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Revision 1503 by gezelter, Sat Oct 2 19:54:41 2010 UTC vs.
Revision 1760 by gezelter, Thu Jun 21 19:26:46 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 +
264      // n_constraints is local, so subtract them on each processor
265      ndf_local -= nConstraints_;
266  
267   #ifdef IS_MPI
268      MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
269 +    MPI_Allreduce(&nfq_local,&nGlobalFluctuatingCharges_,1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
270   #else
271      ndf_ = ndf_local;
272 +    nGlobalFluctuatingCharges_ = nfq_local;
273   #endif
274  
275      // nZconstraints_ is global, as are the 3 COM translations for the
# Line 298 | Line 285 | namespace OpenMD {
285      fdf_ = fdf_local;
286   #endif
287      return fdf_;
288 +  }
289 +  
290 +  unsigned int SimInfo::getNLocalCutoffGroups(){
291 +    int nLocalCutoffAtoms = 0;
292 +    Molecule* mol;
293 +    MoleculeIterator mi;
294 +    CutoffGroup* cg;
295 +    Molecule::CutoffGroupIterator ci;
296 +    
297 +    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
298 +      
299 +      for (cg = mol->beginCutoffGroup(ci); cg != NULL;
300 +           cg = mol->nextCutoffGroup(ci)) {
301 +        nLocalCutoffAtoms += cg->getNumAtom();
302 +        
303 +      }        
304 +    }
305 +    
306 +    return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_;
307    }
308      
309    void SimInfo::calcNdfRaw() {
310      int ndfRaw_local;
311  
312      MoleculeIterator i;
313 <    std::vector<StuntDouble*>::iterator j;
313 >    vector<StuntDouble*>::iterator j;
314      Molecule* mol;
315      StuntDouble* integrableObject;
316  
# Line 353 | Line 359 | namespace OpenMD {
359  
360    void SimInfo::addInteractionPairs(Molecule* mol) {
361      ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
362 <    std::vector<Bond*>::iterator bondIter;
363 <    std::vector<Bend*>::iterator bendIter;
364 <    std::vector<Torsion*>::iterator torsionIter;
365 <    std::vector<Inversion*>::iterator inversionIter;
362 >    vector<Bond*>::iterator bondIter;
363 >    vector<Bend*>::iterator bendIter;
364 >    vector<Torsion*>::iterator torsionIter;
365 >    vector<Inversion*>::iterator inversionIter;
366      Bond* bond;
367      Bend* bend;
368      Torsion* torsion;
# Line 374 | Line 380 | namespace OpenMD {
380      // always be excluded.  These are done at the bottom of this
381      // function.
382  
383 <    std::map<int, std::set<int> > atomGroups;
383 >    map<int, set<int> > atomGroups;
384      Molecule::RigidBodyIterator rbIter;
385      RigidBody* rb;
386      Molecule::IntegrableObjectIterator ii;
# Line 386 | Line 392 | namespace OpenMD {
392        
393        if (integrableObject->isRigidBody()) {
394          rb = static_cast<RigidBody*>(integrableObject);
395 <        std::vector<Atom*> atoms = rb->getAtoms();
396 <        std::set<int> rigidAtoms;
395 >        vector<Atom*> atoms = rb->getAtoms();
396 >        set<int> rigidAtoms;
397          for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
398            rigidAtoms.insert(atoms[i]->getGlobalIndex());
399          }
400          for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
401 <          atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
401 >          atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
402          }      
403        } else {
404 <        std::set<int> oneAtomSet;
404 >        set<int> oneAtomSet;
405          oneAtomSet.insert(integrableObject->getGlobalIndex());
406 <        atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));        
406 >        atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));        
407        }
408      }  
409            
# Line 500 | Line 506 | namespace OpenMD {
506  
507      for (rb = mol->beginRigidBody(rbIter); rb != NULL;
508           rb = mol->nextRigidBody(rbIter)) {
509 <      std::vector<Atom*> atoms = rb->getAtoms();
509 >      vector<Atom*> atoms = rb->getAtoms();
510        for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
511          for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
512            a = atoms[i]->getGlobalIndex();
# Line 514 | Line 520 | namespace OpenMD {
520  
521    void SimInfo::removeInteractionPairs(Molecule* mol) {
522      ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
523 <    std::vector<Bond*>::iterator bondIter;
524 <    std::vector<Bend*>::iterator bendIter;
525 <    std::vector<Torsion*>::iterator torsionIter;
526 <    std::vector<Inversion*>::iterator inversionIter;
523 >    vector<Bond*>::iterator bondIter;
524 >    vector<Bend*>::iterator bendIter;
525 >    vector<Torsion*>::iterator torsionIter;
526 >    vector<Inversion*>::iterator inversionIter;
527      Bond* bond;
528      Bend* bend;
529      Torsion* torsion;
# Line 527 | Line 533 | namespace OpenMD {
533      int c;
534      int d;
535  
536 <    std::map<int, std::set<int> > atomGroups;
536 >    map<int, set<int> > atomGroups;
537      Molecule::RigidBodyIterator rbIter;
538      RigidBody* rb;
539      Molecule::IntegrableObjectIterator ii;
# Line 539 | Line 545 | namespace OpenMD {
545        
546        if (integrableObject->isRigidBody()) {
547          rb = static_cast<RigidBody*>(integrableObject);
548 <        std::vector<Atom*> atoms = rb->getAtoms();
549 <        std::set<int> rigidAtoms;
548 >        vector<Atom*> atoms = rb->getAtoms();
549 >        set<int> rigidAtoms;
550          for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
551            rigidAtoms.insert(atoms[i]->getGlobalIndex());
552          }
553          for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
554 <          atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
554 >          atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
555          }      
556        } else {
557 <        std::set<int> oneAtomSet;
557 >        set<int> oneAtomSet;
558          oneAtomSet.insert(integrableObject->getGlobalIndex());
559 <        atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));        
559 >        atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));        
560        }
561      }  
562  
# Line 653 | Line 659 | namespace OpenMD {
659  
660      for (rb = mol->beginRigidBody(rbIter); rb != NULL;
661           rb = mol->nextRigidBody(rbIter)) {
662 <      std::vector<Atom*> atoms = rb->getAtoms();
662 >      vector<Atom*> atoms = rb->getAtoms();
663        for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
664          for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
665            a = atoms[i]->getGlobalIndex();
# Line 676 | Line 682 | namespace OpenMD {
682      molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
683    }
684  
679 –  void SimInfo::update() {
685  
686 <    setupSimType();
687 <
688 < #ifdef IS_MPI
689 <    setupFortranParallel();
690 < #endif
691 <
692 <    setupFortranSim();
693 <
694 <    //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 <
686 >  /**
687 >   * update
688 >   *
689 >   *  Performs the global checks and variable settings after the
690 >   *  objects have been created.
691 >   *
692 >   */
693 >  void SimInfo::update() {  
694 >    setupSimVariables();
695      calcNdf();
696      calcNdfRaw();
697      calcNdfTrans();
709 –
710 –    fortranInitialized_ = true;
698    }
699 <
700 <  std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
699 >  
700 >  /**
701 >   * getSimulatedAtomTypes
702 >   *
703 >   * Returns an STL set of AtomType* that are actually present in this
704 >   * simulation.  Must query all processors to assemble this information.
705 >   *
706 >   */
707 >  set<AtomType*> SimInfo::getSimulatedAtomTypes() {
708      SimInfo::MoleculeIterator mi;
709      Molecule* mol;
710      Molecule::AtomIterator ai;
711      Atom* atom;
712 <    std::set<AtomType*> atomTypes;
713 <
712 >    set<AtomType*> atomTypes;
713 >    
714      for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
715 <
716 <      for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
715 >      for(atom = mol->beginAtom(ai); atom != NULL;
716 >          atom = mol->nextAtom(ai)) {
717          atomTypes.insert(atom->getAtomType());
718 <      }
719 <        
720 <    }
718 >      }      
719 >    }    
720 >    
721 > #ifdef IS_MPI
722  
723 <    return atomTypes;        
724 <  }
730 <
731 <  void SimInfo::setupSimType() {
732 <    std::set<AtomType*>::iterator i;
733 <    std::set<AtomType*> atomTypes;
734 <    atomTypes = getUniqueAtomTypes();
723 >    // loop over the found atom types on this processor, and add their
724 >    // numerical idents to a vector:
725      
726 <    int useLennardJones = 0;
727 <    int useElectrostatic = 0;
728 <    int useEAM = 0;
729 <    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;
726 >    vector<int> foundTypes;
727 >    set<AtomType*>::iterator i;
728 >    for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
729 >      foundTypes.push_back( (*i)->getIdent() );
730  
731 <    std::string myMethod;
731 >    // count_local holds the number of found types on this processor
732 >    int count_local = foundTypes.size();
733  
734 <    // set the useRF logical
760 <    useRF = 0;
761 <    useSF = 0;
762 <    useSP = 0;
763 <    useBoxDipole = 0;
734 >    int nproc = MPI::COMM_WORLD.Get_size();
735  
736 +    // we need arrays to hold the counts and displacement vectors for
737 +    // all processors
738 +    vector<int> counts(nproc, 0);
739 +    vector<int> disps(nproc, 0);
740  
741 <    if (simParams_->haveElectrostaticSummationMethod()) {
742 <      std::string myMethod = simParams_->getElectrostaticSummationMethod();
743 <      toUpper(myMethod);
744 <      if (myMethod == "REACTION_FIELD"){
745 <        useRF = 1;
746 <      } else if (myMethod == "SHIFTED_FORCE"){
747 <        useSF = 1;
748 <      } else if (myMethod == "SHIFTED_POTENTIAL"){
749 <        useSP = 1;
750 <      }
741 >    // fill the counts array
742 >    MPI::COMM_WORLD.Allgather(&count_local, 1, MPI::INT, &counts[0],
743 >                              1, MPI::INT);
744 >  
745 >    // use the processor counts to compute the displacement array
746 >    disps[0] = 0;    
747 >    int totalCount = counts[0];
748 >    for (int iproc = 1; iproc < nproc; iproc++) {
749 >      disps[iproc] = disps[iproc-1] + counts[iproc-1];
750 >      totalCount += counts[iproc];
751      }
752 +
753 +    // we need a (possibly redundant) set of all found types:
754 +    vector<int> ftGlobal(totalCount);
755      
756 <    if (simParams_->haveAccumulateBoxDipole())
757 <      if (simParams_->getAccumulateBoxDipole())
758 <        useBoxDipole = 1;
756 >    // now spray out the foundTypes to all the other processors:    
757 >    MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
758 >                               &ftGlobal[0], &counts[0], &disps[0],
759 >                               MPI::INT);
760  
761 <    useAtomicVirial_ = simParams_->getUseAtomicVirial();
761 >    vector<int>::iterator j;
762  
763 +    // foundIdents is a stl set, so inserting an already found ident
764 +    // will have no effect.
765 +    set<int> foundIdents;
766 +
767 +    for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
768 +      foundIdents.insert((*j));
769 +    
770 +    // now iterate over the foundIdents and get the actual atom types
771 +    // that correspond to these:
772 +    set<int>::iterator it;
773 +    for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
774 +      atomTypes.insert( forceField_->getAtomType((*it)) );
775 +
776 + #endif
777 +
778 +    return atomTypes;        
779 +  }
780 +
781 +  void SimInfo::setupSimVariables() {
782 +    useAtomicVirial_ = simParams_->getUseAtomicVirial();
783 +    // we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
784 +    calcBoxDipole_ = false;
785 +    if ( simParams_->haveAccumulateBoxDipole() )
786 +      if ( simParams_->getAccumulateBoxDipole() ) {
787 +        calcBoxDipole_ = true;      
788 +      }
789 +    
790 +    set<AtomType*>::iterator i;
791 +    set<AtomType*> atomTypes;
792 +    atomTypes = getSimulatedAtomTypes();    
793 +    int usesElectrostatic = 0;
794 +    int usesMetallic = 0;
795 +    int usesDirectional = 0;
796 +    int usesFluctuatingCharges =  0;
797      //loop over all of the atom types
798      for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
799 <      useLennardJones |= (*i)->isLennardJones();
800 <      useElectrostatic |= (*i)->isElectrostatic();
801 <      useEAM |= (*i)->isEAM();
802 <      useSC |= (*i)->isSC();
790 <      useCharge |= (*i)->isCharge();
791 <      useDirectional |= (*i)->isDirectional();
792 <      useDipole |= (*i)->isDipole();
793 <      useGayBerne |= (*i)->isGayBerne();
794 <      useSticky |= (*i)->isSticky();
795 <      useStickyPower |= (*i)->isStickyPower();
796 <      useShape |= (*i)->isShape();
799 >      usesElectrostatic |= (*i)->isElectrostatic();
800 >      usesMetallic |= (*i)->isMetal();
801 >      usesDirectional |= (*i)->isDirectional();
802 >      usesFluctuatingCharges |= (*i)->isFluctuatingCharge();
803      }
804  
799 –    if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
800 –      useDirectionalAtom = 1;
801 –    }
802 –
803 –    if (useCharge || useDipole) {
804 –      useElectrostatics = 1;
805 –    }
806 –
805   #ifdef IS_MPI    
806      int temp;
807 +    temp = usesDirectional;
808 +    MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
809 +    
810 +    temp = usesMetallic;
811 +    MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
812 +    
813 +    temp = usesElectrostatic;
814 +    MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
815  
816 <    temp = usePBC;
817 <    MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
816 >    temp = usesFluctuatingCharges;
817 >    MPI_Allreduce(&temp, &usesFluctuatingCharges_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
818 > #else
819  
820 <    temp = useDirectionalAtom;
821 <    MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
820 >    usesDirectionalAtoms_ = usesDirectional;
821 >    usesMetallicAtoms_ = usesMetallic;
822 >    usesElectrostaticAtoms_ = usesElectrostatic;
823 >    usesFluctuatingCharges_ = usesFluctuatingCharges;
824  
825 <    temp = useLennardJones;
826 <    MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
825 > #endif
826 >    
827 >    requiresPrepair_ = usesMetallicAtoms_ ? true : false;
828 >    requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
829 >    requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;    
830 >  }
831  
819 –    temp = useElectrostatics;
820 –    MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
832  
833 <    temp = useCharge;
834 <    MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
833 >  vector<int> SimInfo::getGlobalAtomIndices() {
834 >    SimInfo::MoleculeIterator mi;
835 >    Molecule* mol;
836 >    Molecule::AtomIterator ai;
837 >    Atom* atom;
838  
839 <    temp = useDipole;
826 <    MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
827 <
828 <    temp = useSticky;
829 <    MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
830 <
831 <    temp = useStickyPower;
832 <    MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
839 >    vector<int> GlobalAtomIndices(getNAtoms(), 0);
840      
841 <    temp = useGayBerne;
842 <    MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
841 >    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
842 >      
843 >      for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
844 >        GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
845 >      }
846 >    }
847 >    return GlobalAtomIndices;
848 >  }
849  
837 –    temp = useEAM;
838 –    MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
850  
851 <    temp = useSC;
852 <    MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
853 <    
854 <    temp = useShape;
855 <    MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);  
851 >  vector<int> SimInfo::getGlobalGroupIndices() {
852 >    SimInfo::MoleculeIterator mi;
853 >    Molecule* mol;
854 >    Molecule::CutoffGroupIterator ci;
855 >    CutoffGroup* cg;
856  
857 <    temp = useFLARB;
858 <    MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
859 <
860 <    temp = useRF;
861 <    MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
862 <
863 <    temp = useSF;
864 <    MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);  
865 <
866 <    temp = useSP;
867 <    MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
868 <
858 <    temp = useBoxDipole;
859 <    MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
860 <
861 <    temp = useAtomicVirial_;
862 <    MPI_Allreduce(&temp, &useAtomicVirial_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
863 <
864 < #endif
865 <
866 <    fInfo_.SIM_uses_PBC = usePBC;    
867 <    fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
868 <    fInfo_.SIM_uses_LennardJones = useLennardJones;
869 <    fInfo_.SIM_uses_Electrostatics = useElectrostatics;    
870 <    fInfo_.SIM_uses_Charges = useCharge;
871 <    fInfo_.SIM_uses_Dipoles = useDipole;
872 <    fInfo_.SIM_uses_Sticky = useSticky;
873 <    fInfo_.SIM_uses_StickyPower = useStickyPower;
874 <    fInfo_.SIM_uses_GayBerne = useGayBerne;
875 <    fInfo_.SIM_uses_EAM = useEAM;
876 <    fInfo_.SIM_uses_SC = useSC;
877 <    fInfo_.SIM_uses_Shapes = useShape;
878 <    fInfo_.SIM_uses_FLARB = useFLARB;
879 <    fInfo_.SIM_uses_RF = useRF;
880 <    fInfo_.SIM_uses_SF = useSF;
881 <    fInfo_.SIM_uses_SP = useSP;
882 <    fInfo_.SIM_uses_BoxDipole = useBoxDipole;
883 <    fInfo_.SIM_uses_AtomicVirial = useAtomicVirial_;
857 >    vector<int> GlobalGroupIndices;
858 >    
859 >    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
860 >      
861 >      //local index of cutoff group is trivial, it only depends on the
862 >      //order of travesing
863 >      for (cg = mol->beginCutoffGroup(ci); cg != NULL;
864 >           cg = mol->nextCutoffGroup(ci)) {
865 >        GlobalGroupIndices.push_back(cg->getGlobalIndex());
866 >      }        
867 >    }
868 >    return GlobalGroupIndices;
869    }
870  
871 <  void SimInfo::setupFortranSim() {
872 <    int isError;
871 >
872 >  void SimInfo::prepareTopology() {
873      int nExclude, nOneTwo, nOneThree, nOneFour;
889 –    std::vector<int> fortranGlobalGroupMembership;
890 –    
891 –    isError = 0;
874  
893 –    //globalGroupMembership_ is filled by SimCreator    
894 –    for (int i = 0; i < nGlobalAtoms_; i++) {
895 –      fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
896 –    }
897 –
875      //calculate mass ratio of cutoff group
899 –    std::vector<RealType> mfact;
876      SimInfo::MoleculeIterator mi;
877      Molecule* mol;
878      Molecule::CutoffGroupIterator ci;
# Line 905 | Line 881 | namespace OpenMD {
881      Atom* atom;
882      RealType totalMass;
883  
884 <    //to avoid memory reallocation, reserve enough space for mfact
885 <    mfact.reserve(getNCutoffGroups());
884 >    /**
885 >     * The mass factor is the relative mass of an atom to the total
886 >     * mass of the cutoff group it belongs to.  By default, all atoms
887 >     * are their own cutoff groups, and therefore have mass factors of
888 >     * 1.  We need some special handling for massless atoms, which
889 >     * will be treated as carrying the entire mass of the cutoff
890 >     * group.
891 >     */
892 >    massFactors_.clear();
893 >    massFactors_.resize(getNAtoms(), 1.0);
894      
895      for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {        
896 <      for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
896 >      for (cg = mol->beginCutoffGroup(ci); cg != NULL;
897 >           cg = mol->nextCutoffGroup(ci)) {
898  
899          totalMass = cg->getMass();
900          for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
901            // Check for massless groups - set mfact to 1 if true
902 <          if (totalMass != 0)
903 <            mfact.push_back(atom->getMass()/totalMass);
902 >          if (totalMass != 0)
903 >            massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
904            else
905 <            mfact.push_back( 1.0 );
905 >            massFactors_[atom->getLocalIndex()] = 1.0;
906          }
907        }      
908      }
909  
910 <    //fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
926 <    std::vector<int> identArray;
910 >    // Build the identArray_
911  
912 <    //to avoid memory reallocation, reserve enough space identArray
913 <    identArray.reserve(getNAtoms());
930 <    
912 >    identArray_.clear();
913 >    identArray_.reserve(getNAtoms());    
914      for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {        
915        for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
916 <        identArray.push_back(atom->getIdent());
916 >        identArray_.push_back(atom->getIdent());
917        }
918      }    
936 –
937 –    //fill molMembershipArray
938 –    //molMembershipArray is filled by SimCreator    
939 –    std::vector<int> molMembershipArray(nGlobalAtoms_);
940 –    for (int i = 0; i < nGlobalAtoms_; i++) {
941 –      molMembershipArray[i] = globalMolMembership_[i] + 1;
942 –    }
919      
920 <    //setup fortran simulation
920 >    //scan topology
921  
922      nExclude = excludedInteractions_.getSize();
923      nOneTwo = oneTwoInteractions_.getSize();
# Line 953 | Line 929 | namespace OpenMD {
929      int* oneThreeList = oneThreeInteractions_.getPairList();
930      int* oneFourList = oneFourInteractions_.getPairList();
931  
932 <    setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
957 <                   &nExclude, excludeList,
958 <                   &nOneTwo, oneTwoList,
959 <                   &nOneThree, oneThreeList,
960 <                   &nOneFour, oneFourList,
961 <                   &molMembershipArray[0], &mfact[0], &nCutoffGroups_,
962 <                   &fortranGlobalGroupMembership[0], &isError);
963 <    
964 <    if( isError ){
965 <      
966 <      sprintf( painCave.errMsg,
967 <               "There was an error setting the simulation information in fortran.\n" );
968 <      painCave.isFatal = 1;
969 <      painCave.severity = OPENMD_ERROR;
970 <      simError();
971 <    }
972 <    
973 <    
974 <    sprintf( checkPointMsg,
975 <             "succesfully sent the simulation information to fortran.\n");
976 <    
977 <    errorCheckPoint();
978 <    
979 <    // Setup number of neighbors in neighbor list if present
980 <    if (simParams_->haveNeighborListNeighbors()) {
981 <      int nlistNeighbors = simParams_->getNeighborListNeighbors();
982 <      setNeighbors(&nlistNeighbors);
983 <    }
984 <  
985 <
986 <  }
987 <
988 <
989 <  void SimInfo::setupFortranParallel() {
990 < #ifdef IS_MPI    
991 <    //SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
992 <    std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
993 <    std::vector<int> localToGlobalCutoffGroupIndex;
994 <    SimInfo::MoleculeIterator mi;
995 <    Molecule::AtomIterator ai;
996 <    Molecule::CutoffGroupIterator ci;
997 <    Molecule* mol;
998 <    Atom* atom;
999 <    CutoffGroup* cg;
1000 <    mpiSimData parallelData;
1001 <    int isError;
1002 <
1003 <    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
1004 <
1005 <      //local index(index in DataStorge) of atom is important
1006 <      for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
1007 <        localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
1008 <      }
1009 <
1010 <      //local index of cutoff group is trivial, it only depends on the order of travesing
1011 <      for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
1012 <        localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
1013 <      }        
1014 <        
1015 <    }
1016 <
1017 <    //fill up mpiSimData struct
1018 <    parallelData.nMolGlobal = getNGlobalMolecules();
1019 <    parallelData.nMolLocal = getNMolecules();
1020 <    parallelData.nAtomsGlobal = getNGlobalAtoms();
1021 <    parallelData.nAtomsLocal = getNAtoms();
1022 <    parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
1023 <    parallelData.nGroupsLocal = getNCutoffGroups();
1024 <    parallelData.myNode = worldRank;
1025 <    MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
1026 <
1027 <    //pass mpiSimData struct and index arrays to fortran
1028 <    setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
1029 <                    &localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
1030 <                    &localToGlobalCutoffGroupIndex[0], &isError);
1031 <
1032 <    if (isError) {
1033 <      sprintf(painCave.errMsg,
1034 <              "mpiRefresh errror: fortran didn't like something we gave it.\n");
1035 <      painCave.isFatal = 1;
1036 <      simError();
1037 <    }
1038 <
1039 <    sprintf(checkPointMsg, " mpiRefresh successful.\n");
1040 <    errorCheckPoint();
1041 <
1042 < #endif
1043 <  }
1044 <
1045 <  void SimInfo::setupCutoff() {          
1046 <    
1047 <    ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
1048 <
1049 <    // Check the cutoff policy
1050 <    int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
1051 <
1052 <    // Set LJ shifting bools to false
1053 <    ljsp_ = 0;
1054 <    ljsf_ = 0;
1055 <
1056 <    std::string myPolicy;
1057 <    if (forceFieldOptions_.haveCutoffPolicy()){
1058 <      myPolicy = forceFieldOptions_.getCutoffPolicy();
1059 <    }else if (simParams_->haveCutoffPolicy()) {
1060 <      myPolicy = simParams_->getCutoffPolicy();
1061 <    }
1062 <
1063 <    if (!myPolicy.empty()){
1064 <      toUpper(myPolicy);
1065 <      if (myPolicy == "MIX") {
1066 <        cp = MIX_CUTOFF_POLICY;
1067 <      } else {
1068 <        if (myPolicy == "MAX") {
1069 <          cp = MAX_CUTOFF_POLICY;
1070 <        } else {
1071 <          if (myPolicy == "TRADITIONAL") {            
1072 <            cp = TRADITIONAL_CUTOFF_POLICY;
1073 <          } else {
1074 <            // throw error        
1075 <            sprintf( painCave.errMsg,
1076 <                     "SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
1077 <            painCave.isFatal = 1;
1078 <            simError();
1079 <          }    
1080 <        }          
1081 <      }
1082 <    }          
1083 <    notifyFortranCutoffPolicy(&cp);
1084 <
1085 <    // Check the Skin Thickness for neighborlists
1086 <    RealType skin;
1087 <    if (simParams_->haveSkinThickness()) {
1088 <      skin = simParams_->getSkinThickness();
1089 <      notifyFortranSkinThickness(&skin);
1090 <    }            
1091 <        
1092 <    // Check if the cutoff was set explicitly:
1093 <    if (simParams_->haveCutoffRadius()) {
1094 <      rcut_ = simParams_->getCutoffRadius();
1095 <      if (simParams_->haveSwitchingRadius()) {
1096 <        rsw_  = simParams_->getSwitchingRadius();
1097 <      } else {
1098 <        if (fInfo_.SIM_uses_Charges |
1099 <            fInfo_.SIM_uses_Dipoles |
1100 <            fInfo_.SIM_uses_RF) {
1101 <          
1102 <          rsw_ = 0.85 * rcut_;
1103 <          sprintf(painCave.errMsg,
1104 <                  "SimCreator Warning: No value was set for the switchingRadius.\n"
1105 <                  "\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
1106 <                  "\tswitchingRadius = %f. for this simulation\n", rsw_);
1107 <        painCave.isFatal = 0;
1108 <        simError();
1109 <        } else {
1110 <          rsw_ = rcut_;
1111 <          sprintf(painCave.errMsg,
1112 <                  "SimCreator Warning: No value was set for the switchingRadius.\n"
1113 <                  "\tOpenMD will use the same value as the cutoffRadius.\n"
1114 <                  "\tswitchingRadius = %f. for this simulation\n", rsw_);
1115 <          painCave.isFatal = 0;
1116 <          simError();
1117 <        }
1118 <      }
1119 <
1120 <      if (simParams_->haveElectrostaticSummationMethod()) {
1121 <        std::string myMethod = simParams_->getElectrostaticSummationMethod();
1122 <        toUpper(myMethod);
1123 <        
1124 <        if (myMethod == "SHIFTED_POTENTIAL") {
1125 <          ljsp_ = 1;
1126 <        } else if (myMethod == "SHIFTED_FORCE") {
1127 <          ljsf_ = 1;
1128 <        }
1129 <      }
1130 <
1131 <      notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1132 <      
1133 <    } else {
1134 <      
1135 <      // For electrostatic atoms, we'll assume a large safe value:
1136 <      if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
1137 <        sprintf(painCave.errMsg,
1138 <                "SimCreator Warning: No value was set for the cutoffRadius.\n"
1139 <                "\tOpenMD will use a default value of 15.0 angstroms"
1140 <                "\tfor the cutoffRadius.\n");
1141 <        painCave.isFatal = 0;
1142 <        simError();
1143 <        rcut_ = 15.0;
1144 <      
1145 <        if (simParams_->haveElectrostaticSummationMethod()) {
1146 <          std::string myMethod = simParams_->getElectrostaticSummationMethod();
1147 <          toUpper(myMethod);
1148 <          
1149 <          // For the time being, we're tethering the LJ shifted behavior to the
1150 <          // electrostaticSummationMethod keyword options
1151 <          if (myMethod == "SHIFTED_POTENTIAL") {
1152 <            ljsp_ = 1;
1153 <          } else if (myMethod == "SHIFTED_FORCE") {
1154 <            ljsf_ = 1;
1155 <          }
1156 <          if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1157 <            if (simParams_->haveSwitchingRadius()){
1158 <              sprintf(painCave.errMsg,
1159 <                      "SimInfo Warning: A value was set for the switchingRadius\n"
1160 <                      "\teven though the electrostaticSummationMethod was\n"
1161 <                      "\tset to %s\n", myMethod.c_str());
1162 <              painCave.isFatal = 1;
1163 <              simError();            
1164 <            }
1165 <          }
1166 <        }
1167 <      
1168 <        if (simParams_->haveSwitchingRadius()){
1169 <          rsw_ = simParams_->getSwitchingRadius();
1170 <        } else {        
1171 <          sprintf(painCave.errMsg,
1172 <                  "SimCreator Warning: No value was set for switchingRadius.\n"
1173 <                  "\tOpenMD will use a default value of\n"
1174 <                  "\t0.85 * cutoffRadius for the switchingRadius\n");
1175 <          painCave.isFatal = 0;
1176 <          simError();
1177 <          rsw_ = 0.85 * rcut_;
1178 <        }
1179 <
1180 <        Electrostatic::setElectrostaticCutoffRadius(rcut_, rsw_);
1181 <        notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1182 <
1183 <      } else {
1184 <        // We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1185 <        // We'll punt and let fortran figure out the cutoffs later.
1186 <        
1187 <        notifyFortranYouAreOnYourOwn();
1188 <
1189 <      }
1190 <    }
932 >    topologyDone_ = true;
933    }
934  
1193 –  void SimInfo::setupElectrostaticSummationMethod( int isError ) {    
1194 –    
1195 –    int errorOut;
1196 –    ElectrostaticSummationMethod esm = NONE;
1197 –    ElectrostaticScreeningMethod sm = UNDAMPED;
1198 –    RealType alphaVal;
1199 –    RealType dielectric;
1200 –    
1201 –    errorOut = isError;
1202 –
1203 –    if (simParams_->haveElectrostaticSummationMethod()) {
1204 –      std::string myMethod = simParams_->getElectrostaticSummationMethod();
1205 –      toUpper(myMethod);
1206 –      if (myMethod == "NONE") {
1207 –        esm = NONE;
1208 –      } else {
1209 –        if (myMethod == "SWITCHING_FUNCTION") {
1210 –          esm = SWITCHING_FUNCTION;
1211 –        } else {
1212 –          if (myMethod == "SHIFTED_POTENTIAL") {
1213 –            esm = SHIFTED_POTENTIAL;
1214 –          } else {
1215 –            if (myMethod == "SHIFTED_FORCE") {            
1216 –              esm = SHIFTED_FORCE;
1217 –            } else {
1218 –              if (myMethod == "REACTION_FIELD") {
1219 –                esm = REACTION_FIELD;
1220 –                dielectric = simParams_->getDielectric();
1221 –                if (!simParams_->haveDielectric()) {
1222 –                  // throw warning
1223 –                  sprintf( painCave.errMsg,
1224 –                           "SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
1225 –                           "\tA default value of %f will be used for the dielectric.\n", dielectric);
1226 –                  painCave.isFatal = 0;
1227 –                  simError();
1228 –                }
1229 –              } else {
1230 –                // throw error        
1231 –                sprintf( painCave.errMsg,
1232 –                         "SimInfo error: Unknown electrostaticSummationMethod.\n"
1233 –                         "\t(Input file specified %s .)\n"
1234 –                         "\telectrostaticSummationMethod must be one of: \"none\",\n"
1235 –                         "\t\"shifted_potential\", \"shifted_force\", or \n"
1236 –                         "\t\"reaction_field\".\n", myMethod.c_str() );
1237 –                painCave.isFatal = 1;
1238 –                simError();
1239 –              }    
1240 –            }          
1241 –          }
1242 –        }
1243 –      }
1244 –    }
1245 –    
1246 –    if (simParams_->haveElectrostaticScreeningMethod()) {
1247 –      std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1248 –      toUpper(myScreen);
1249 –      if (myScreen == "UNDAMPED") {
1250 –        sm = UNDAMPED;
1251 –      } else {
1252 –        if (myScreen == "DAMPED") {
1253 –          sm = DAMPED;
1254 –          if (!simParams_->haveDampingAlpha()) {
1255 –            // first set a cutoff dependent alpha value
1256 –            // we assume alpha depends linearly with rcut from 0 to 20.5 ang
1257 –            alphaVal = 0.5125 - rcut_* 0.025;
1258 –            // for values rcut > 20.5, alpha is zero
1259 –            if (alphaVal < 0) alphaVal = 0;
1260 –
1261 –            // throw warning
1262 –            sprintf( painCave.errMsg,
1263 –                     "SimInfo warning: dampingAlpha was not specified in the input file.\n"
1264 –                     "\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1265 –            painCave.isFatal = 0;
1266 –            simError();
1267 –          } else {
1268 –            alphaVal = simParams_->getDampingAlpha();
1269 –          }
1270 –          
1271 –        } else {
1272 –          // throw error        
1273 –          sprintf( painCave.errMsg,
1274 –                   "SimInfo error: Unknown electrostaticScreeningMethod.\n"
1275 –                   "\t(Input file specified %s .)\n"
1276 –                   "\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1277 –                   "or \"damped\".\n", myScreen.c_str() );
1278 –          painCave.isFatal = 1;
1279 –          simError();
1280 –        }
1281 –      }
1282 –    }
1283 –    
1284 –
1285 –    Electrostatic::setElectrostaticSummationMethod( esm );
1286 –    Electrostatic::setElectrostaticScreeningMethod( sm );
1287 –    Electrostatic::setDampingAlpha( alphaVal );
1288 –    Electrostatic::setReactionFieldDielectric( dielectric );
1289 –    initFortranFF( &errorOut );
1290 –  }
1291 –
1292 –  void SimInfo::setupSwitchingFunction() {    
1293 –    int ft = CUBIC;
1294 –
1295 –    if (simParams_->haveSwitchingFunctionType()) {
1296 –      std::string funcType = simParams_->getSwitchingFunctionType();
1297 –      toUpper(funcType);
1298 –      if (funcType == "CUBIC") {
1299 –        ft = CUBIC;
1300 –      } else {
1301 –        if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1302 –          ft = FIFTH_ORDER_POLY;
1303 –        } else {
1304 –          // throw error        
1305 –          sprintf( painCave.errMsg,
1306 –                   "SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1307 –          painCave.isFatal = 1;
1308 –          simError();
1309 –        }          
1310 –      }
1311 –    }
1312 –
1313 –    // send switching function notification to switcheroo
1314 –    setFunctionType(&ft);
1315 –
1316 –  }
1317 –
1318 –  void SimInfo::setupAccumulateBoxDipole() {    
1319 –
1320 –    // we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1321 –    if ( simParams_->haveAccumulateBoxDipole() )
1322 –      if ( simParams_->getAccumulateBoxDipole() ) {
1323 –        setAccumulateBoxDipole();
1324 –        calcBoxDipole_ = true;
1325 –      }
1326 –
1327 –  }
1328 –
935    void SimInfo::addProperty(GenericData* genData) {
936      properties_.addProperty(genData);  
937    }
938  
939 <  void SimInfo::removeProperty(const std::string& propName) {
939 >  void SimInfo::removeProperty(const string& propName) {
940      properties_.removeProperty(propName);  
941    }
942  
# Line 1338 | Line 944 | namespace OpenMD {
944      properties_.clearProperties();
945    }
946  
947 <  std::vector<std::string> SimInfo::getPropertyNames() {
947 >  vector<string> SimInfo::getPropertyNames() {
948      return properties_.getPropertyNames();  
949    }
950        
951 <  std::vector<GenericData*> SimInfo::getProperties() {
951 >  vector<GenericData*> SimInfo::getProperties() {
952      return properties_.getProperties();
953    }
954  
955 <  GenericData* SimInfo::getPropertyByName(const std::string& propName) {
955 >  GenericData* SimInfo::getPropertyByName(const string& propName) {
956      return properties_.getPropertyByName(propName);
957    }
958  
# Line 1360 | Line 966 | namespace OpenMD {
966      Molecule* mol;
967      RigidBody* rb;
968      Atom* atom;
969 +    CutoffGroup* cg;
970      SimInfo::MoleculeIterator mi;
971      Molecule::RigidBodyIterator rbIter;
972 <    Molecule::AtomIterator atomIter;;
972 >    Molecule::AtomIterator atomIter;
973 >    Molecule::CutoffGroupIterator cgIter;
974  
975      for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
976          
# Line 1372 | Line 980 | namespace OpenMD {
980          
981        for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
982          rb->setSnapshotManager(sman_);
983 +      }
984 +
985 +      for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
986 +        cg->setSnapshotManager(sman_);
987        }
988      }    
989      
# Line 1429 | Line 1041 | namespace OpenMD {
1041  
1042    }        
1043  
1044 <  std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1044 >  ostream& operator <<(ostream& o, SimInfo& info) {
1045  
1046      return o;
1047    }
# Line 1472 | Line 1084 | namespace OpenMD {
1084  
1085  
1086         [  Ixx -Ixy  -Ixz ]
1087 <  J =| -Iyx  Iyy  -Iyz |
1087 >    J =| -Iyx  Iyy  -Iyz |
1088         [ -Izx -Iyz   Izz ]
1089      */
1090  
# Line 1579 | Line 1191 | namespace OpenMD {
1191      return IOIndexToIntegrableObject.at(index);
1192    }
1193    
1194 <  void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1194 >  void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1195      IOIndexToIntegrableObject= v;
1196    }
1197  
# Line 1601 | Line 1213 | namespace OpenMD {
1213      
1214      det = intTensor.determinant();
1215      sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1216 <    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1216 >    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,geomCnst)*sqrt(det);
1217      return;
1218    }
1219  
# Line 1617 | Line 1229 | namespace OpenMD {
1229      
1230      detI = intTensor.determinant();
1231      sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1232 <    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1232 >    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,geomCnst)*sqrt(detI);
1233      return;
1234    }
1235   /*
1236 <   void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1236 >   void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1237        assert( v.size() == nAtoms_ + nRigidBodies_);
1238        sdByGlobalIndex_ = v;
1239      }
# Line 1631 | Line 1243 | namespace OpenMD {
1243        return sdByGlobalIndex_.at(index);
1244      }  
1245   */  
1246 +  int SimInfo::getNGlobalConstraints() {
1247 +    int nGlobalConstraints;
1248 + #ifdef IS_MPI
1249 +    MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1250 +                  MPI_COMM_WORLD);    
1251 + #else
1252 +    nGlobalConstraints =  nConstraints_;
1253 + #endif
1254 +    return nGlobalConstraints;
1255 +  }
1256 +
1257   }//end namespace OpenMD
1258  

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