "CUBIC") {
1302 <        ft = CUBIC;
1303 <      } else {
1304 <        if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1305 <          ft = FIFTH_ORDER_POLY;
1306 <        } else {
1307 <          // throw error        
1308 <          sprintf( painCave.errMsg,
1309 <                   "SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1310 <          painCave.isFatal = 1;
1311 <          simError();
1312 <        }          
1313 <      }
1314 <    }
1315 <
1316 <    // send switching function notification to switcheroo
1317 <    setFunctionType(&ft);
1318 <
912 >    topologyDone_ = true;
913    }
914  
1321 –  void SimInfo::setupAccumulateBoxDipole() {    
1322 –
1323 –    // we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1324 –    if ( simParams_->haveAccumulateBoxDipole() )
1325 –      if ( simParams_->getAccumulateBoxDipole() ) {
1326 –        setAccumulateBoxDipole();
1327 –        calcBoxDipole_ = true;
1328 –      }
1329 –
1330 –  }
1331 –
915    void SimInfo::addProperty(GenericData* genData) {
916      properties_.addProperty(genData);  
917    }
918  
919 <  void SimInfo::removeProperty(const std::string& propName) {
919 >  void SimInfo::removeProperty(const string& propName) {
920      properties_.removeProperty(propName);  
921    }
922  
# Line 1341 | Line 924 | namespace OpenMD {
924      properties_.clearProperties();
925    }
926  
927 <  std::vector<std::string> SimInfo::getPropertyNames() {
927 >  vector<string> SimInfo::getPropertyNames() {
928      return properties_.getPropertyNames();  
929    }
930        
931 <  std::vector<GenericData*> SimInfo::getProperties() {
931 >  vector<GenericData*> SimInfo::getProperties() {
932      return properties_.getProperties();
933    }
934  
935 <  GenericData* SimInfo::getPropertyByName(const std::string& propName) {
935 >  GenericData* SimInfo::getPropertyByName(const string& propName) {
936      return properties_.getPropertyByName(propName);
937    }
938  
# Line 1363 | Line 946 | namespace OpenMD {
946      Molecule* mol;
947      RigidBody* rb;
948      Atom* atom;
949 +    CutoffGroup* cg;
950      SimInfo::MoleculeIterator mi;
951      Molecule::RigidBodyIterator rbIter;
952 <    Molecule::AtomIterator atomIter;;
952 >    Molecule::AtomIterator atomIter;
953 >    Molecule::CutoffGroupIterator cgIter;
954  
955      for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
956          
# Line 1376 | Line 961 | namespace OpenMD {
961        for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
962          rb->setSnapshotManager(sman_);
963        }
964 +
965 +      for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
966 +        cg->setSnapshotManager(sman_);
967 +      }
968      }    
969      
970    }
# Line 1432 | Line 1021 | namespace OpenMD {
1021  
1022    }        
1023  
1024 <  std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1024 >  ostream& operator <<(ostream& o, SimInfo& info) {
1025  
1026      return o;
1027    }
# Line 1475 | Line 1064 | namespace OpenMD {
1064  
1065  
1066         [  Ixx -Ixy  -Ixz ]
1067 <  J =| -Iyx  Iyy  -Iyz |
1067 >    J =| -Iyx  Iyy  -Iyz |
1068         [ -Izx -Iyz   Izz ]
1069      */
1070  
# Line 1582 | Line 1171 | namespace OpenMD {
1171      return IOIndexToIntegrableObject.at(index);
1172    }
1173    
1174 <  void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1174 >  void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1175      IOIndexToIntegrableObject= v;
1176    }
1177  
# Line 1624 | Line 1213 | namespace OpenMD {
1213      return;
1214    }
1215   /*
1216 <   void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1216 >   void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1217        assert( v.size() == nAtoms_ + nRigidBodies_);
1218        sdByGlobalIndex_ = v;
1219      }
# Line 1634 | Line 1223 | namespace OpenMD {
1223        return sdByGlobalIndex_.at(index);
1224      }  
1225   */  
1226 +  int SimInfo::getNGlobalConstraints() {
1227 +    int nGlobalConstraints;
1228 + #ifdef IS_MPI
1229 +    MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1230 +                  MPI_COMM_WORLD);    
1231 + #else
1232 +    nGlobalConstraints =  nConstraints_;
1233 + #endif
1234 +    return nGlobalConstraints;
1235 +  }
1236 +
1237   }//end namespace OpenMD
1238  

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