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Revision 1530 by gezelter, Tue Dec 28 21:47:55 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/fCutoffPolicy.h"
58 – #include "UseTheForce/doForces_interface.h"
59 – #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"
66 –
67 –
64   #ifdef IS_MPI
65 < #include "UseTheForce/mpiComponentPlan.h"
66 < #include "UseTheForce/DarkSide/simParallel_interface.h"
71 < #endif
65 > #include <mpi.h>
66 > #endif
67  
68   using namespace std;
69   namespace OpenMD {
# Line 77 | 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 93 | 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 134 | 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 229 | 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)) {
241 –      for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
242 –           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          }
253 –            
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 271 | 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)) {
293 –      for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
294 –           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 307 | 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 320 | 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 356 | 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;
363 <         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 374 | 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 509 | 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;
516 <         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 527 | 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 658 | 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() {
666 <    
697 >  void SimInfo::update() {  
698      setupSimVariables();
668 –    setupCutoffs();
669 –    setupSwitching();
670 –    setupElectrostatics();
671 –    setupNeighborlists();
672 –
673 – #ifdef IS_MPI
674 –    setupFortranParallel();
675 – #endif
676 –    setupFortranSim();
677 –    fortranInitialized_ = true;
678 –
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 688 | 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
701 <   *
702 <   * Sets the values of cutoffRadius and cutoffMethod
703 <   *
704 <   * cutoffRadius : realType
705 <   *  If the cutoffRadius was explicitly set, use that value.
706 <   *  If the cutoffRadius was not explicitly set:
707 <   *      Are there electrostatic atoms?  Use 12.0 Angstroms.
708 <   *      No electrostatic atoms?  Poll the atom types present in the
709 <   *      simulation for suggested cutoff values (e.g. 2.5 * sigma).
710 <   *      Use the maximum suggested value that was found.
711 <   *
712 <   * cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE, SHIFTED_POTENTIAL)
713 <   *      If cutoffMethod was explicitly set, use that choice.
714 <   *      If cutoffMethod was not explicitly set, use SHIFTED_FORCE
715 <   */
716 <  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_) {
722 <        sprintf(painCave.errMsg,
723 <                "SimInfo: No value was set for the cutoffRadius.\n"
724 <                "\tOpenMD will use a default value of 12.0 angstroms"
725 <                "\tfor the cutoffRadius.\n");
726 <        painCave.isFatal = 0;
727 <        painCave.severity = OPENMD_INFO;
728 <        simError();
729 <        cutoffRadius_ = 12.0;
730 <      } else {
731 <        RealType thisCut;
732 <        set<AtomType*>::iterator i;
733 <        set<AtomType*> atomTypes;
734 <        atomTypes = getSimulatedAtomTypes();        
735 <        for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
736 <          thisCut = InteractionManager::Instance()->getSuggestedCutoffRadius((*i));
737 <          cutoffRadius_ = max(thisCut, cutoffRadius_);
738 <        }
739 <        sprintf(painCave.errMsg,
740 <                "SimInfo: No value was set for the cutoffRadius.\n"
741 <                "\tOpenMD will use %lf angstroms.\n",
742 <                cutoffRadius_);
743 <        painCave.isFatal = 0;
744 <        painCave.severity = OPENMD_INFO;
745 <        simError();
746 <      }            
747 <    }
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 <    InteractionManager::Instance()->setCutoffRadius(cutoffRadius_);
735 >    // count_local holds the number of found types on this processor
736 >    int count_local = foundTypes.size();
737  
738 <    map<string, CutoffMethod> stringToCutoffMethod;
739 <    stringToCutoffMethod["HARD"] = HARD;
740 <    stringToCutoffMethod["SWITCHING_FUNCTION"] = SWITCHING_FUNCTION;
741 <    stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;    
742 <    stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
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,
763 <                "SimInfo: Could not find chosen cutoffMethod %s\n"
764 <                "\tShould be one of: "
765 <                "HARD, SWITCHING_FUNCTION, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n",
766 <                cutMeth.c_str());
767 <        painCave.isFatal = 1;
768 <        painCave.severity = OPENMD_ERROR;
769 <        simError();
770 <      } else {
771 <        cutoffMethod_ = i->second;
772 <      }
773 <    } else {
774 <      sprintf(painCave.errMsg,
775 <              "SimInfo: No value was set for the cutoffMethod.\n"
776 <              "\tOpenMD will use SHIFTED_FORCE.\n");
777 <        painCave.isFatal = 0;
778 <        painCave.severity = OPENMD_INFO;
779 <        simError();
780 <        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 <    InteractionManager::Instance()->setCutoffMethod(cutoffMethod_);
758 <  }
785 <  
786 <  /**
787 <   * setupSwitching
788 <   *
789 <   * Sets the values of switchingRadius and
790 <   *  If the switchingRadius was explicitly set, use that value (but check it)
791 <   *  If the switchingRadius was not explicitly set: use 0.85 * cutoffRadius_
792 <   */
793 <  void SimInfo::setupSwitching() {
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,
799 <                "SimInfo: switchingRadius (%f) is larger than cutoffRadius(%f)\n",
800 <                switchingRadius_, cutoffRadius_);
801 <        painCave.isFatal = 1;
802 <        painCave.severity = OPENMD_ERROR;
803 <        simError();
804 <      }
805 <    } else {      
806 <      switchingRadius_ = 0.85 * cutoffRadius_;
807 <      sprintf(painCave.errMsg,
808 <              "SimInfo: No value was set for the switchingRadius.\n"
809 <              "\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
810 <              "\tswitchingRadius = %f. for this simulation\n", switchingRadius_);
811 <      painCave.isFatal = 0;
812 <      painCave.severity = OPENMD_WARNING;
813 <      simError();
814 <    }          
815 <  
816 <    InteractionManager::Instance()->setSwitchingRadius(switchingRadius_);
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 <    SwitchingFunctionType ft;
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 <        ft = cubic;
779 <      } else {
780 <        if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
827 <          ft = fifth_order_poly;
828 <        } else {
829 <          // throw error        
830 <          sprintf( painCave.errMsg,
831 <                   "SimInfo : Unknown switchingFunctionType. (Input file specified %s .)\n"
832 <                   "\tswitchingFunctionType must be one of: "
833 <                   "\"cubic\" or \"fifth_order_polynomial\".",
834 <                   funcType.c_str() );
835 <          painCave.isFatal = 1;
836 <          painCave.severity = OPENMD_ERROR;
837 <          simError();
838 <        }          
839 <      }
840 <    }
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 <    InteractionManager::Instance()->setSwitchingFunctionType(ft);
782 >    return atomTypes;        
783    }
784  
785 <  /**
786 <   * setupSkinThickness
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::setupSkinThickness() {    
792 <    if (simParams_->haveSkinThickness()) {
793 <      skinThickness_ = simParams_->getSkinThickness();
794 <    } else {      
795 <      skinThickness_ = 1.0;
796 <      sprintf(painCave.errMsg,
797 <              "SimInfo Warning: No value was set for the skinThickness.\n"
798 <              "\tOpenMD will use a default value of %f Angstroms\n"
859 <              "\tfor this simulation\n", skinThickness_);
860 <      painCave.isFatal = 0;
861 <      simError();
862 <    }            
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::setupSimType() {
801 >  void SimInfo::setupSimVariables() {
802 >    useAtomicVirial_ = simParams_->getUseAtomicVirial();
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 >    
811      set<AtomType*>::iterator i;
812      set<AtomType*> atomTypes;
813 <    atomTypes = getSimulatedAtomTypes();
814 <
815 <    useAtomicVirial_ = simParams_->getUseAtomicVirial();
816 <
817 <    int usesElectrostatic = 0;
873 <    int usesMetallic = 0;
874 <    int usesDirectional = 0;
813 >    atomTypes = getSimulatedAtomTypes();    
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_;
897 <    fInfo_.SIM_requires_SelfCorrection = usesElectrostaticAtoms_;
898 <    fInfo_.SIM_uses_AtomicVirial = usesAtomicVirial_;
851 >    
852 >    requiresPrepair_ = usesMetallicAtoms_ ? true : false;
853 >    requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
854 >    requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;    
855    }
856  
857 <  void SimInfo::setupFortranSim() {
858 <    int isError;
859 <    int nExclude, nOneTwo, nOneThree, nOneFour;
860 <    vector<int> fortranGlobalGroupMembership;
857 >
858 >  vector<int> SimInfo::getGlobalAtomIndices() {
859 >    SimInfo::MoleculeIterator mi;
860 >    Molecule* mol;
861 >    Molecule::AtomIterator ai;
862 >    Atom* atom;
863 >
864 >    vector<int> GlobalAtomIndices(getNAtoms(), 0);
865      
866 <    notifyFortranSkinThickness(&skinThickness_);
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  
908 –    int ljsp = cutoffMethod_ == SHIFTED_POTENTIAL ? 1 : 0;
909 –    int ljsf = cutoffMethod_ == SHIFTED_FORCE ? 1 : 0;
910 –    notifyFortranCutoffs(&cutoffRadius_, &switchingRadius_, &ljsp, &ljsf);
875  
876 <    isError = 0;
876 >  vector<int> SimInfo::getGlobalGroupIndices() {
877 >    SimInfo::MoleculeIterator mi;
878 >    Molecule* mol;
879 >    Molecule::CutoffGroupIterator ci;
880 >    CutoffGroup* cg;
881  
882 <    //globalGroupMembership_ is filled by SimCreator    
883 <    for (int i = 0; i < nGlobalAtoms_; i++) {
884 <      fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
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
920 –    vector<RealType> mfact;
900      SimInfo::MoleculeIterator mi;
901      Molecule* mol;
902      Molecule::CutoffGroupIterator ci;
# Line 926 | 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 !!!)
947 <    vector<int> identArray;
934 >    // Build the identArray_
935  
936 <    //to avoid memory reallocation, reserve enough space identArray
937 <    identArray.reserve(getNAtoms());
951 <    
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      }    
957 –
958 –    //fill molMembershipArray
959 –    //molMembershipArray is filled by SimCreator    
960 –    vector<int> molMembershipArray(nGlobalAtoms_);
961 –    for (int i = 0; i < nGlobalAtoms_; i++) {
962 –      molMembershipArray[i] = globalMolMembership_[i] + 1;
963 –    }
943      
944 <    //setup fortran simulation
966 <
967 <    nExclude = excludedInteractions_.getSize();
968 <    nOneTwo = oneTwoInteractions_.getSize();
969 <    nOneThree = oneThreeInteractions_.getSize();
970 <    nOneFour = oneFourInteractions_.getSize();
971 <
972 <    int* excludeList = excludedInteractions_.getPairList();
973 <    int* oneTwoList = oneTwoInteractions_.getPairList();
974 <    int* oneThreeList = oneThreeInteractions_.getPairList();
975 <    int* oneFourList = oneFourInteractions_.getPairList();
976 <
977 <    setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
978 <                   &nExclude, excludeList,
979 <                   &nOneTwo, oneTwoList,
980 <                   &nOneThree, oneThreeList,
981 <                   &nOneFour, oneFourList,
982 <                   &molMembershipArray[0], &mfact[0], &nCutoffGroups_,
983 <                   &fortranGlobalGroupMembership[0], &isError);
984 <    
985 <    if( isError ){
986 <      
987 <      sprintf( painCave.errMsg,
988 <               "There was an error setting the simulation information in fortran.\n" );
989 <      painCave.isFatal = 1;
990 <      painCave.severity = OPENMD_ERROR;
991 <      simError();
992 <    }
993 <    
994 <    
995 <    sprintf( checkPointMsg,
996 <             "succesfully sent the simulation information to fortran.\n");
997 <    
998 <    errorCheckPoint();
999 <    
1000 <    // Setup number of neighbors in neighbor list if present
1001 <    if (simParams_->haveNeighborListNeighbors()) {
1002 <      int nlistNeighbors = simParams_->getNeighborListNeighbors();
1003 <      setNeighbors(&nlistNeighbors);
1004 <    }
1005 <  
1006 <
944 >    topologyDone_ = true;
945    }
946  
1009 –
1010 –  void SimInfo::setupFortranParallel() {
1011 – #ifdef IS_MPI    
1012 –    //SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
1013 –    vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
1014 –    vector<int> localToGlobalCutoffGroupIndex;
1015 –    SimInfo::MoleculeIterator mi;
1016 –    Molecule::AtomIterator ai;
1017 –    Molecule::CutoffGroupIterator ci;
1018 –    Molecule* mol;
1019 –    Atom* atom;
1020 –    CutoffGroup* cg;
1021 –    mpiSimData parallelData;
1022 –    int isError;
1023 –
1024 –    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
1025 –
1026 –      //local index(index in DataStorge) of atom is important
1027 –      for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
1028 –        localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
1029 –      }
1030 –
1031 –      //local index of cutoff group is trivial, it only depends on the order of travesing
1032 –      for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
1033 –        localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
1034 –      }        
1035 –        
1036 –    }
1037 –
1038 –    //fill up mpiSimData struct
1039 –    parallelData.nMolGlobal = getNGlobalMolecules();
1040 –    parallelData.nMolLocal = getNMolecules();
1041 –    parallelData.nAtomsGlobal = getNGlobalAtoms();
1042 –    parallelData.nAtomsLocal = getNAtoms();
1043 –    parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
1044 –    parallelData.nGroupsLocal = getNCutoffGroups();
1045 –    parallelData.myNode = worldRank;
1046 –    MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
1047 –
1048 –    //pass mpiSimData struct and index arrays to fortran
1049 –    setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
1050 –                    &localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
1051 –                    &localToGlobalCutoffGroupIndex[0], &isError);
1052 –
1053 –    if (isError) {
1054 –      sprintf(painCave.errMsg,
1055 –              "mpiRefresh errror: fortran didn't like something we gave it.\n");
1056 –      painCave.isFatal = 1;
1057 –      simError();
1058 –    }
1059 –
1060 –    sprintf(checkPointMsg, " mpiRefresh successful.\n");
1061 –    errorCheckPoint();
1062 –
1063 – #endif
1064 –  }
1065 –
1066 –
1067 –  void SimInfo::setupSwitchingFunction() {    
1068 –
1069 –  }
1070 –
1071 –  void SimInfo::setupAccumulateBoxDipole() {    
1072 –
1073 –    // we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1074 –    if ( simParams_->haveAccumulateBoxDipole() )
1075 –      if ( simParams_->getAccumulateBoxDipole() ) {
1076 –        calcBoxDipole_ = true;
1077 –      }
1078 –
1079 –  }
1080 –
947    void SimInfo::addProperty(GenericData* genData) {
948      properties_.addProperty(genData);  
949    }
# Line 1112 | 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    }
1131 –
1132 –  Vector3d SimInfo::getComVel(){
1133 –    SimInfo::MoleculeIterator i;
1134 –    Molecule* mol;
1135 –
1136 –    Vector3d comVel(0.0);
1137 –    RealType totalMass = 0.0;
1138 –    
1139 –
1140 –    for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1141 –      RealType mass = mol->getMass();
1142 –      totalMass += mass;
1143 –      comVel += mass * mol->getComVel();
1144 –    }  
1145 –
1146 – #ifdef IS_MPI
1147 –    RealType tmpMass = totalMass;
1148 –    Vector3d tmpComVel(comVel);    
1149 –    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1150 –    MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1151 – #endif
1152 –
1153 –    comVel /= totalMass;
1154 –
1155 –    return comVel;
1156 –  }
1157 –
1158 –  Vector3d SimInfo::getCom(){
1159 –    SimInfo::MoleculeIterator i;
1160 –    Molecule* mol;
1161 –
1162 –    Vector3d com(0.0);
1163 –    RealType totalMass = 0.0;
1164 –    
1165 –    for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1166 –      RealType mass = mol->getMass();
1167 –      totalMass += mass;
1168 –      com += mass * mol->getCom();
1169 –    }  
1006  
1171 – #ifdef IS_MPI
1172 –    RealType tmpMass = totalMass;
1173 –    Vector3d tmpCom(com);    
1174 –    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1175 –    MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1176 – #endif
1007  
1178 –    com /= totalMass;
1179 –
1180 –    return com;
1181 –
1182 –  }        
1183 –
1008    ostream& operator <<(ostream& o, SimInfo& info) {
1009  
1010      return o;
1011    }
1012    
1013 <  
1190 <   /*
1191 <   Returns center of mass and center of mass velocity in one function call.
1192 <   */
1193 <  
1194 <   void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1195 <      SimInfo::MoleculeIterator i;
1196 <      Molecule* mol;
1197 <      
1198 <    
1199 <      RealType totalMass = 0.0;
1200 <    
1201 <
1202 <      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1203 <         RealType mass = mol->getMass();
1204 <         totalMass += mass;
1205 <         com += mass * mol->getCom();
1206 <         comVel += mass * mol->getComVel();          
1207 <      }  
1208 <      
1209 < #ifdef IS_MPI
1210 <      RealType tmpMass = totalMass;
1211 <      Vector3d tmpCom(com);  
1212 <      Vector3d tmpComVel(comVel);
1213 <      MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1214 <      MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1215 <      MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1216 < #endif
1217 <      
1218 <      com /= totalMass;
1219 <      comVel /= totalMass;
1220 <   }        
1221 <  
1222 <   /*
1223 <   Return intertia tensor for entire system and angular momentum Vector.
1224 <
1225 <
1226 <       [  Ixx -Ixy  -Ixz ]
1227 <    J =| -Iyx  Iyy  -Iyz |
1228 <       [ -Izx -Iyz   Izz ]
1229 <    */
1230 <
1231 <   void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1232 <      
1233 <
1234 <      RealType xx = 0.0;
1235 <      RealType yy = 0.0;
1236 <      RealType zz = 0.0;
1237 <      RealType xy = 0.0;
1238 <      RealType xz = 0.0;
1239 <      RealType yz = 0.0;
1240 <      Vector3d com(0.0);
1241 <      Vector3d comVel(0.0);
1242 <      
1243 <      getComAll(com, comVel);
1244 <      
1245 <      SimInfo::MoleculeIterator i;
1246 <      Molecule* mol;
1247 <      
1248 <      Vector3d thisq(0.0);
1249 <      Vector3d thisv(0.0);
1250 <
1251 <      RealType thisMass = 0.0;
1252 <    
1253 <      
1254 <      
1255 <  
1256 <      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1257 <        
1258 <         thisq = mol->getCom()-com;
1259 <         thisv = mol->getComVel()-comVel;
1260 <         thisMass = mol->getMass();
1261 <         // Compute moment of intertia coefficients.
1262 <         xx += thisq[0]*thisq[0]*thisMass;
1263 <         yy += thisq[1]*thisq[1]*thisMass;
1264 <         zz += thisq[2]*thisq[2]*thisMass;
1265 <        
1266 <         // compute products of intertia
1267 <         xy += thisq[0]*thisq[1]*thisMass;
1268 <         xz += thisq[0]*thisq[2]*thisMass;
1269 <         yz += thisq[1]*thisq[2]*thisMass;
1270 <            
1271 <         angularMomentum += cross( thisq, thisv ) * thisMass;
1272 <            
1273 <      }  
1274 <      
1275 <      
1276 <      inertiaTensor(0,0) = yy + zz;
1277 <      inertiaTensor(0,1) = -xy;
1278 <      inertiaTensor(0,2) = -xz;
1279 <      inertiaTensor(1,0) = -xy;
1280 <      inertiaTensor(1,1) = xx + zz;
1281 <      inertiaTensor(1,2) = -yz;
1282 <      inertiaTensor(2,0) = -xz;
1283 <      inertiaTensor(2,1) = -yz;
1284 <      inertiaTensor(2,2) = xx + yy;
1285 <      
1286 < #ifdef IS_MPI
1287 <      Mat3x3d tmpI(inertiaTensor);
1288 <      Vector3d tmpAngMom;
1289 <      MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1290 <      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1291 < #endif
1292 <              
1293 <      return;
1294 <   }
1295 <
1296 <   //Returns the angular momentum of the system
1297 <   Vector3d SimInfo::getAngularMomentum(){
1298 <      
1299 <      Vector3d com(0.0);
1300 <      Vector3d comVel(0.0);
1301 <      Vector3d angularMomentum(0.0);
1302 <      
1303 <      getComAll(com,comVel);
1304 <      
1305 <      SimInfo::MoleculeIterator i;
1306 <      Molecule* mol;
1307 <      
1308 <      Vector3d thisr(0.0);
1309 <      Vector3d thisp(0.0);
1310 <      
1311 <      RealType thisMass;
1312 <      
1313 <      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {        
1314 <        thisMass = mol->getMass();
1315 <        thisr = mol->getCom()-com;
1316 <        thisp = (mol->getComVel()-comVel)*thisMass;
1317 <        
1318 <        angularMomentum += cross( thisr, thisp );
1319 <        
1320 <      }  
1321 <      
1322 < #ifdef IS_MPI
1323 <      Vector3d tmpAngMom;
1324 <      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1325 < #endif
1326 <      
1327 <      return angularMomentum;
1328 <   }
1329 <  
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  
1338 –  /* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1339 –     based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1340 –     where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1341 –     V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1342 –  */
1343 –  void SimInfo::getGyrationalVolume(RealType &volume){
1344 –    Mat3x3d intTensor;
1345 –    RealType det;
1346 –    Vector3d dummyAngMom;
1347 –    RealType sysconstants;
1348 –    RealType geomCnst;
1349 –
1350 –    geomCnst = 3.0/2.0;
1351 –    /* Get the inertial tensor and angular momentum for free*/
1352 –    getInertiaTensor(intTensor,dummyAngMom);
1353 –    
1354 –    det = intTensor.determinant();
1355 –    sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1356 –    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1357 –    return;
1358 –  }
1359 –
1360 –  void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1361 –    Mat3x3d intTensor;
1362 –    Vector3d dummyAngMom;
1363 –    RealType sysconstants;
1364 –    RealType geomCnst;
1365 –
1366 –    geomCnst = 3.0/2.0;
1367 –    /* Get the inertial tensor and angular momentum for free*/
1368 –    getInertiaTensor(intTensor,dummyAngMom);
1369 –    
1370 –    detI = intTensor.determinant();
1371 –    sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1372 –    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1373 –    return;
1374 –  }
1375 – /*
1376 –   void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1377 –      assert( v.size() == nAtoms_ + nRigidBodies_);
1378 –      sdByGlobalIndex_ = v;
1379 –    }
1380 –
1381 –    StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1382 –      //assert(index < nAtoms_ + nRigidBodies_);
1383 –      return sdByGlobalIndex_.at(index);
1384 –    }  
1385 – */  
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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