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Revision 1505 by gezelter, Sun Oct 3 22:18:59 2010 UTC vs.
Revision 1744 by gezelter, Tue Jun 5 18:07:08 2012 UTC

# Line 36 | Line 36
36   * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).            
37   * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
38   * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
39 < * [4]  Vardeman & Gezelter, in progress (2009).                        
39 > * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40 > * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
42  
43   /**
# Line 54 | Line 55
55   #include "math/Vector3.hpp"
56   #include "primitives/Molecule.hpp"
57   #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"
58   #include "utils/MemoryUtils.hpp"
59   #include "utils/simError.h"
60   #include "selection/SelectionManager.hpp"
61   #include "io/ForceFieldOptions.hpp"
62 < #include "UseTheForce/ForceField.hpp"
63 <
68 <
62 > #include "brains/ForceField.hpp"
63 > #include "nonbonded/SwitchingFunction.hpp"
64   #ifdef IS_MPI
65 < #include "UseTheForce/mpiComponentPlan.h"
66 < #include "UseTheForce/DarkSide/simParallel_interface.h"
72 < #endif
65 > #include <mpi.h>
66 > #endif
67  
68 + using namespace std;
69   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 –  }
70    
71    SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
72      forceField_(ff), simParams_(simParams),
73      ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
74      nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
75 <    nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
75 >    nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0), nGlobalFluctuatingCharges_(0),
76      nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
77      nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
78 <    nConstraints_(0), sman_(NULL), fortranInitialized_(false),
79 <    calcBoxDipole_(false), useAtomicVirial_(true) {
80 <
81 <
82 <      MoleculeStamp* molStamp;
83 <      int nMolWithSameStamp;
84 <      int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
85 <      int nGroups = 0;      //total cutoff groups defined in meta-data file
86 <      CutoffGroupStamp* cgStamp;    
87 <      RigidBodyStamp* rbStamp;
88 <      int nRigidAtoms = 0;
89 <
90 <      std::vector<Component*> components = simParams->getComponents();
78 >    nConstraints_(0), nFluctuatingCharges_(0), sman_(NULL), topologyDone_(false),
79 >    calcBoxDipole_(false), useAtomicVirial_(true) {    
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 >    vector<Component*> components = simParams->getComponents();
90 >    
91 >    for (vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
92 >      molStamp = (*i)->getMoleculeStamp();
93 >      nMolWithSameStamp = (*i)->getNMol();
94        
95 <      for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
96 <        molStamp = (*i)->getMoleculeStamp();
97 <        nMolWithSameStamp = (*i)->getNMol();
98 <        
99 <        addMoleculeStamp(molStamp, nMolWithSameStamp);
100 <
101 <        //calculate atoms in molecules
102 <        nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;  
103 <
104 <        //calculate atoms in cutoff groups
105 <        int nAtomsInGroups = 0;
106 <        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 <        
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();
103 >      
104 >      for (int j=0; j < nCutoffGroupsInStamp; j++) {
105 >        cgStamp = molStamp->getCutoffGroupStamp(j);
106 >        nAtomsInGroups += cgStamp->getNMembers();
107        }
108 <
109 <      //every free atom (atom does not belong to cutoff groups) is a cutoff
110 <      //group therefore the total number of cutoff groups in the system is
111 <      //equal to the total number of atoms minus number of atoms belong to
112 <      //cutoff group defined in meta-data file plus the number of cutoff
113 <      //groups defined in meta-data file
114 <      nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
115 <
116 <      //every free atom (atom does not belong to rigid bodies) is an
117 <      //integrable object therefore the total number of integrable objects
118 <      //in the system is equal to the total number of atoms minus number of
119 <      //atoms belong to rigid body defined in meta-data file plus the number
120 <      //of rigid bodies defined in meta-data file
121 <      nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
122 <                                                + nGlobalRigidBodies_;
123 <  
124 <      nGlobalMols_ = molStampIds_.size();
158 <      molToProcMap_.resize(nGlobalMols_);
108 >      
109 >      nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
110 >      
111 >      nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;            
112 >      
113 >      //calculate atoms in rigid bodies
114 >      int nAtomsInRigidBodies = 0;
115 >      int nRigidBodiesInStamp = molStamp->getNRigidBodies();
116 >      
117 >      for (int j=0; j < nRigidBodiesInStamp; j++) {
118 >        rbStamp = molStamp->getRigidBodyStamp(j);
119 >        nAtomsInRigidBodies += rbStamp->getNMembers();
120 >      }
121 >      
122 >      nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
123 >      nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;            
124 >      
125      }
126 +    
127 +    //every free atom (atom does not belong to cutoff groups) is a cutoff
128 +    //group therefore the total number of cutoff groups in the system is
129 +    //equal to the total number of atoms minus number of atoms belong to
130 +    //cutoff group defined in meta-data file plus the number of cutoff
131 +    //groups defined in meta-data file
132  
133 +    nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
134 +    
135 +    //every free atom (atom does not belong to rigid bodies) is an
136 +    //integrable object therefore the total number of integrable objects
137 +    //in the system is equal to the total number of atoms minus number of
138 +    //atoms belong to rigid body defined in meta-data file plus the number
139 +    //of rigid bodies defined in meta-data file
140 +    nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
141 +      + nGlobalRigidBodies_;
142 +    
143 +    nGlobalMols_ = molStampIds_.size();
144 +    molToProcMap_.resize(nGlobalMols_);
145 +  }
146 +  
147    SimInfo::~SimInfo() {
148 <    std::map<int, Molecule*>::iterator i;
148 >    map<int, Molecule*>::iterator i;
149      for (i = molecules_.begin(); i != molecules_.end(); ++i) {
150        delete i->second;
151      }
# Line 170 | Line 156 | namespace OpenMD {
156      delete forceField_;
157    }
158  
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 –  }
159  
160    bool SimInfo::addMolecule(Molecule* mol) {
161      MoleculeIterator i;
162 <
162 >    
163      i = molecules_.find(mol->getGlobalIndex());
164      if (i == molecules_.end() ) {
165 <
166 <      molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
167 <        
165 >      
166 >      molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
167 >      
168        nAtoms_ += mol->getNAtoms();
169        nBonds_ += mol->getNBonds();
170        nBends_ += mol->getNBends();
# Line 198 | Line 174 | namespace OpenMD {
174        nIntegrableObjects_ += mol->getNIntegrableObjects();
175        nCutoffGroups_ += mol->getNCutoffGroups();
176        nConstraints_ += mol->getNConstraintPairs();
177 <
177 >      
178        addInteractionPairs(mol);
179 <  
179 >      
180        return true;
181      } else {
182        return false;
183      }
184    }
185 <
185 >  
186    bool SimInfo::removeMolecule(Molecule* mol) {
187      MoleculeIterator i;
188      i = molecules_.find(mol->getGlobalIndex());
# Line 234 | Line 210 | namespace OpenMD {
210      } else {
211        return false;
212      }
237 –
238 –
213    }    
214  
215          
# Line 251 | Line 225 | namespace OpenMD {
225  
226  
227    void SimInfo::calcNdf() {
228 <    int ndf_local;
228 >    int ndf_local, nfq_local;
229      MoleculeIterator i;
230 <    std::vector<StuntDouble*>::iterator j;
230 >    vector<StuntDouble*>::iterator j;
231 >    vector<Atom*>::iterator k;
232 >
233      Molecule* mol;
234      StuntDouble* integrableObject;
235 +    Atom* atom;
236  
237      ndf_local = 0;
238 +    nfq_local = 0;
239      
240      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
241        for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
# Line 272 | Line 250 | namespace OpenMD {
250              ndf_local += 3;
251            }
252          }
275 –            
253        }
254 +      for (atom = mol->beginFluctuatingCharge(k); atom != NULL;
255 +           atom = mol->nextFluctuatingCharge(k)) {
256 +        if (atom->isFluctuatingCharge()) {
257 +          nfq_local++;
258 +        }
259 +      }
260      }
261      
262 +    ndfLocal_ = ndf_local;
263 +    cerr << "ndfLocal_ = " << ndfLocal_ << "\n";
264 +
265      // n_constraints is local, so subtract them on each processor
266      ndf_local -= nConstraints_;
267  
268   #ifdef IS_MPI
269      MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
270 +    MPI_Allreduce(&nfq_local,&nGlobalFluctuatingCharges_,1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
271   #else
272      ndf_ = ndf_local;
273 +    nGlobalFluctuatingCharges_ = nfq_local;
274   #endif
275  
276      // nZconstraints_ is global, as are the 3 COM translations for the
# Line 298 | Line 286 | namespace OpenMD {
286      fdf_ = fdf_local;
287   #endif
288      return fdf_;
289 +  }
290 +  
291 +  unsigned int SimInfo::getNLocalCutoffGroups(){
292 +    int nLocalCutoffAtoms = 0;
293 +    Molecule* mol;
294 +    MoleculeIterator mi;
295 +    CutoffGroup* cg;
296 +    Molecule::CutoffGroupIterator ci;
297 +    
298 +    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
299 +      
300 +      for (cg = mol->beginCutoffGroup(ci); cg != NULL;
301 +           cg = mol->nextCutoffGroup(ci)) {
302 +        nLocalCutoffAtoms += cg->getNumAtom();
303 +        
304 +      }        
305 +    }
306 +    
307 +    return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_;
308    }
309      
310    void SimInfo::calcNdfRaw() {
311      int ndfRaw_local;
312  
313      MoleculeIterator i;
314 <    std::vector<StuntDouble*>::iterator j;
314 >    vector<StuntDouble*>::iterator j;
315      Molecule* mol;
316      StuntDouble* integrableObject;
317  
# Line 353 | Line 360 | namespace OpenMD {
360  
361    void SimInfo::addInteractionPairs(Molecule* mol) {
362      ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
363 <    std::vector<Bond*>::iterator bondIter;
364 <    std::vector<Bend*>::iterator bendIter;
365 <    std::vector<Torsion*>::iterator torsionIter;
366 <    std::vector<Inversion*>::iterator inversionIter;
363 >    vector<Bond*>::iterator bondIter;
364 >    vector<Bend*>::iterator bendIter;
365 >    vector<Torsion*>::iterator torsionIter;
366 >    vector<Inversion*>::iterator inversionIter;
367      Bond* bond;
368      Bend* bend;
369      Torsion* torsion;
# Line 374 | Line 381 | namespace OpenMD {
381      // always be excluded.  These are done at the bottom of this
382      // function.
383  
384 <    std::map<int, std::set<int> > atomGroups;
384 >    map<int, set<int> > atomGroups;
385      Molecule::RigidBodyIterator rbIter;
386      RigidBody* rb;
387      Molecule::IntegrableObjectIterator ii;
# Line 386 | Line 393 | namespace OpenMD {
393        
394        if (integrableObject->isRigidBody()) {
395          rb = static_cast<RigidBody*>(integrableObject);
396 <        std::vector<Atom*> atoms = rb->getAtoms();
397 <        std::set<int> rigidAtoms;
396 >        vector<Atom*> atoms = rb->getAtoms();
397 >        set<int> rigidAtoms;
398          for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
399            rigidAtoms.insert(atoms[i]->getGlobalIndex());
400          }
401          for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
402 <          atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
402 >          atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
403          }      
404        } else {
405 <        std::set<int> oneAtomSet;
405 >        set<int> oneAtomSet;
406          oneAtomSet.insert(integrableObject->getGlobalIndex());
407 <        atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));        
407 >        atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));        
408        }
409      }  
410            
# Line 500 | Line 507 | namespace OpenMD {
507  
508      for (rb = mol->beginRigidBody(rbIter); rb != NULL;
509           rb = mol->nextRigidBody(rbIter)) {
510 <      std::vector<Atom*> atoms = rb->getAtoms();
510 >      vector<Atom*> atoms = rb->getAtoms();
511        for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
512          for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
513            a = atoms[i]->getGlobalIndex();
# Line 514 | Line 521 | namespace OpenMD {
521  
522    void SimInfo::removeInteractionPairs(Molecule* mol) {
523      ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
524 <    std::vector<Bond*>::iterator bondIter;
525 <    std::vector<Bend*>::iterator bendIter;
526 <    std::vector<Torsion*>::iterator torsionIter;
527 <    std::vector<Inversion*>::iterator inversionIter;
524 >    vector<Bond*>::iterator bondIter;
525 >    vector<Bend*>::iterator bendIter;
526 >    vector<Torsion*>::iterator torsionIter;
527 >    vector<Inversion*>::iterator inversionIter;
528      Bond* bond;
529      Bend* bend;
530      Torsion* torsion;
# Line 527 | Line 534 | namespace OpenMD {
534      int c;
535      int d;
536  
537 <    std::map<int, std::set<int> > atomGroups;
537 >    map<int, set<int> > atomGroups;
538      Molecule::RigidBodyIterator rbIter;
539      RigidBody* rb;
540      Molecule::IntegrableObjectIterator ii;
# Line 539 | Line 546 | namespace OpenMD {
546        
547        if (integrableObject->isRigidBody()) {
548          rb = static_cast<RigidBody*>(integrableObject);
549 <        std::vector<Atom*> atoms = rb->getAtoms();
550 <        std::set<int> rigidAtoms;
549 >        vector<Atom*> atoms = rb->getAtoms();
550 >        set<int> rigidAtoms;
551          for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
552            rigidAtoms.insert(atoms[i]->getGlobalIndex());
553          }
554          for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
555 <          atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
555 >          atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
556          }      
557        } else {
558 <        std::set<int> oneAtomSet;
558 >        set<int> oneAtomSet;
559          oneAtomSet.insert(integrableObject->getGlobalIndex());
560 <        atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));        
560 >        atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));        
561        }
562      }  
563  
# Line 653 | Line 660 | namespace OpenMD {
660  
661      for (rb = mol->beginRigidBody(rbIter); rb != NULL;
662           rb = mol->nextRigidBody(rbIter)) {
663 <      std::vector<Atom*> atoms = rb->getAtoms();
663 >      vector<Atom*> atoms = rb->getAtoms();
664        for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
665          for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
666            a = atoms[i]->getGlobalIndex();
# Line 676 | Line 683 | namespace OpenMD {
683      molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
684    }
685  
679 –  void SimInfo::update() {
686  
687 <    setupSimType();
688 <
689 < #ifdef IS_MPI
690 <    setupFortranParallel();
691 < #endif
692 <
693 <    setupFortranSim();
694 <
695 <    //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 <
687 >  /**
688 >   * update
689 >   *
690 >   *  Performs the global checks and variable settings after the
691 >   *  objects have been created.
692 >   *
693 >   */
694 >  void SimInfo::update() {  
695 >    setupSimVariables();
696      calcNdf();
697      calcNdfRaw();
698      calcNdfTrans();
709 –
710 –    fortranInitialized_ = true;
699    }
700 <
701 <  std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
700 >  
701 >  /**
702 >   * getSimulatedAtomTypes
703 >   *
704 >   * Returns an STL set of AtomType* that are actually present in this
705 >   * simulation.  Must query all processors to assemble this information.
706 >   *
707 >   */
708 >  set<AtomType*> SimInfo::getSimulatedAtomTypes() {
709      SimInfo::MoleculeIterator mi;
710      Molecule* mol;
711      Molecule::AtomIterator ai;
712      Atom* atom;
713 <    std::set<AtomType*> atomTypes;
714 <
713 >    set<AtomType*> atomTypes;
714 >    
715      for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
716 <
717 <      for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
716 >      for(atom = mol->beginAtom(ai); atom != NULL;
717 >          atom = mol->nextAtom(ai)) {
718          atomTypes.insert(atom->getAtomType());
719 <      }
720 <        
721 <    }
719 >      }      
720 >    }    
721 >    
722 > #ifdef IS_MPI
723  
724 <    return atomTypes;        
725 <  }
730 <
731 <  void SimInfo::setupSimType() {
732 <    std::set<AtomType*>::iterator i;
733 <    std::set<AtomType*> atomTypes;
734 <    atomTypes = getUniqueAtomTypes();
724 >    // loop over the found atom types on this processor, and add their
725 >    // numerical idents to a vector:
726      
727 <    int useLennardJones = 0;
728 <    int useElectrostatic = 0;
729 <    int useEAM = 0;
730 <    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;
727 >    vector<int> foundTypes;
728 >    set<AtomType*>::iterator i;
729 >    for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
730 >      foundTypes.push_back( (*i)->getIdent() );
731  
732 <    std::string myMethod;
732 >    // count_local holds the number of found types on this processor
733 >    int count_local = foundTypes.size();
734  
735 <    // set the useRF logical
760 <    useRF = 0;
761 <    useSF = 0;
762 <    useSP = 0;
763 <    useBoxDipole = 0;
735 >    int nproc = MPI::COMM_WORLD.Get_size();
736  
737 <    if (simParams_->haveElectrostaticSummationMethod()) {
738 <      std::string myMethod = simParams_->getElectrostaticSummationMethod();
739 <      toUpper(myMethod);
740 <      if (myMethod == "REACTION_FIELD"){
741 <        useRF = 1;
742 <      } else if (myMethod == "SHIFTED_FORCE"){
743 <        useSF = 1;
744 <      } else if (myMethod == "SHIFTED_POTENTIAL"){
745 <        useSP = 1;
746 <      }
737 >    // we need arrays to hold the counts and displacement vectors for
738 >    // all processors
739 >    vector<int> counts(nproc, 0);
740 >    vector<int> disps(nproc, 0);
741 >
742 >    // fill the counts array
743 >    MPI::COMM_WORLD.Allgather(&count_local, 1, MPI::INT, &counts[0],
744 >                              1, MPI::INT);
745 >  
746 >    // use the processor counts to compute the displacement array
747 >    disps[0] = 0;    
748 >    int totalCount = counts[0];
749 >    for (int iproc = 1; iproc < nproc; iproc++) {
750 >      disps[iproc] = disps[iproc-1] + counts[iproc-1];
751 >      totalCount += counts[iproc];
752      }
753 +
754 +    // we need a (possibly redundant) set of all found types:
755 +    vector<int> ftGlobal(totalCount);
756      
757 <    if (simParams_->haveAccumulateBoxDipole())
758 <      if (simParams_->getAccumulateBoxDipole())
759 <        useBoxDipole = 1;
757 >    // now spray out the foundTypes to all the other processors:    
758 >    MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
759 >                               &ftGlobal[0], &counts[0], &disps[0],
760 >                               MPI::INT);
761  
762 <    useAtomicVirial_ = simParams_->getUseAtomicVirial();
762 >    vector<int>::iterator j;
763  
764 <    //loop over all of the atom types
765 <    for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
766 <      useLennardJones |= (*i)->isLennardJones();
786 <      useElectrostatic |= (*i)->isElectrostatic();
787 <      useEAM |= (*i)->isEAM();
788 <      useSC |= (*i)->isSC();
789 <      useCharge |= (*i)->isCharge();
790 <      useDirectional |= (*i)->isDirectional();
791 <      useDipole |= (*i)->isDipole();
792 <      useGayBerne |= (*i)->isGayBerne();
793 <      useSticky |= (*i)->isSticky();
794 <      useStickyPower |= (*i)->isStickyPower();
795 <      useShape |= (*i)->isShape();
796 <    }
764 >    // foundIdents is a stl set, so inserting an already found ident
765 >    // will have no effect.
766 >    set<int> foundIdents;
767  
768 <    if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
769 <      useDirectionalAtom = 1;
770 <    }
768 >    for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
769 >      foundIdents.insert((*j));
770 >    
771 >    // now iterate over the foundIdents and get the actual atom types
772 >    // that correspond to these:
773 >    set<int>::iterator it;
774 >    for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
775 >      atomTypes.insert( forceField_->getAtomType((*it)) );
776 >
777 > #endif
778  
779 <    if (useCharge || useDipole) {
780 <      useElectrostatics = 1;
804 <    }
779 >    return atomTypes;        
780 >  }
781  
782 +  void SimInfo::setupSimVariables() {
783 +    useAtomicVirial_ = simParams_->getUseAtomicVirial();
784 +    // we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
785 +    calcBoxDipole_ = false;
786 +    if ( simParams_->haveAccumulateBoxDipole() )
787 +      if ( simParams_->getAccumulateBoxDipole() ) {
788 +        calcBoxDipole_ = true;      
789 +      }
790 +    
791 +    set<AtomType*>::iterator i;
792 +    set<AtomType*> atomTypes;
793 +    atomTypes = getSimulatedAtomTypes();    
794 +    int usesElectrostatic = 0;
795 +    int usesMetallic = 0;
796 +    int usesDirectional = 0;
797 +    int usesFluctuatingCharges =  0;
798 +    //loop over all of the atom types
799 +    for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
800 +      usesElectrostatic |= (*i)->isElectrostatic();
801 +      usesMetallic |= (*i)->isMetal();
802 +      usesDirectional |= (*i)->isDirectional();
803 +      usesFluctuatingCharges |= (*i)->isFluctuatingCharge();
804 +    }
805 +    
806   #ifdef IS_MPI    
807      int temp;
808 +    temp = usesDirectional;
809 +    MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
810 +    
811 +    temp = usesMetallic;
812 +    MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
813 +    
814 +    temp = usesElectrostatic;
815 +    MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
816  
817 <    temp = usePBC;
818 <    MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
817 >    temp = usesFluctuatingCharges;
818 >    MPI_Allreduce(&temp, &usesFluctuatingCharges_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
819 > #else
820  
821 <    temp = useDirectionalAtom;
822 <    MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
821 >    usesDirectionalAtoms_ = usesDirectional;
822 >    usesMetallicAtoms_ = usesMetallic;
823 >    usesElectrostaticAtoms_ = usesElectrostatic;
824 >    usesFluctuatingCharges_ = usesFluctuatingCharges;
825  
826 <    temp = useLennardJones;
827 <    MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
826 > #endif
827 >    
828 >    requiresPrepair_ = usesMetallicAtoms_ ? true : false;
829 >    requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
830 >    requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;    
831 >  }
832  
818 –    temp = useElectrostatics;
819 –    MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
833  
834 <    temp = useCharge;
835 <    MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
834 >  vector<int> SimInfo::getGlobalAtomIndices() {
835 >    SimInfo::MoleculeIterator mi;
836 >    Molecule* mol;
837 >    Molecule::AtomIterator ai;
838 >    Atom* atom;
839  
840 <    temp = useDipole;
825 <    MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
826 <
827 <    temp = useSticky;
828 <    MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
829 <
830 <    temp = useStickyPower;
831 <    MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
840 >    vector<int> GlobalAtomIndices(getNAtoms(), 0);
841      
842 <    temp = useGayBerne;
843 <    MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
842 >    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
843 >      
844 >      for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
845 >        GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
846 >      }
847 >    }
848 >    return GlobalAtomIndices;
849 >  }
850  
836 –    temp = useEAM;
837 –    MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
851  
852 <    temp = useSC;
853 <    MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
854 <    
855 <    temp = useShape;
856 <    MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);  
852 >  vector<int> SimInfo::getGlobalGroupIndices() {
853 >    SimInfo::MoleculeIterator mi;
854 >    Molecule* mol;
855 >    Molecule::CutoffGroupIterator ci;
856 >    CutoffGroup* cg;
857  
858 <    temp = useFLARB;
859 <    MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
860 <
861 <    temp = useRF;
862 <    MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
863 <
864 <    temp = useSF;
865 <    MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);  
866 <
867 <    temp = useSP;
868 <    MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
869 <
857 <    temp = useBoxDipole;
858 <    MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
859 <
860 <    temp = useAtomicVirial_;
861 <    MPI_Allreduce(&temp, &useAtomicVirial_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
862 <
863 < #endif
864 <    fInfo_.SIM_uses_PBC = usePBC;    
865 <    fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
866 <    fInfo_.SIM_uses_LennardJones = useLennardJones;
867 <    fInfo_.SIM_uses_Electrostatics = useElectrostatics;    
868 <    fInfo_.SIM_uses_Charges = useCharge;
869 <    fInfo_.SIM_uses_Dipoles = useDipole;
870 <    fInfo_.SIM_uses_Sticky = useSticky;
871 <    fInfo_.SIM_uses_StickyPower = useStickyPower;
872 <    fInfo_.SIM_uses_GayBerne = useGayBerne;
873 <    fInfo_.SIM_uses_EAM = useEAM;
874 <    fInfo_.SIM_uses_SC = useSC;
875 <    fInfo_.SIM_uses_Shapes = useShape;
876 <    fInfo_.SIM_uses_FLARB = useFLARB;
877 <    fInfo_.SIM_uses_RF = useRF;
878 <    fInfo_.SIM_uses_SF = useSF;
879 <    fInfo_.SIM_uses_SP = useSP;
880 <    fInfo_.SIM_uses_BoxDipole = useBoxDipole;
881 <    fInfo_.SIM_uses_AtomicVirial = useAtomicVirial_;
858 >    vector<int> GlobalGroupIndices;
859 >    
860 >    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
861 >      
862 >      //local index of cutoff group is trivial, it only depends on the
863 >      //order of travesing
864 >      for (cg = mol->beginCutoffGroup(ci); cg != NULL;
865 >           cg = mol->nextCutoffGroup(ci)) {
866 >        GlobalGroupIndices.push_back(cg->getGlobalIndex());
867 >      }        
868 >    }
869 >    return GlobalGroupIndices;
870    }
871  
872 <  void SimInfo::setupFortranSim() {
873 <    int isError;
872 >
873 >  void SimInfo::prepareTopology() {
874      int nExclude, nOneTwo, nOneThree, nOneFour;
887 –    std::vector<int> fortranGlobalGroupMembership;
888 –    
889 –    isError = 0;
875  
891 –    //globalGroupMembership_ is filled by SimCreator    
892 –    for (int i = 0; i < nGlobalAtoms_; i++) {
893 –      fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
894 –    }
895 –
876      //calculate mass ratio of cutoff group
897 –    std::vector<RealType> mfact;
877      SimInfo::MoleculeIterator mi;
878      Molecule* mol;
879      Molecule::CutoffGroupIterator ci;
# Line 903 | Line 882 | namespace OpenMD {
882      Atom* atom;
883      RealType totalMass;
884  
885 <    //to avoid memory reallocation, reserve enough space for mfact
886 <    mfact.reserve(getNCutoffGroups());
885 >    /**
886 >     * The mass factor is the relative mass of an atom to the total
887 >     * mass of the cutoff group it belongs to.  By default, all atoms
888 >     * are their own cutoff groups, and therefore have mass factors of
889 >     * 1.  We need some special handling for massless atoms, which
890 >     * will be treated as carrying the entire mass of the cutoff
891 >     * group.
892 >     */
893 >    massFactors_.clear();
894 >    massFactors_.resize(getNAtoms(), 1.0);
895      
896      for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {        
897 <      for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
897 >      for (cg = mol->beginCutoffGroup(ci); cg != NULL;
898 >           cg = mol->nextCutoffGroup(ci)) {
899  
900          totalMass = cg->getMass();
901          for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
902            // Check for massless groups - set mfact to 1 if true
903 <          if (totalMass != 0)
904 <            mfact.push_back(atom->getMass()/totalMass);
903 >          if (totalMass != 0)
904 >            massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
905            else
906 <            mfact.push_back( 1.0 );
906 >            massFactors_[atom->getLocalIndex()] = 1.0;
907          }
908        }      
909      }
910  
911 <    //fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
924 <    std::vector<int> identArray;
911 >    // Build the identArray_
912  
913 <    //to avoid memory reallocation, reserve enough space identArray
914 <    identArray.reserve(getNAtoms());
928 <    
913 >    identArray_.clear();
914 >    identArray_.reserve(getNAtoms());    
915      for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {        
916        for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
917 <        identArray.push_back(atom->getIdent());
917 >        identArray_.push_back(atom->getIdent());
918        }
919      }    
934 –
935 –    //fill molMembershipArray
936 –    //molMembershipArray is filled by SimCreator    
937 –    std::vector<int> molMembershipArray(nGlobalAtoms_);
938 –    for (int i = 0; i < nGlobalAtoms_; i++) {
939 –      molMembershipArray[i] = globalMolMembership_[i] + 1;
940 –    }
920      
921 <    //setup fortran simulation
921 >    //scan topology
922  
923      nExclude = excludedInteractions_.getSize();
924      nOneTwo = oneTwoInteractions_.getSize();
# Line 951 | Line 930 | namespace OpenMD {
930      int* oneThreeList = oneThreeInteractions_.getPairList();
931      int* oneFourList = oneFourInteractions_.getPairList();
932  
933 <    setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
955 <                   &nExclude, excludeList,
956 <                   &nOneTwo, oneTwoList,
957 <                   &nOneThree, oneThreeList,
958 <                   &nOneFour, oneFourList,
959 <                   &molMembershipArray[0], &mfact[0], &nCutoffGroups_,
960 <                   &fortranGlobalGroupMembership[0], &isError);
961 <    
962 <    if( isError ){
963 <      
964 <      sprintf( painCave.errMsg,
965 <               "There was an error setting the simulation information in fortran.\n" );
966 <      painCave.isFatal = 1;
967 <      painCave.severity = OPENMD_ERROR;
968 <      simError();
969 <    }
970 <    
971 <    
972 <    sprintf( checkPointMsg,
973 <             "succesfully sent the simulation information to fortran.\n");
974 <    
975 <    errorCheckPoint();
976 <    
977 <    // Setup number of neighbors in neighbor list if present
978 <    if (simParams_->haveNeighborListNeighbors()) {
979 <      int nlistNeighbors = simParams_->getNeighborListNeighbors();
980 <      setNeighbors(&nlistNeighbors);
981 <    }
982 <  
983 <
984 <  }
985 <
986 <
987 <  void SimInfo::setupFortranParallel() {
988 < #ifdef IS_MPI    
989 <    //SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
990 <    std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
991 <    std::vector<int> localToGlobalCutoffGroupIndex;
992 <    SimInfo::MoleculeIterator mi;
993 <    Molecule::AtomIterator ai;
994 <    Molecule::CutoffGroupIterator ci;
995 <    Molecule* mol;
996 <    Atom* atom;
997 <    CutoffGroup* cg;
998 <    mpiSimData parallelData;
999 <    int isError;
1000 <
1001 <    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
1002 <
1003 <      //local index(index in DataStorge) of atom is important
1004 <      for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
1005 <        localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
1006 <      }
1007 <
1008 <      //local index of cutoff group is trivial, it only depends on the order of travesing
1009 <      for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
1010 <        localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
1011 <      }        
1012 <        
1013 <    }
1014 <
1015 <    //fill up mpiSimData struct
1016 <    parallelData.nMolGlobal = getNGlobalMolecules();
1017 <    parallelData.nMolLocal = getNMolecules();
1018 <    parallelData.nAtomsGlobal = getNGlobalAtoms();
1019 <    parallelData.nAtomsLocal = getNAtoms();
1020 <    parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
1021 <    parallelData.nGroupsLocal = getNCutoffGroups();
1022 <    parallelData.myNode = worldRank;
1023 <    MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
1024 <
1025 <    //pass mpiSimData struct and index arrays to fortran
1026 <    setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
1027 <                    &localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
1028 <                    &localToGlobalCutoffGroupIndex[0], &isError);
1029 <
1030 <    if (isError) {
1031 <      sprintf(painCave.errMsg,
1032 <              "mpiRefresh errror: fortran didn't like something we gave it.\n");
1033 <      painCave.isFatal = 1;
1034 <      simError();
1035 <    }
1036 <
1037 <    sprintf(checkPointMsg, " mpiRefresh successful.\n");
1038 <    errorCheckPoint();
1039 <
1040 < #endif
1041 <  }
1042 <
1043 <  void SimInfo::setupCutoff() {          
1044 <    
1045 <    ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
1046 <
1047 <    // Check the cutoff policy
1048 <    int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
1049 <
1050 <    // Set LJ shifting bools to false
1051 <    ljsp_ = 0;
1052 <    ljsf_ = 0;
1053 <
1054 <    std::string myPolicy;
1055 <    if (forceFieldOptions_.haveCutoffPolicy()){
1056 <      myPolicy = forceFieldOptions_.getCutoffPolicy();
1057 <    }else if (simParams_->haveCutoffPolicy()) {
1058 <      myPolicy = simParams_->getCutoffPolicy();
1059 <    }
1060 <
1061 <    if (!myPolicy.empty()){
1062 <      toUpper(myPolicy);
1063 <      if (myPolicy == "MIX") {
1064 <        cp = MIX_CUTOFF_POLICY;
1065 <      } else {
1066 <        if (myPolicy == "MAX") {
1067 <          cp = MAX_CUTOFF_POLICY;
1068 <        } else {
1069 <          if (myPolicy == "TRADITIONAL") {            
1070 <            cp = TRADITIONAL_CUTOFF_POLICY;
1071 <          } else {
1072 <            // throw error        
1073 <            sprintf( painCave.errMsg,
1074 <                     "SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
1075 <            painCave.isFatal = 1;
1076 <            simError();
1077 <          }    
1078 <        }          
1079 <      }
1080 <    }          
1081 <    notifyFortranCutoffPolicy(&cp);
1082 <
1083 <    // Check the Skin Thickness for neighborlists
1084 <    RealType skin;
1085 <    if (simParams_->haveSkinThickness()) {
1086 <      skin = simParams_->getSkinThickness();
1087 <      notifyFortranSkinThickness(&skin);
1088 <    }            
1089 <        
1090 <    // Check if the cutoff was set explicitly:
1091 <    if (simParams_->haveCutoffRadius()) {
1092 <      rcut_ = simParams_->getCutoffRadius();
1093 <      if (simParams_->haveSwitchingRadius()) {
1094 <        rsw_  = simParams_->getSwitchingRadius();
1095 <      } else {
1096 <        if (fInfo_.SIM_uses_Charges |
1097 <            fInfo_.SIM_uses_Dipoles |
1098 <            fInfo_.SIM_uses_RF) {
1099 <          
1100 <          rsw_ = 0.85 * rcut_;
1101 <          sprintf(painCave.errMsg,
1102 <                  "SimCreator Warning: No value was set for the switchingRadius.\n"
1103 <                  "\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
1104 <                  "\tswitchingRadius = %f. for this simulation\n", rsw_);
1105 <        painCave.isFatal = 0;
1106 <        simError();
1107 <        } else {
1108 <          rsw_ = rcut_;
1109 <          sprintf(painCave.errMsg,
1110 <                  "SimCreator Warning: No value was set for the switchingRadius.\n"
1111 <                  "\tOpenMD will use the same value as the cutoffRadius.\n"
1112 <                  "\tswitchingRadius = %f. for this simulation\n", rsw_);
1113 <          painCave.isFatal = 0;
1114 <          simError();
1115 <        }
1116 <      }
1117 <
1118 <      if (simParams_->haveElectrostaticSummationMethod()) {
1119 <        std::string myMethod = simParams_->getElectrostaticSummationMethod();
1120 <        toUpper(myMethod);
1121 <        
1122 <        if (myMethod == "SHIFTED_POTENTIAL") {
1123 <          ljsp_ = 1;
1124 <        } else if (myMethod == "SHIFTED_FORCE") {
1125 <          ljsf_ = 1;
1126 <        }
1127 <      }
1128 <
1129 <      notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1130 <      
1131 <    } else {
1132 <      
1133 <      // For electrostatic atoms, we'll assume a large safe value:
1134 <      if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
1135 <        sprintf(painCave.errMsg,
1136 <                "SimCreator Warning: No value was set for the cutoffRadius.\n"
1137 <                "\tOpenMD will use a default value of 15.0 angstroms"
1138 <                "\tfor the cutoffRadius.\n");
1139 <        painCave.isFatal = 0;
1140 <        simError();
1141 <        rcut_ = 15.0;
1142 <      
1143 <        if (simParams_->haveElectrostaticSummationMethod()) {
1144 <          std::string myMethod = simParams_->getElectrostaticSummationMethod();
1145 <          toUpper(myMethod);
1146 <          
1147 <          // For the time being, we're tethering the LJ shifted behavior to the
1148 <          // electrostaticSummationMethod keyword options
1149 <          if (myMethod == "SHIFTED_POTENTIAL") {
1150 <            ljsp_ = 1;
1151 <          } else if (myMethod == "SHIFTED_FORCE") {
1152 <            ljsf_ = 1;
1153 <          }
1154 <          if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1155 <            if (simParams_->haveSwitchingRadius()){
1156 <              sprintf(painCave.errMsg,
1157 <                      "SimInfo Warning: A value was set for the switchingRadius\n"
1158 <                      "\teven though the electrostaticSummationMethod was\n"
1159 <                      "\tset to %s\n", myMethod.c_str());
1160 <              painCave.isFatal = 1;
1161 <              simError();            
1162 <            }
1163 <          }
1164 <        }
1165 <      
1166 <        if (simParams_->haveSwitchingRadius()){
1167 <          rsw_ = simParams_->getSwitchingRadius();
1168 <        } else {        
1169 <          sprintf(painCave.errMsg,
1170 <                  "SimCreator Warning: No value was set for switchingRadius.\n"
1171 <                  "\tOpenMD will use a default value of\n"
1172 <                  "\t0.85 * cutoffRadius for the switchingRadius\n");
1173 <          painCave.isFatal = 0;
1174 <          simError();
1175 <          rsw_ = 0.85 * rcut_;
1176 <        }
1177 <
1178 <        Electrostatic::setElectrostaticCutoffRadius(rcut_, rsw_);
1179 <        notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1180 <
1181 <      } else {
1182 <        // We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1183 <        // We'll punt and let fortran figure out the cutoffs later.
1184 <        
1185 <        notifyFortranYouAreOnYourOwn();
1186 <
1187 <      }
1188 <    }
1189 <  }
1190 <
1191 <  void SimInfo::setupElectrostaticSummationMethod( int isError ) {    
1192 <    
1193 <    int errorOut;
1194 <    ElectrostaticSummationMethod esm = NONE;
1195 <    ElectrostaticScreeningMethod sm = UNDAMPED;
1196 <    RealType alphaVal;
1197 <    RealType dielectric;
1198 <    
1199 <    errorOut = isError;
1200 <
1201 <    if (simParams_->haveElectrostaticSummationMethod()) {
1202 <      std::string myMethod = simParams_->getElectrostaticSummationMethod();
1203 <      toUpper(myMethod);
1204 <      if (myMethod == "NONE") {
1205 <        esm = NONE;
1206 <      } else {
1207 <        if (myMethod == "SWITCHING_FUNCTION") {
1208 <          esm = SWITCHING_FUNCTION;
1209 <        } else {
1210 <          if (myMethod == "SHIFTED_POTENTIAL") {
1211 <            esm = SHIFTED_POTENTIAL;
1212 <          } else {
1213 <            if (myMethod == "SHIFTED_FORCE") {            
1214 <              esm = SHIFTED_FORCE;
1215 <            } else {
1216 <              if (myMethod == "REACTION_FIELD") {
1217 <                esm = REACTION_FIELD;
1218 <                dielectric = simParams_->getDielectric();
1219 <                if (!simParams_->haveDielectric()) {
1220 <                  // throw warning
1221 <                  sprintf( painCave.errMsg,
1222 <                           "SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
1223 <                           "\tA default value of %f will be used for the dielectric.\n", dielectric);
1224 <                  painCave.isFatal = 0;
1225 <                  simError();
1226 <                }
1227 <              } else {
1228 <                // throw error        
1229 <                sprintf( painCave.errMsg,
1230 <                         "SimInfo error: Unknown electrostaticSummationMethod.\n"
1231 <                         "\t(Input file specified %s .)\n"
1232 <                         "\telectrostaticSummationMethod must be one of: \"none\",\n"
1233 <                         "\t\"shifted_potential\", \"shifted_force\", or \n"
1234 <                         "\t\"reaction_field\".\n", myMethod.c_str() );
1235 <                painCave.isFatal = 1;
1236 <                simError();
1237 <              }    
1238 <            }          
1239 <          }
1240 <        }
1241 <      }
1242 <    }
1243 <    
1244 <    if (simParams_->haveElectrostaticScreeningMethod()) {
1245 <      std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1246 <      toUpper(myScreen);
1247 <      if (myScreen == "UNDAMPED") {
1248 <        sm = UNDAMPED;
1249 <      } else {
1250 <        if (myScreen == "DAMPED") {
1251 <          sm = DAMPED;
1252 <          if (!simParams_->haveDampingAlpha()) {
1253 <            // first set a cutoff dependent alpha value
1254 <            // we assume alpha depends linearly with rcut from 0 to 20.5 ang
1255 <            alphaVal = 0.5125 - rcut_* 0.025;
1256 <            // for values rcut > 20.5, alpha is zero
1257 <            if (alphaVal < 0) alphaVal = 0;
1258 <
1259 <            // throw warning
1260 <            sprintf( painCave.errMsg,
1261 <                     "SimInfo warning: dampingAlpha was not specified in the input file.\n"
1262 <                     "\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1263 <            painCave.isFatal = 0;
1264 <            simError();
1265 <          } else {
1266 <            alphaVal = simParams_->getDampingAlpha();
1267 <          }
1268 <          
1269 <        } else {
1270 <          // throw error        
1271 <          sprintf( painCave.errMsg,
1272 <                   "SimInfo error: Unknown electrostaticScreeningMethod.\n"
1273 <                   "\t(Input file specified %s .)\n"
1274 <                   "\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1275 <                   "or \"damped\".\n", myScreen.c_str() );
1276 <          painCave.isFatal = 1;
1277 <          simError();
1278 <        }
1279 <      }
1280 <    }
1281 <    
1282 <
1283 <    Electrostatic::setElectrostaticSummationMethod( esm );
1284 <    Electrostatic::setElectrostaticScreeningMethod( sm );
1285 <    Electrostatic::setDampingAlpha( alphaVal );
1286 <    Electrostatic::setReactionFieldDielectric( dielectric );
1287 <    initFortranFF( &errorOut );
1288 <  }
1289 <
1290 <  void SimInfo::setupSwitchingFunction() {    
1291 <    int ft = CUBIC;
1292 <
1293 <    if (simParams_->haveSwitchingFunctionType()) {
1294 <      std::string funcType = simParams_->getSwitchingFunctionType();
1295 <      toUpper(funcType);
1296 <      if (funcType == "CUBIC") {
1297 <        ft = CUBIC;
1298 <      } else {
1299 <        if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1300 <          ft = FIFTH_ORDER_POLY;
1301 <        } else {
1302 <          // throw error        
1303 <          sprintf( painCave.errMsg,
1304 <                   "SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1305 <          painCave.isFatal = 1;
1306 <          simError();
1307 <        }          
1308 <      }
1309 <    }
1310 <
1311 <    // send switching function notification to switcheroo
1312 <    setFunctionType(&ft);
1313 <
933 >    topologyDone_ = true;
934    }
935  
1316 –  void SimInfo::setupAccumulateBoxDipole() {    
1317 –
1318 –    // we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1319 –    if ( simParams_->haveAccumulateBoxDipole() )
1320 –      if ( simParams_->getAccumulateBoxDipole() ) {
1321 –        setAccumulateBoxDipole();
1322 –        calcBoxDipole_ = true;
1323 –      }
1324 –
1325 –  }
1326 –
936    void SimInfo::addProperty(GenericData* genData) {
937      properties_.addProperty(genData);  
938    }
939  
940 <  void SimInfo::removeProperty(const std::string& propName) {
940 >  void SimInfo::removeProperty(const string& propName) {
941      properties_.removeProperty(propName);  
942    }
943  
# Line 1336 | Line 945 | namespace OpenMD {
945      properties_.clearProperties();
946    }
947  
948 <  std::vector<std::string> SimInfo::getPropertyNames() {
948 >  vector<string> SimInfo::getPropertyNames() {
949      return properties_.getPropertyNames();  
950    }
951        
952 <  std::vector<GenericData*> SimInfo::getProperties() {
952 >  vector<GenericData*> SimInfo::getProperties() {
953      return properties_.getProperties();
954    }
955  
956 <  GenericData* SimInfo::getPropertyByName(const std::string& propName) {
956 >  GenericData* SimInfo::getPropertyByName(const string& propName) {
957      return properties_.getPropertyByName(propName);
958    }
959  
# Line 1358 | Line 967 | namespace OpenMD {
967      Molecule* mol;
968      RigidBody* rb;
969      Atom* atom;
970 +    CutoffGroup* cg;
971      SimInfo::MoleculeIterator mi;
972      Molecule::RigidBodyIterator rbIter;
973 <    Molecule::AtomIterator atomIter;;
973 >    Molecule::AtomIterator atomIter;
974 >    Molecule::CutoffGroupIterator cgIter;
975  
976      for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
977          
# Line 1370 | Line 981 | namespace OpenMD {
981          
982        for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
983          rb->setSnapshotManager(sman_);
984 +      }
985 +
986 +      for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
987 +        cg->setSnapshotManager(sman_);
988        }
989      }    
990      
# Line 1427 | Line 1042 | namespace OpenMD {
1042  
1043    }        
1044  
1045 <  std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1045 >  ostream& operator <<(ostream& o, SimInfo& info) {
1046  
1047      return o;
1048    }
# Line 1577 | Line 1192 | namespace OpenMD {
1192      return IOIndexToIntegrableObject.at(index);
1193    }
1194    
1195 <  void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1195 >  void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1196      IOIndexToIntegrableObject= v;
1197    }
1198  
# Line 1599 | Line 1214 | namespace OpenMD {
1214      
1215      det = intTensor.determinant();
1216      sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1217 <    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1217 >    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,geomCnst)*sqrt(det);
1218      return;
1219    }
1220  
# Line 1615 | Line 1230 | namespace OpenMD {
1230      
1231      detI = intTensor.determinant();
1232      sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1233 <    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1233 >    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,geomCnst)*sqrt(detI);
1234      return;
1235    }
1236   /*
1237 <   void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1237 >   void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1238        assert( v.size() == nAtoms_ + nRigidBodies_);
1239        sdByGlobalIndex_ = v;
1240      }
# Line 1629 | Line 1244 | namespace OpenMD {
1244        return sdByGlobalIndex_.at(index);
1245      }  
1246   */  
1247 +  int SimInfo::getNGlobalConstraints() {
1248 +    int nGlobalConstraints;
1249 + #ifdef IS_MPI
1250 +    MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1251 +                  MPI_COMM_WORLD);    
1252 + #else
1253 +    nGlobalConstraints =  nConstraints_;
1254 + #endif
1255 +    return nGlobalConstraints;
1256 +  }
1257 +
1258   }//end namespace OpenMD
1259  

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