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Revision 1534 by gezelter, Wed Dec 29 21:53:28 2010 UTC vs.
Revision 1874 by gezelter, Wed May 15 15:09:35 2013 UTC

# Line 35 | Line 35
35   *                                                                      
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).                        
38 > * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
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/doForces_interface.h"
58 – #include "UseTheForce/DarkSide/neighborLists_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"
62 > #include "brains/ForceField.hpp"
63   #include "nonbonded/SwitchingFunction.hpp"
65 –
64   #ifdef IS_MPI
65 < #include "UseTheForce/mpiComponentPlan.h"
66 < #include "UseTheForce/DarkSide/simParallel_interface.h"
69 < #endif
65 > #include <mpi.h>
66 > #endif
67  
68   using namespace std;
69   namespace OpenMD {
# Line 75 | Line 72 | namespace OpenMD {
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),
78 >    nConstraints_(0), nFluctuatingCharges_(0), sman_(NULL), topologyDone_(false),
79      calcBoxDipole_(false), useAtomicVirial_(true) {    
80      
81      MoleculeStamp* molStamp;
# Line 91 | Line 88 | namespace OpenMD {
88      
89      vector<Component*> components = simParams->getComponents();
90      
91 <    for (vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
91 >    for (vector<Component*>::iterator i = components.begin();
92 >         i !=components.end(); ++i) {
93        molStamp = (*i)->getMoleculeStamp();
94        nMolWithSameStamp = (*i)->getNMol();
95        
# Line 132 | Line 130 | namespace OpenMD {
130      //equal to the total number of atoms minus number of atoms belong to
131      //cutoff group defined in meta-data file plus the number of cutoff
132      //groups defined in meta-data file
133 +
134      nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
135      
136      //every free atom (atom does not belong to rigid bodies) is an
# Line 227 | Line 226 | namespace OpenMD {
226  
227  
228    void SimInfo::calcNdf() {
229 <    int ndf_local;
229 >    int ndf_local, nfq_local;
230      MoleculeIterator i;
231      vector<StuntDouble*>::iterator j;
232 +    vector<Atom*>::iterator k;
233 +
234      Molecule* mol;
235 <    StuntDouble* integrableObject;
235 >    StuntDouble* sd;
236 >    Atom* atom;
237  
238      ndf_local = 0;
239 +    nfq_local = 0;
240      
241      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
242 <      for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
243 <           integrableObject = mol->nextIntegrableObject(j)) {
242 >
243 >      for (sd = mol->beginIntegrableObject(j); sd != NULL;
244 >           sd = mol->nextIntegrableObject(j)) {
245  
246          ndf_local += 3;
247  
248 <        if (integrableObject->isDirectional()) {
249 <          if (integrableObject->isLinear()) {
248 >        if (sd->isDirectional()) {
249 >          if (sd->isLinear()) {
250              ndf_local += 2;
251            } else {
252              ndf_local += 3;
253            }
254          }
251 –            
255        }
256 +
257 +      for (atom = mol->beginFluctuatingCharge(k); atom != NULL;
258 +           atom = mol->nextFluctuatingCharge(k)) {
259 +        if (atom->isFluctuatingCharge()) {
260 +          nfq_local++;
261 +        }
262 +      }
263      }
264      
265 +    ndfLocal_ = ndf_local;
266 +
267      // n_constraints is local, so subtract them on each processor
268      ndf_local -= nConstraints_;
269  
270   #ifdef IS_MPI
271 <    MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
271 >    MPI::COMM_WORLD.Allreduce(&ndf_local, &ndf_, 1, MPI::INT,MPI::SUM);
272 >    MPI::COMM_WORLD.Allreduce(&nfq_local, &nGlobalFluctuatingCharges_, 1,
273 >                              MPI::INT, MPI::SUM);
274   #else
275      ndf_ = ndf_local;
276 +    nGlobalFluctuatingCharges_ = nfq_local;
277   #endif
278  
279      // nZconstraints_ is global, as are the 3 COM translations for the
# Line 269 | Line 284 | namespace OpenMD {
284  
285    int SimInfo::getFdf() {
286   #ifdef IS_MPI
287 <    MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
287 >    MPI::COMM_WORLD.Allreduce(&fdf_local, &fdf_, 1, MPI::INT, MPI::SUM);
288   #else
289      fdf_ = fdf_local;
290   #endif
291      return fdf_;
292    }
293 +  
294 +  unsigned int SimInfo::getNLocalCutoffGroups(){
295 +    int nLocalCutoffAtoms = 0;
296 +    Molecule* mol;
297 +    MoleculeIterator mi;
298 +    CutoffGroup* cg;
299 +    Molecule::CutoffGroupIterator ci;
300      
301 +    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
302 +      
303 +      for (cg = mol->beginCutoffGroup(ci); cg != NULL;
304 +           cg = mol->nextCutoffGroup(ci)) {
305 +        nLocalCutoffAtoms += cg->getNumAtom();
306 +        
307 +      }        
308 +    }
309 +    
310 +    return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_;
311 +  }
312 +    
313    void SimInfo::calcNdfRaw() {
314      int ndfRaw_local;
315  
316      MoleculeIterator i;
317      vector<StuntDouble*>::iterator j;
318      Molecule* mol;
319 <    StuntDouble* integrableObject;
319 >    StuntDouble* sd;
320  
321      // Raw degrees of freedom that we have to set
322      ndfRaw_local = 0;
323      
324      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
291 –      for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
292 –           integrableObject = mol->nextIntegrableObject(j)) {
325  
326 +      for (sd = mol->beginIntegrableObject(j); sd != NULL;
327 +           sd = mol->nextIntegrableObject(j)) {
328 +
329          ndfRaw_local += 3;
330  
331 <        if (integrableObject->isDirectional()) {
332 <          if (integrableObject->isLinear()) {
331 >        if (sd->isDirectional()) {
332 >          if (sd->isLinear()) {
333              ndfRaw_local += 2;
334            } else {
335              ndfRaw_local += 3;
# Line 305 | Line 340 | namespace OpenMD {
340      }
341      
342   #ifdef IS_MPI
343 <    MPI_Allreduce(&ndfRaw_local,&ndfRaw_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
343 >    MPI::COMM_WORLD.Allreduce(&ndfRaw_local, &ndfRaw_, 1, MPI::INT, MPI::SUM);
344   #else
345      ndfRaw_ = ndfRaw_local;
346   #endif
# Line 318 | Line 353 | namespace OpenMD {
353  
354  
355   #ifdef IS_MPI
356 <    MPI_Allreduce(&ndfTrans_local,&ndfTrans_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
356 >    MPI::COMM_WORLD.Allreduce(&ndfTrans_local, &ndfTrans_, 1,
357 >                              MPI::INT, MPI::SUM);
358   #else
359      ndfTrans_ = ndfTrans_local;
360   #endif
# Line 354 | Line 390 | namespace OpenMD {
390      Molecule::RigidBodyIterator rbIter;
391      RigidBody* rb;
392      Molecule::IntegrableObjectIterator ii;
393 <    StuntDouble* integrableObject;
393 >    StuntDouble* sd;
394      
395 <    for (integrableObject = mol->beginIntegrableObject(ii);
396 <         integrableObject != NULL;
361 <         integrableObject = mol->nextIntegrableObject(ii)) {
395 >    for (sd = mol->beginIntegrableObject(ii); sd != NULL;
396 >         sd = mol->nextIntegrableObject(ii)) {
397        
398 <      if (integrableObject->isRigidBody()) {
399 <        rb = static_cast<RigidBody*>(integrableObject);
398 >      if (sd->isRigidBody()) {
399 >        rb = static_cast<RigidBody*>(sd);
400          vector<Atom*> atoms = rb->getAtoms();
401          set<int> rigidAtoms;
402          for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
# Line 372 | Line 407 | namespace OpenMD {
407          }      
408        } else {
409          set<int> oneAtomSet;
410 <        oneAtomSet.insert(integrableObject->getGlobalIndex());
411 <        atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));        
410 >        oneAtomSet.insert(sd->getGlobalIndex());
411 >        atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));        
412        }
413      }  
414            
# Line 507 | Line 542 | namespace OpenMD {
542      Molecule::RigidBodyIterator rbIter;
543      RigidBody* rb;
544      Molecule::IntegrableObjectIterator ii;
545 <    StuntDouble* integrableObject;
545 >    StuntDouble* sd;
546      
547 <    for (integrableObject = mol->beginIntegrableObject(ii);
548 <         integrableObject != NULL;
514 <         integrableObject = mol->nextIntegrableObject(ii)) {
547 >    for (sd = mol->beginIntegrableObject(ii); sd != NULL;
548 >         sd = mol->nextIntegrableObject(ii)) {
549        
550 <      if (integrableObject->isRigidBody()) {
551 <        rb = static_cast<RigidBody*>(integrableObject);
550 >      if (sd->isRigidBody()) {
551 >        rb = static_cast<RigidBody*>(sd);
552          vector<Atom*> atoms = rb->getAtoms();
553          set<int> rigidAtoms;
554          for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
# Line 525 | Line 559 | namespace OpenMD {
559          }      
560        } else {
561          set<int> oneAtomSet;
562 <        oneAtomSet.insert(integrableObject->getGlobalIndex());
563 <        atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));        
562 >        oneAtomSet.insert(sd->getGlobalIndex());
563 >        atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));        
564        }
565      }  
566  
# Line 656 | Line 690 | namespace OpenMD {
690    /**
691     * update
692     *
693 <   *  Performs the global checks and variable settings after the objects have been
694 <   *  created.
693 >   *  Performs the global checks and variable settings after the
694 >   *  objects have been created.
695     *
696     */
697 <  void SimInfo::update() {
664 <    
697 >  void SimInfo::update() {  
698      setupSimVariables();
666 –    setupCutoffs();
667 –    setupSwitching();
668 –    setupElectrostatics();
669 –    setupNeighborlists();
670 –
671 – #ifdef IS_MPI
672 –    setupFortranParallel();
673 – #endif
674 –    setupFortranSim();
675 –    fortranInitialized_ = true;
676 –
699      calcNdf();
700      calcNdfRaw();
701      calcNdfTrans();
702    }
703    
704 +  /**
705 +   * getSimulatedAtomTypes
706 +   *
707 +   * Returns an STL set of AtomType* that are actually present in this
708 +   * simulation.  Must query all processors to assemble this information.
709 +   *
710 +   */
711    set<AtomType*> SimInfo::getSimulatedAtomTypes() {
712      SimInfo::MoleculeIterator mi;
713      Molecule* mol;
# Line 686 | Line 715 | namespace OpenMD {
715      Atom* atom;
716      set<AtomType*> atomTypes;
717      
718 <    for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {      
719 <      for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
718 >    for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
719 >      for(atom = mol->beginAtom(ai); atom != NULL;
720 >          atom = mol->nextAtom(ai)) {
721          atomTypes.insert(atom->getAtomType());
722        }      
723      }    
724 <    return atomTypes;        
725 <  }
724 >    
725 > #ifdef IS_MPI
726  
727 <  /**
728 <   * setupCutoffs
699 <   *
700 <   * Sets the values of cutoffRadius and cutoffMethod
701 <   *
702 <   * cutoffRadius : realType
703 <   *  If the cutoffRadius was explicitly set, use that value.
704 <   *  If the cutoffRadius was not explicitly set:
705 <   *      Are there electrostatic atoms?  Use 12.0 Angstroms.
706 <   *      No electrostatic atoms?  Poll the atom types present in the
707 <   *      simulation for suggested cutoff values (e.g. 2.5 * sigma).
708 <   *      Use the maximum suggested value that was found.
709 <   *
710 <   * cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE, SHIFTED_POTENTIAL)
711 <   *      If cutoffMethod was explicitly set, use that choice.
712 <   *      If cutoffMethod was not explicitly set, use SHIFTED_FORCE
713 <   */
714 <  void SimInfo::setupCutoffs() {
727 >    // loop over the found atom types on this processor, and add their
728 >    // numerical idents to a vector:
729      
730 <    if (simParams_->haveCutoffRadius()) {
731 <      cutoffRadius_ = simParams_->getCutoffRadius();
732 <    } else {      
733 <      if (usesElectrostaticAtoms_) {
720 <        sprintf(painCave.errMsg,
721 <                "SimInfo: No value was set for the cutoffRadius.\n"
722 <                "\tOpenMD will use a default value of 12.0 angstroms"
723 <                "\tfor the cutoffRadius.\n");
724 <        painCave.isFatal = 0;
725 <        painCave.severity = OPENMD_INFO;
726 <        simError();
727 <        cutoffRadius_ = 12.0;
728 <      } else {
729 <        RealType thisCut;
730 <        set<AtomType*>::iterator i;
731 <        set<AtomType*> atomTypes;
732 <        atomTypes = getSimulatedAtomTypes();        
733 <        for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
734 <          thisCut = InteractionManager::Instance()->getSuggestedCutoffRadius((*i));
735 <          cutoffRadius_ = max(thisCut, cutoffRadius_);
736 <        }
737 <        sprintf(painCave.errMsg,
738 <                "SimInfo: No value was set for the cutoffRadius.\n"
739 <                "\tOpenMD will use %lf angstroms.\n",
740 <                cutoffRadius_);
741 <        painCave.isFatal = 0;
742 <        painCave.severity = OPENMD_INFO;
743 <        simError();
744 <      }            
745 <    }
730 >    vector<int> foundTypes;
731 >    set<AtomType*>::iterator i;
732 >    for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
733 >      foundTypes.push_back( (*i)->getIdent() );
734  
735 <    map<string, CutoffMethod> stringToCutoffMethod;
736 <    stringToCutoffMethod["HARD"] = HARD;
737 <    stringToCutoffMethod["SWITCHING_FUNCTION"] = SWITCHING_FUNCTION;
738 <    stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;    
739 <    stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
735 >    // count_local holds the number of found types on this processor
736 >    int count_local = foundTypes.size();
737 >
738 >    int nproc = MPI::COMM_WORLD.Get_size();
739 >
740 >    // we need arrays to hold the counts and displacement vectors for
741 >    // all processors
742 >    vector<int> counts(nproc, 0);
743 >    vector<int> disps(nproc, 0);
744 >
745 >    // fill the counts array
746 >    MPI::COMM_WORLD.Allgather(&count_local, 1, MPI::INT, &counts[0],
747 >                              1, MPI::INT);
748    
749 <    if (simParams_->haveCutoffMethod()) {
750 <      string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
751 <      map<string, CutoffMethod>::iterator i;
752 <      i = stringToCutoffMethod.find(cutMeth);
753 <      if (i == stringToCutoffMethod.end()) {
754 <        sprintf(painCave.errMsg,
759 <                "SimInfo: Could not find chosen cutoffMethod %s\n"
760 <                "\tShould be one of: "
761 <                "HARD, SWITCHING_FUNCTION, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n",
762 <                cutMeth.c_str());
763 <        painCave.isFatal = 1;
764 <        painCave.severity = OPENMD_ERROR;
765 <        simError();
766 <      } else {
767 <        cutoffMethod_ = i->second;
768 <      }
769 <    } else {
770 <      sprintf(painCave.errMsg,
771 <              "SimInfo: No value was set for the cutoffMethod.\n"
772 <              "\tOpenMD will use SHIFTED_FORCE.\n");
773 <        painCave.isFatal = 0;
774 <        painCave.severity = OPENMD_INFO;
775 <        simError();
776 <        cutoffMethod_ = SHIFTED_FORCE;        
749 >    // use the processor counts to compute the displacement array
750 >    disps[0] = 0;    
751 >    int totalCount = counts[0];
752 >    for (int iproc = 1; iproc < nproc; iproc++) {
753 >      disps[iproc] = disps[iproc-1] + counts[iproc-1];
754 >      totalCount += counts[iproc];
755      }
756 <  }
757 <  
758 <  /**
781 <   * setupSwitching
782 <   *
783 <   * Sets the values of switchingRadius and
784 <   *  If the switchingRadius was explicitly set, use that value (but check it)
785 <   *  If the switchingRadius was not explicitly set: use 0.85 * cutoffRadius_
786 <   */
787 <  void SimInfo::setupSwitching() {
756 >
757 >    // we need a (possibly redundant) set of all found types:
758 >    vector<int> ftGlobal(totalCount);
759      
760 <    if (simParams_->haveSwitchingRadius()) {
761 <      switchingRadius_ = simParams_->getSwitchingRadius();
762 <      if (switchingRadius_ > cutoffRadius_) {        
763 <        sprintf(painCave.errMsg,
764 <                "SimInfo: switchingRadius (%f) is larger than cutoffRadius(%f)\n",
765 <                switchingRadius_, cutoffRadius_);
766 <        painCave.isFatal = 1;
767 <        painCave.severity = OPENMD_ERROR;
768 <        simError();
769 <      }
770 <    } else {      
771 <      switchingRadius_ = 0.85 * cutoffRadius_;
772 <      sprintf(painCave.errMsg,
802 <              "SimInfo: No value was set for the switchingRadius.\n"
803 <              "\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
804 <              "\tswitchingRadius = %f. for this simulation\n", switchingRadius_);
805 <      painCave.isFatal = 0;
806 <      painCave.severity = OPENMD_WARNING;
807 <      simError();
808 <    }          
760 >    // now spray out the foundTypes to all the other processors:    
761 >    MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
762 >                               &ftGlobal[0], &counts[0], &disps[0],
763 >                               MPI::INT);
764 >
765 >    vector<int>::iterator j;
766 >
767 >    // foundIdents is a stl set, so inserting an already found ident
768 >    // will have no effect.
769 >    set<int> foundIdents;
770 >
771 >    for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
772 >      foundIdents.insert((*j));
773      
774 <    if (simParams_->haveSwitchingFunctionType()) {
775 <      string funcType = simParams_->getSwitchingFunctionType();
776 <      toUpper(funcType);
777 <      if (funcType == "CUBIC") {
778 <        sft_ = cubic;
779 <      } else {
780 <        if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
781 <          sft_ = fifth_order_poly;
782 <        } else {
819 <          // throw error        
820 <          sprintf( painCave.errMsg,
821 <                   "SimInfo : Unknown switchingFunctionType. (Input file specified %s .)\n"
822 <                   "\tswitchingFunctionType must be one of: "
823 <                   "\"cubic\" or \"fifth_order_polynomial\".",
824 <                   funcType.c_str() );
825 <          painCave.isFatal = 1;
826 <          painCave.severity = OPENMD_ERROR;
827 <          simError();
828 <        }          
829 <      }
830 <    }
774 >    // now iterate over the foundIdents and get the actual atom types
775 >    // that correspond to these:
776 >    set<int>::iterator it;
777 >    for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
778 >      atomTypes.insert( forceField_->getAtomType((*it)) );
779 >
780 > #endif
781 >
782 >    return atomTypes;        
783    }
784  
785 <  /**
786 <   * setupNeighborlists
787 <   *
788 <   *  If the skinThickness was explicitly set, use that value (but check it)
789 <   *  If the skinThickness was not explicitly set: use 1.0 angstroms
790 <   */
791 <  void SimInfo::setupNeighborlists() {    
792 <    if (simParams_->haveSkinThickness()) {
793 <      skinThickness_ = simParams_->getSkinThickness();
794 <    } else {      
795 <      skinThickness_ = 1.0;
796 <      sprintf(painCave.errMsg,
797 <              "SimInfo: No value was set for the skinThickness.\n"
798 <              "\tOpenMD will use a default value of %f Angstroms\n"
847 <              "\tfor this simulation\n", skinThickness_);
848 <      painCave.severity = OPENMD_INFO;
849 <      painCave.isFatal = 0;
850 <      simError();
851 <    }            
785 >
786 >  int getGlobalCountOfType(AtomType* atype) {
787 >    /*
788 >    set<AtomType*> atypes = getSimulatedAtomTypes();
789 >    map<AtomType*, int> counts_;
790 >
791 >    for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
792 >      for(atom = mol->beginAtom(ai); atom != NULL;
793 >          atom = mol->nextAtom(ai)) {
794 >        atom->getAtomType();
795 >      }      
796 >    }    
797 >    */
798 >    return 0;
799    }
800  
801    void SimInfo::setupSimVariables() {
802      useAtomicVirial_ = simParams_->getUseAtomicVirial();
803 <    // we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
803 >    // we only call setAccumulateBoxDipole if the accumulateBoxDipole
804 >    // parameter is true
805      calcBoxDipole_ = false;
806      if ( simParams_->haveAccumulateBoxDipole() )
807        if ( simParams_->getAccumulateBoxDipole() ) {
808          calcBoxDipole_ = true;      
809        }
810 <
810 >    
811      set<AtomType*>::iterator i;
812      set<AtomType*> atomTypes;
813      atomTypes = getSimulatedAtomTypes();    
814 <    int usesElectrostatic = 0;
815 <    int usesMetallic = 0;
816 <    int usesDirectional = 0;
814 >    bool usesElectrostatic = false;
815 >    bool usesMetallic = false;
816 >    bool usesDirectional = false;
817 >    bool usesFluctuatingCharges =  false;
818      //loop over all of the atom types
819      for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
820        usesElectrostatic |= (*i)->isElectrostatic();
821        usesMetallic |= (*i)->isMetal();
822        usesDirectional |= (*i)->isDirectional();
823 +      usesFluctuatingCharges |= (*i)->isFluctuatingCharge();
824      }
825  
826 < #ifdef IS_MPI    
827 <    int temp;
826 > #ifdef IS_MPI
827 >    bool temp;
828      temp = usesDirectional;
829 <    MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
830 <
829 >    MPI::COMM_WORLD.Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI::BOOL,
830 >                              MPI::LOR);
831 >        
832      temp = usesMetallic;
833 <    MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
834 <
833 >    MPI::COMM_WORLD.Allreduce(&temp, &usesMetallicAtoms_, 1, MPI::BOOL,
834 >                              MPI::LOR);
835 >    
836      temp = usesElectrostatic;
837 <    MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
837 >    MPI::COMM_WORLD.Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI::BOOL,
838 >                              MPI::LOR);
839 >
840 >    temp = usesFluctuatingCharges;
841 >    MPI::COMM_WORLD.Allreduce(&temp, &usesFluctuatingCharges_, 1, MPI::BOOL,
842 >                              MPI::LOR);
843 > #else
844 >
845 >    usesDirectionalAtoms_ = usesDirectional;
846 >    usesMetallicAtoms_ = usesMetallic;
847 >    usesElectrostaticAtoms_ = usesElectrostatic;
848 >    usesFluctuatingCharges_ = usesFluctuatingCharges;
849 >
850   #endif
851 <    fInfo_.SIM_uses_PBC = usesPeriodicBoundaries_;    
852 <    fInfo_.SIM_uses_DirectionalAtoms = usesDirectionalAtoms_;
853 <    fInfo_.SIM_uses_MetallicAtoms = usesMetallicAtoms_;
854 <    fInfo_.SIM_requires_SkipCorrection = usesElectrostaticAtoms_;
891 <    fInfo_.SIM_requires_SelfCorrection = usesElectrostaticAtoms_;
892 <    fInfo_.SIM_uses_AtomicVirial = usesAtomicVirial_;
851 >    
852 >    requiresPrepair_ = usesMetallicAtoms_ ? true : false;
853 >    requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
854 >    requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;    
855    }
856  
895 –  void SimInfo::setupFortranSim() {
896 –    int isError;
897 –    int nExclude, nOneTwo, nOneThree, nOneFour;
898 –    vector<int> fortranGlobalGroupMembership;
899 –    
900 –    notifyFortranSkinThickness(&skinThickness_);
857  
858 <    int ljsp = cutoffMethod_ == SHIFTED_POTENTIAL ? 1 : 0;
859 <    int ljsf = cutoffMethod_ == SHIFTED_FORCE ? 1 : 0;
860 <    notifyFortranCutoffs(&cutoffRadius_, &switchingRadius_, &ljsp, &ljsf);
858 >  vector<int> SimInfo::getGlobalAtomIndices() {
859 >    SimInfo::MoleculeIterator mi;
860 >    Molecule* mol;
861 >    Molecule::AtomIterator ai;
862 >    Atom* atom;
863  
864 <    isError = 0;
864 >    vector<int> GlobalAtomIndices(getNAtoms(), 0);
865 >    
866 >    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
867 >      
868 >      for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
869 >        GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
870 >      }
871 >    }
872 >    return GlobalAtomIndices;
873 >  }
874  
875 <    //globalGroupMembership_ is filled by SimCreator    
876 <    for (int i = 0; i < nGlobalAtoms_; i++) {
877 <      fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
875 >
876 >  vector<int> SimInfo::getGlobalGroupIndices() {
877 >    SimInfo::MoleculeIterator mi;
878 >    Molecule* mol;
879 >    Molecule::CutoffGroupIterator ci;
880 >    CutoffGroup* cg;
881 >
882 >    vector<int> GlobalGroupIndices;
883 >    
884 >    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
885 >      
886 >      //local index of cutoff group is trivial, it only depends on the
887 >      //order of travesing
888 >      for (cg = mol->beginCutoffGroup(ci); cg != NULL;
889 >           cg = mol->nextCutoffGroup(ci)) {
890 >        GlobalGroupIndices.push_back(cg->getGlobalIndex());
891 >      }        
892      }
893 +    return GlobalGroupIndices;
894 +  }
895  
896 +
897 +  void SimInfo::prepareTopology() {
898 +
899      //calculate mass ratio of cutoff group
914 –    vector<RealType> mfact;
900      SimInfo::MoleculeIterator mi;
901      Molecule* mol;
902      Molecule::CutoffGroupIterator ci;
# Line 920 | Line 905 | namespace OpenMD {
905      Atom* atom;
906      RealType totalMass;
907  
908 <    //to avoid memory reallocation, reserve enough space for mfact
909 <    mfact.reserve(getNCutoffGroups());
908 >    /**
909 >     * The mass factor is the relative mass of an atom to the total
910 >     * mass of the cutoff group it belongs to.  By default, all atoms
911 >     * are their own cutoff groups, and therefore have mass factors of
912 >     * 1.  We need some special handling for massless atoms, which
913 >     * will be treated as carrying the entire mass of the cutoff
914 >     * group.
915 >     */
916 >    massFactors_.clear();
917 >    massFactors_.resize(getNAtoms(), 1.0);
918      
919      for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {        
920 <      for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
920 >      for (cg = mol->beginCutoffGroup(ci); cg != NULL;
921 >           cg = mol->nextCutoffGroup(ci)) {
922  
923          totalMass = cg->getMass();
924          for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
925            // Check for massless groups - set mfact to 1 if true
926 <          if (totalMass != 0)
927 <            mfact.push_back(atom->getMass()/totalMass);
926 >          if (totalMass != 0)
927 >            massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
928            else
929 <            mfact.push_back( 1.0 );
929 >            massFactors_[atom->getLocalIndex()] = 1.0;
930          }
931        }      
932      }
933  
934 <    //fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
941 <    vector<int> identArray;
934 >    // Build the identArray_
935  
936 <    //to avoid memory reallocation, reserve enough space identArray
937 <    identArray.reserve(getNAtoms());
945 <    
936 >    identArray_.clear();
937 >    identArray_.reserve(getNAtoms());    
938      for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {        
939        for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
940 <        identArray.push_back(atom->getIdent());
940 >        identArray_.push_back(atom->getIdent());
941        }
942      }    
951 –
952 –    //fill molMembershipArray
953 –    //molMembershipArray is filled by SimCreator    
954 –    vector<int> molMembershipArray(nGlobalAtoms_);
955 –    for (int i = 0; i < nGlobalAtoms_; i++) {
956 –      molMembershipArray[i] = globalMolMembership_[i] + 1;
957 –    }
943      
944 <    //setup fortran simulation
960 <
961 <    nExclude = excludedInteractions_.getSize();
962 <    nOneTwo = oneTwoInteractions_.getSize();
963 <    nOneThree = oneThreeInteractions_.getSize();
964 <    nOneFour = oneFourInteractions_.getSize();
965 <
966 <    int* excludeList = excludedInteractions_.getPairList();
967 <    int* oneTwoList = oneTwoInteractions_.getPairList();
968 <    int* oneThreeList = oneThreeInteractions_.getPairList();
969 <    int* oneFourList = oneFourInteractions_.getPairList();
970 <
971 <    setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
972 <                   &nExclude, excludeList,
973 <                   &nOneTwo, oneTwoList,
974 <                   &nOneThree, oneThreeList,
975 <                   &nOneFour, oneFourList,
976 <                   &molMembershipArray[0], &mfact[0], &nCutoffGroups_,
977 <                   &fortranGlobalGroupMembership[0], &isError);
978 <    
979 <    if( isError ){
980 <      
981 <      sprintf( painCave.errMsg,
982 <               "There was an error setting the simulation information in fortran.\n" );
983 <      painCave.isFatal = 1;
984 <      painCave.severity = OPENMD_ERROR;
985 <      simError();
986 <    }
987 <    
988 <    
989 <    sprintf( checkPointMsg,
990 <             "succesfully sent the simulation information to fortran.\n");
991 <    
992 <    errorCheckPoint();
993 <    
994 <    // Setup number of neighbors in neighbor list if present
995 <    if (simParams_->haveNeighborListNeighbors()) {
996 <      int nlistNeighbors = simParams_->getNeighborListNeighbors();
997 <      setNeighbors(&nlistNeighbors);
998 <    }
999 <  
1000 <
944 >    topologyDone_ = true;
945    }
946  
1003 –
1004 –  void SimInfo::setupFortranParallel() {
1005 – #ifdef IS_MPI    
1006 –    //SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
1007 –    vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
1008 –    vector<int> localToGlobalCutoffGroupIndex;
1009 –    SimInfo::MoleculeIterator mi;
1010 –    Molecule::AtomIterator ai;
1011 –    Molecule::CutoffGroupIterator ci;
1012 –    Molecule* mol;
1013 –    Atom* atom;
1014 –    CutoffGroup* cg;
1015 –    mpiSimData parallelData;
1016 –    int isError;
1017 –
1018 –    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
1019 –
1020 –      //local index(index in DataStorge) of atom is important
1021 –      for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
1022 –        localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
1023 –      }
1024 –
1025 –      //local index of cutoff group is trivial, it only depends on the order of travesing
1026 –      for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
1027 –        localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
1028 –      }        
1029 –        
1030 –    }
1031 –
1032 –    //fill up mpiSimData struct
1033 –    parallelData.nMolGlobal = getNGlobalMolecules();
1034 –    parallelData.nMolLocal = getNMolecules();
1035 –    parallelData.nAtomsGlobal = getNGlobalAtoms();
1036 –    parallelData.nAtomsLocal = getNAtoms();
1037 –    parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
1038 –    parallelData.nGroupsLocal = getNCutoffGroups();
1039 –    parallelData.myNode = worldRank;
1040 –    MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
1041 –
1042 –    //pass mpiSimData struct and index arrays to fortran
1043 –    setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
1044 –                    &localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
1045 –                    &localToGlobalCutoffGroupIndex[0], &isError);
1046 –
1047 –    if (isError) {
1048 –      sprintf(painCave.errMsg,
1049 –              "mpiRefresh errror: fortran didn't like something we gave it.\n");
1050 –      painCave.isFatal = 1;
1051 –      simError();
1052 –    }
1053 –
1054 –    sprintf(checkPointMsg, " mpiRefresh successful.\n");
1055 –    errorCheckPoint();
1056 –
1057 – #endif
1058 –  }
1059 –
1060 –
1061 –  void SimInfo::setupAccumulateBoxDipole() {    
1062 –
1063 –
1064 –  }
1065 –
947    void SimInfo::addProperty(GenericData* genData) {
948      properties_.addProperty(genData);  
949    }
# Line 1097 | Line 978 | namespace OpenMD {
978      Molecule* mol;
979      RigidBody* rb;
980      Atom* atom;
981 +    CutoffGroup* cg;
982      SimInfo::MoleculeIterator mi;
983      Molecule::RigidBodyIterator rbIter;
984 <    Molecule::AtomIterator atomIter;;
984 >    Molecule::AtomIterator atomIter;
985 >    Molecule::CutoffGroupIterator cgIter;
986  
987      for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
988          
989 <      for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
989 >      for (atom = mol->beginAtom(atomIter); atom != NULL;
990 >           atom = mol->nextAtom(atomIter)) {
991          atom->setSnapshotManager(sman_);
992        }
993          
994 <      for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
994 >      for (rb = mol->beginRigidBody(rbIter); rb != NULL;
995 >           rb = mol->nextRigidBody(rbIter)) {
996          rb->setSnapshotManager(sman_);
997        }
998 +
999 +      for (cg = mol->beginCutoffGroup(cgIter); cg != NULL;
1000 +           cg = mol->nextCutoffGroup(cgIter)) {
1001 +        cg->setSnapshotManager(sman_);
1002 +      }
1003      }    
1004      
1005    }
1006  
1117 –  Vector3d SimInfo::getComVel(){
1118 –    SimInfo::MoleculeIterator i;
1119 –    Molecule* mol;
1007  
1121 –    Vector3d comVel(0.0);
1122 –    RealType totalMass = 0.0;
1123 –    
1124 –
1125 –    for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1126 –      RealType mass = mol->getMass();
1127 –      totalMass += mass;
1128 –      comVel += mass * mol->getComVel();
1129 –    }  
1130 –
1131 – #ifdef IS_MPI
1132 –    RealType tmpMass = totalMass;
1133 –    Vector3d tmpComVel(comVel);    
1134 –    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1135 –    MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1136 – #endif
1137 –
1138 –    comVel /= totalMass;
1139 –
1140 –    return comVel;
1141 –  }
1142 –
1143 –  Vector3d SimInfo::getCom(){
1144 –    SimInfo::MoleculeIterator i;
1145 –    Molecule* mol;
1146 –
1147 –    Vector3d com(0.0);
1148 –    RealType totalMass = 0.0;
1149 –    
1150 –    for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1151 –      RealType mass = mol->getMass();
1152 –      totalMass += mass;
1153 –      com += mass * mol->getCom();
1154 –    }  
1155 –
1156 – #ifdef IS_MPI
1157 –    RealType tmpMass = totalMass;
1158 –    Vector3d tmpCom(com);    
1159 –    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1160 –    MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1161 – #endif
1162 –
1163 –    com /= totalMass;
1164 –
1165 –    return com;
1166 –
1167 –  }        
1168 –
1008    ostream& operator <<(ostream& o, SimInfo& info) {
1009  
1010      return o;
1011    }
1012    
1013 <  
1175 <   /*
1176 <   Returns center of mass and center of mass velocity in one function call.
1177 <   */
1178 <  
1179 <   void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1180 <      SimInfo::MoleculeIterator i;
1181 <      Molecule* mol;
1182 <      
1183 <    
1184 <      RealType totalMass = 0.0;
1185 <    
1186 <
1187 <      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1188 <         RealType mass = mol->getMass();
1189 <         totalMass += mass;
1190 <         com += mass * mol->getCom();
1191 <         comVel += mass * mol->getComVel();          
1192 <      }  
1193 <      
1194 < #ifdef IS_MPI
1195 <      RealType tmpMass = totalMass;
1196 <      Vector3d tmpCom(com);  
1197 <      Vector3d tmpComVel(comVel);
1198 <      MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1199 <      MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1200 <      MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1201 < #endif
1202 <      
1203 <      com /= totalMass;
1204 <      comVel /= totalMass;
1205 <   }        
1206 <  
1207 <   /*
1208 <   Return intertia tensor for entire system and angular momentum Vector.
1209 <
1210 <
1211 <       [  Ixx -Ixy  -Ixz ]
1212 <    J =| -Iyx  Iyy  -Iyz |
1213 <       [ -Izx -Iyz   Izz ]
1214 <    */
1215 <
1216 <   void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1217 <      
1218 <
1219 <      RealType xx = 0.0;
1220 <      RealType yy = 0.0;
1221 <      RealType zz = 0.0;
1222 <      RealType xy = 0.0;
1223 <      RealType xz = 0.0;
1224 <      RealType yz = 0.0;
1225 <      Vector3d com(0.0);
1226 <      Vector3d comVel(0.0);
1227 <      
1228 <      getComAll(com, comVel);
1229 <      
1230 <      SimInfo::MoleculeIterator i;
1231 <      Molecule* mol;
1232 <      
1233 <      Vector3d thisq(0.0);
1234 <      Vector3d thisv(0.0);
1235 <
1236 <      RealType thisMass = 0.0;
1237 <    
1238 <      
1239 <      
1240 <  
1241 <      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1242 <        
1243 <         thisq = mol->getCom()-com;
1244 <         thisv = mol->getComVel()-comVel;
1245 <         thisMass = mol->getMass();
1246 <         // Compute moment of intertia coefficients.
1247 <         xx += thisq[0]*thisq[0]*thisMass;
1248 <         yy += thisq[1]*thisq[1]*thisMass;
1249 <         zz += thisq[2]*thisq[2]*thisMass;
1250 <        
1251 <         // compute products of intertia
1252 <         xy += thisq[0]*thisq[1]*thisMass;
1253 <         xz += thisq[0]*thisq[2]*thisMass;
1254 <         yz += thisq[1]*thisq[2]*thisMass;
1255 <            
1256 <         angularMomentum += cross( thisq, thisv ) * thisMass;
1257 <            
1258 <      }  
1259 <      
1260 <      
1261 <      inertiaTensor(0,0) = yy + zz;
1262 <      inertiaTensor(0,1) = -xy;
1263 <      inertiaTensor(0,2) = -xz;
1264 <      inertiaTensor(1,0) = -xy;
1265 <      inertiaTensor(1,1) = xx + zz;
1266 <      inertiaTensor(1,2) = -yz;
1267 <      inertiaTensor(2,0) = -xz;
1268 <      inertiaTensor(2,1) = -yz;
1269 <      inertiaTensor(2,2) = xx + yy;
1270 <      
1271 < #ifdef IS_MPI
1272 <      Mat3x3d tmpI(inertiaTensor);
1273 <      Vector3d tmpAngMom;
1274 <      MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1275 <      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1276 < #endif
1277 <              
1278 <      return;
1279 <   }
1280 <
1281 <   //Returns the angular momentum of the system
1282 <   Vector3d SimInfo::getAngularMomentum(){
1283 <      
1284 <      Vector3d com(0.0);
1285 <      Vector3d comVel(0.0);
1286 <      Vector3d angularMomentum(0.0);
1287 <      
1288 <      getComAll(com,comVel);
1289 <      
1290 <      SimInfo::MoleculeIterator i;
1291 <      Molecule* mol;
1292 <      
1293 <      Vector3d thisr(0.0);
1294 <      Vector3d thisp(0.0);
1295 <      
1296 <      RealType thisMass;
1297 <      
1298 <      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {        
1299 <        thisMass = mol->getMass();
1300 <        thisr = mol->getCom()-com;
1301 <        thisp = (mol->getComVel()-comVel)*thisMass;
1302 <        
1303 <        angularMomentum += cross( thisr, thisp );
1304 <        
1305 <      }  
1306 <      
1307 < #ifdef IS_MPI
1308 <      Vector3d tmpAngMom;
1309 <      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1310 < #endif
1311 <      
1312 <      return angularMomentum;
1313 <   }
1314 <  
1013 >  
1014    StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1015 <    return IOIndexToIntegrableObject.at(index);
1015 >    if (index >= int(IOIndexToIntegrableObject.size())) {
1016 >      sprintf(painCave.errMsg,
1017 >              "SimInfo::getIOIndexToIntegrableObject Error: Integrable Object\n"
1018 >              "\tindex exceeds number of known objects!\n");
1019 >      painCave.isFatal = 1;
1020 >      simError();
1021 >      return NULL;
1022 >    } else
1023 >      return IOIndexToIntegrableObject.at(index);
1024    }
1025    
1026    void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1027      IOIndexToIntegrableObject= v;
1028    }
1029  
1323 –  /* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1324 –     based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1325 –     where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1326 –     V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1327 –  */
1328 –  void SimInfo::getGyrationalVolume(RealType &volume){
1329 –    Mat3x3d intTensor;
1330 –    RealType det;
1331 –    Vector3d dummyAngMom;
1332 –    RealType sysconstants;
1333 –    RealType geomCnst;
1334 –
1335 –    geomCnst = 3.0/2.0;
1336 –    /* Get the inertial tensor and angular momentum for free*/
1337 –    getInertiaTensor(intTensor,dummyAngMom);
1338 –    
1339 –    det = intTensor.determinant();
1340 –    sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1341 –    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1342 –    return;
1343 –  }
1344 –
1345 –  void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1346 –    Mat3x3d intTensor;
1347 –    Vector3d dummyAngMom;
1348 –    RealType sysconstants;
1349 –    RealType geomCnst;
1350 –
1351 –    geomCnst = 3.0/2.0;
1352 –    /* Get the inertial tensor and angular momentum for free*/
1353 –    getInertiaTensor(intTensor,dummyAngMom);
1354 –    
1355 –    detI = intTensor.determinant();
1356 –    sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1357 –    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1358 –    return;
1359 –  }
1360 – /*
1361 –   void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1362 –      assert( v.size() == nAtoms_ + nRigidBodies_);
1363 –      sdByGlobalIndex_ = v;
1364 –    }
1365 –
1366 –    StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1367 –      //assert(index < nAtoms_ + nRigidBodies_);
1368 –      return sdByGlobalIndex_.at(index);
1369 –    }  
1370 – */  
1030    int SimInfo::getNGlobalConstraints() {
1031      int nGlobalConstraints;
1032   #ifdef IS_MPI
1033 <    MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1034 <                  MPI_COMM_WORLD);    
1033 >    MPI::COMM_WORLD.Allreduce(&nConstraints_, &nGlobalConstraints, 1,
1034 >                              MPI::INT, MPI::SUM);
1035   #else
1036      nGlobalConstraints =  nConstraints_;
1037   #endif

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