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Revision 1569 by gezelter, Thu May 26 13:55:04 2011 UTC vs.
Revision 1779 by gezelter, Mon Aug 20 17:51:39 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 58 | Line 59
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"
64 + #ifdef IS_MPI
65 + #include <mpi.h>
66 + #endif
67  
68   using namespace std;
69   namespace OpenMD {
# Line 68 | 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), topologyDone_(false),
78 >    nConstraints_(0), nFluctuatingCharges_(0), sman_(NULL), topologyDone_(false),
79      calcBoxDipole_(false), useAtomicVirial_(true) {    
80      
81      MoleculeStamp* molStamp;
# Line 84 | 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 125 | 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
128 –    std::cerr << "nGA = " << nGlobalAtoms_ << "\n";
129 –    std::cerr << "nCA = " << nCutoffAtoms << "\n";
130 –    std::cerr << "nG = " << nGroups << "\n";
133  
134      nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
133 –
134 –    std::cerr << "nGCG = " << nGlobalCutoffGroups_ << "\n";
135      
136      //every free atom (atom does not belong to rigid bodies) is an
137      //integrable object therefore the total number of integrable objects
# Line 226 | 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)) {
238 –      for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
239 –           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          }
250 –            
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);
272 +    MPI_Allreduce(&nfq_local,&nGlobalFluctuatingCharges_,1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
273   #else
274      ndf_ = ndf_local;
275 +    nGlobalFluctuatingCharges_ = nfq_local;
276   #endif
277  
278      // nZconstraints_ is global, as are the 3 COM translations for the
# Line 274 | Line 289 | namespace OpenMD {
289   #endif
290      return fdf_;
291    }
292 +  
293 +  unsigned int SimInfo::getNLocalCutoffGroups(){
294 +    int nLocalCutoffAtoms = 0;
295 +    Molecule* mol;
296 +    MoleculeIterator mi;
297 +    CutoffGroup* cg;
298 +    Molecule::CutoffGroupIterator ci;
299      
300 +    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
301 +      
302 +      for (cg = mol->beginCutoffGroup(ci); cg != NULL;
303 +           cg = mol->nextCutoffGroup(ci)) {
304 +        nLocalCutoffAtoms += cg->getNumAtom();
305 +        
306 +      }        
307 +    }
308 +    
309 +    return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_;
310 +  }
311 +    
312    void SimInfo::calcNdfRaw() {
313      int ndfRaw_local;
314  
315      MoleculeIterator i;
316      vector<StuntDouble*>::iterator j;
317      Molecule* mol;
318 <    StuntDouble* integrableObject;
318 >    StuntDouble* sd;
319  
320      // Raw degrees of freedom that we have to set
321      ndfRaw_local = 0;
322      
323      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
290 –      for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
291 –           integrableObject = mol->nextIntegrableObject(j)) {
324  
325 +      for (sd = mol->beginIntegrableObject(j); sd != NULL;
326 +           sd = mol->nextIntegrableObject(j)) {
327 +
328          ndfRaw_local += 3;
329  
330 <        if (integrableObject->isDirectional()) {
331 <          if (integrableObject->isLinear()) {
330 >        if (sd->isDirectional()) {
331 >          if (sd->isLinear()) {
332              ndfRaw_local += 2;
333            } else {
334              ndfRaw_local += 3;
# Line 353 | Line 388 | namespace OpenMD {
388      Molecule::RigidBodyIterator rbIter;
389      RigidBody* rb;
390      Molecule::IntegrableObjectIterator ii;
391 <    StuntDouble* integrableObject;
391 >    StuntDouble* sd;
392      
393 <    for (integrableObject = mol->beginIntegrableObject(ii);
394 <         integrableObject != NULL;
360 <         integrableObject = mol->nextIntegrableObject(ii)) {
393 >    for (sd = mol->beginIntegrableObject(ii); sd != NULL;
394 >         sd = mol->nextIntegrableObject(ii)) {
395        
396 <      if (integrableObject->isRigidBody()) {
397 <        rb = static_cast<RigidBody*>(integrableObject);
396 >      if (sd->isRigidBody()) {
397 >        rb = static_cast<RigidBody*>(sd);
398          vector<Atom*> atoms = rb->getAtoms();
399          set<int> rigidAtoms;
400          for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
# Line 371 | Line 405 | namespace OpenMD {
405          }      
406        } else {
407          set<int> oneAtomSet;
408 <        oneAtomSet.insert(integrableObject->getGlobalIndex());
409 <        atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));        
408 >        oneAtomSet.insert(sd->getGlobalIndex());
409 >        atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));        
410        }
411      }  
412            
# Line 506 | Line 540 | namespace OpenMD {
540      Molecule::RigidBodyIterator rbIter;
541      RigidBody* rb;
542      Molecule::IntegrableObjectIterator ii;
543 <    StuntDouble* integrableObject;
543 >    StuntDouble* sd;
544      
545 <    for (integrableObject = mol->beginIntegrableObject(ii);
546 <         integrableObject != NULL;
513 <         integrableObject = mol->nextIntegrableObject(ii)) {
545 >    for (sd = mol->beginIntegrableObject(ii); sd != NULL;
546 >         sd = mol->nextIntegrableObject(ii)) {
547        
548 <      if (integrableObject->isRigidBody()) {
549 <        rb = static_cast<RigidBody*>(integrableObject);
548 >      if (sd->isRigidBody()) {
549 >        rb = static_cast<RigidBody*>(sd);
550          vector<Atom*> atoms = rb->getAtoms();
551          set<int> rigidAtoms;
552          for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
# Line 524 | Line 557 | namespace OpenMD {
557          }      
558        } else {
559          set<int> oneAtomSet;
560 <        oneAtomSet.insert(integrableObject->getGlobalIndex());
561 <        atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));        
560 >        oneAtomSet.insert(sd->getGlobalIndex());
561 >        atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));        
562        }
563      }  
564  
# Line 680 | Line 713 | namespace OpenMD {
713      Atom* atom;
714      set<AtomType*> atomTypes;
715      
716 <    for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {      
717 <      for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
716 >    for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
717 >      for(atom = mol->beginAtom(ai); atom != NULL;
718 >          atom = mol->nextAtom(ai)) {
719          atomTypes.insert(atom->getAtomType());
720        }      
721      }    
722 <
722 >    
723   #ifdef IS_MPI
724  
725      // loop over the found atom types on this processor, and add their
726      // numerical idents to a vector:
727 <
727 >    
728      vector<int> foundTypes;
729      set<AtomType*>::iterator i;
730      for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
# Line 699 | Line 733 | namespace OpenMD {
733      // count_local holds the number of found types on this processor
734      int count_local = foundTypes.size();
735  
702 –    // count holds the total number of found types on all processors
703 –    // (some will be redundant with the ones found locally):
704 –    int count;
705 –    MPI::COMM_WORLD.Allreduce(&count_local, &count, 1, MPI::INT, MPI::SUM);
706 –
707 –    // create a vector to hold the globally found types, and resize it:
708 –    vector<int> ftGlobal;
709 –    ftGlobal.resize(count);
710 –    vector<int> counts;
711 –
736      int nproc = MPI::COMM_WORLD.Get_size();
713 –    counts.resize(nproc);
714 –    vector<int> disps;
715 –    disps.resize(nproc);
737  
738 <    // now spray out the foundTypes to all the other processors:
738 >    // we need arrays to hold the counts and displacement vectors for
739 >    // all processors
740 >    vector<int> counts(nproc, 0);
741 >    vector<int> disps(nproc, 0);
742 >
743 >    // fill the counts array
744 >    MPI::COMM_WORLD.Allgather(&count_local, 1, MPI::INT, &counts[0],
745 >                              1, MPI::INT);
746 >  
747 >    // use the processor counts to compute the displacement array
748 >    disps[0] = 0;    
749 >    int totalCount = counts[0];
750 >    for (int iproc = 1; iproc < nproc; iproc++) {
751 >      disps[iproc] = disps[iproc-1] + counts[iproc-1];
752 >      totalCount += counts[iproc];
753 >    }
754 >
755 >    // we need a (possibly redundant) set of all found types:
756 >    vector<int> ftGlobal(totalCount);
757      
758 +    // now spray out the foundTypes to all the other processors:    
759      MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
760 <                               &ftGlobal[0], &counts[0], &disps[0], MPI::INT);
760 >                               &ftGlobal[0], &counts[0], &disps[0],
761 >                               MPI::INT);
762  
763 +    vector<int>::iterator j;
764 +
765      // foundIdents is a stl set, so inserting an already found ident
766      // will have no effect.
767      set<int> foundIdents;
768 <    vector<int>::iterator j;
768 >
769      for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
770        foundIdents.insert((*j));
771      
772      // now iterate over the foundIdents and get the actual atom types
773      // that correspond to these:
774      set<int>::iterator it;
775 <    for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
775 >    for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
776        atomTypes.insert( forceField_->getAtomType((*it)) );
777  
778   #endif
779 <    
779 >
780      return atomTypes;        
781    }
782  
783    void SimInfo::setupSimVariables() {
784      useAtomicVirial_ = simParams_->getUseAtomicVirial();
785 <    // we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
785 >    // we only call setAccumulateBoxDipole if the accumulateBoxDipole
786 >    // parameter is true
787      calcBoxDipole_ = false;
788      if ( simParams_->haveAccumulateBoxDipole() )
789        if ( simParams_->getAccumulateBoxDipole() ) {
790          calcBoxDipole_ = true;      
791        }
792 <
792 >    
793      set<AtomType*>::iterator i;
794      set<AtomType*> atomTypes;
795      atomTypes = getSimulatedAtomTypes();    
796 <    int usesElectrostatic = 0;
797 <    int usesMetallic = 0;
798 <    int usesDirectional = 0;
796 >    bool usesElectrostatic = false;
797 >    bool usesMetallic = false;
798 >    bool usesDirectional = false;
799 >    bool usesFluctuatingCharges =  false;
800      //loop over all of the atom types
801      for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
802        usesElectrostatic |= (*i)->isElectrostatic();
803        usesMetallic |= (*i)->isMetal();
804        usesDirectional |= (*i)->isDirectional();
805 +      usesFluctuatingCharges |= (*i)->isFluctuatingCharge();
806      }
807  
808 < #ifdef IS_MPI    
809 <    int temp;
808 > #ifdef IS_MPI
809 >    bool temp;
810      temp = usesDirectional;
811 <    MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
812 <
811 >    MPI::COMM_WORLD.Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI::BOOL,
812 >                              MPI::LOR);
813 >        
814      temp = usesMetallic;
815 <    MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
816 <
815 >    MPI::COMM_WORLD.Allreduce(&temp, &usesMetallicAtoms_, 1, MPI::BOOL,
816 >                              MPI::LOR);
817 >    
818      temp = usesElectrostatic;
819 <    MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
819 >    MPI::COMM_WORLD.Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI::BOOL,
820 >                              MPI::LOR);
821 >
822 >    temp = usesFluctuatingCharges;
823 >    MPI::COMM_WORLD.Allreduce(&temp, &usesFluctuatingCharges_, 1, MPI::BOOL,
824 >                              MPI::LOR);
825 > #else
826 >
827 >    usesDirectionalAtoms_ = usesDirectional;
828 >    usesMetallicAtoms_ = usesMetallic;
829 >    usesElectrostaticAtoms_ = usesElectrostatic;
830 >    usesFluctuatingCharges_ = usesFluctuatingCharges;
831 >
832   #endif
833 +    
834 +    requiresPrepair_ = usesMetallicAtoms_ ? true : false;
835 +    requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
836 +    requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;    
837    }
838  
839  
# Line 824 | Line 888 | namespace OpenMD {
888      Atom* atom;
889      RealType totalMass;
890  
891 <    //to avoid memory reallocation, reserve enough space for massFactors_
891 >    /**
892 >     * The mass factor is the relative mass of an atom to the total
893 >     * mass of the cutoff group it belongs to.  By default, all atoms
894 >     * are their own cutoff groups, and therefore have mass factors of
895 >     * 1.  We need some special handling for massless atoms, which
896 >     * will be treated as carrying the entire mass of the cutoff
897 >     * group.
898 >     */
899      massFactors_.clear();
900 <    massFactors_.reserve(getNCutoffGroups());
900 >    massFactors_.resize(getNAtoms(), 1.0);
901      
902      for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {        
903        for (cg = mol->beginCutoffGroup(ci); cg != NULL;
# Line 835 | Line 906 | namespace OpenMD {
906          totalMass = cg->getMass();
907          for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
908            // Check for massless groups - set mfact to 1 if true
909 <          if (totalMass != 0)
910 <            massFactors_.push_back(atom->getMass()/totalMass);
909 >          if (totalMass != 0)
910 >            massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
911            else
912 <            massFactors_.push_back( 1.0 );
912 >            massFactors_[atom->getLocalIndex()] = 1.0;
913          }
914        }      
915      }
# Line 865 | Line 936 | namespace OpenMD {
936      int* oneThreeList = oneThreeInteractions_.getPairList();
937      int* oneFourList = oneFourInteractions_.getPairList();
938  
868 –    //setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray_[0],
869 –    //               &nExclude, excludeList,
870 –    //               &nOneTwo, oneTwoList,
871 –    //               &nOneThree, oneThreeList,
872 –    //               &nOneFour, oneFourList,
873 –    //               &molMembershipArray[0], &mfact[0], &nCutoffGroups_,
874 –    //               &fortranGlobalGroupMembership[0], &isError);
875 –    
939      topologyDone_ = true;
940    }
941  
# Line 918 | Line 981 | namespace OpenMD {
981  
982      for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
983          
984 <      for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
984 >      for (atom = mol->beginAtom(atomIter); atom != NULL;
985 >           atom = mol->nextAtom(atomIter)) {
986          atom->setSnapshotManager(sman_);
987        }
988          
989 <      for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
989 >      for (rb = mol->beginRigidBody(rbIter); rb != NULL;
990 >           rb = mol->nextRigidBody(rbIter)) {
991          rb->setSnapshotManager(sman_);
992        }
993  
994 <      for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
994 >      for (cg = mol->beginCutoffGroup(cgIter); cg != NULL;
995 >           cg = mol->nextCutoffGroup(cgIter)) {
996          cg->setSnapshotManager(sman_);
997        }
998      }    
999      
1000    }
1001  
936 –  Vector3d SimInfo::getComVel(){
937 –    SimInfo::MoleculeIterator i;
938 –    Molecule* mol;
1002  
940 –    Vector3d comVel(0.0);
941 –    RealType totalMass = 0.0;
942 –    
943 –
944 –    for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
945 –      RealType mass = mol->getMass();
946 –      totalMass += mass;
947 –      comVel += mass * mol->getComVel();
948 –    }  
949 –
950 – #ifdef IS_MPI
951 –    RealType tmpMass = totalMass;
952 –    Vector3d tmpComVel(comVel);    
953 –    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
954 –    MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
955 – #endif
956 –
957 –    comVel /= totalMass;
958 –
959 –    return comVel;
960 –  }
961 –
962 –  Vector3d SimInfo::getCom(){
963 –    SimInfo::MoleculeIterator i;
964 –    Molecule* mol;
965 –
966 –    Vector3d com(0.0);
967 –    RealType totalMass = 0.0;
968 –    
969 –    for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
970 –      RealType mass = mol->getMass();
971 –      totalMass += mass;
972 –      com += mass * mol->getCom();
973 –    }  
974 –
975 – #ifdef IS_MPI
976 –    RealType tmpMass = totalMass;
977 –    Vector3d tmpCom(com);    
978 –    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
979 –    MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
980 – #endif
981 –
982 –    com /= totalMass;
983 –
984 –    return com;
985 –
986 –  }        
987 –
1003    ostream& operator <<(ostream& o, SimInfo& info) {
1004  
1005      return o;
1006    }
1007    
1008 <  
994 <   /*
995 <   Returns center of mass and center of mass velocity in one function call.
996 <   */
997 <  
998 <   void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
999 <      SimInfo::MoleculeIterator i;
1000 <      Molecule* mol;
1001 <      
1002 <    
1003 <      RealType totalMass = 0.0;
1004 <    
1005 <
1006 <      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1007 <         RealType mass = mol->getMass();
1008 <         totalMass += mass;
1009 <         com += mass * mol->getCom();
1010 <         comVel += mass * mol->getComVel();          
1011 <      }  
1012 <      
1013 < #ifdef IS_MPI
1014 <      RealType tmpMass = totalMass;
1015 <      Vector3d tmpCom(com);  
1016 <      Vector3d tmpComVel(comVel);
1017 <      MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1018 <      MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1019 <      MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1020 < #endif
1021 <      
1022 <      com /= totalMass;
1023 <      comVel /= totalMass;
1024 <   }        
1025 <  
1026 <   /*
1027 <   Return intertia tensor for entire system and angular momentum Vector.
1028 <
1029 <
1030 <       [  Ixx -Ixy  -Ixz ]
1031 <    J =| -Iyx  Iyy  -Iyz |
1032 <       [ -Izx -Iyz   Izz ]
1033 <    */
1034 <
1035 <   void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1036 <      
1037 <
1038 <      RealType xx = 0.0;
1039 <      RealType yy = 0.0;
1040 <      RealType zz = 0.0;
1041 <      RealType xy = 0.0;
1042 <      RealType xz = 0.0;
1043 <      RealType yz = 0.0;
1044 <      Vector3d com(0.0);
1045 <      Vector3d comVel(0.0);
1046 <      
1047 <      getComAll(com, comVel);
1048 <      
1049 <      SimInfo::MoleculeIterator i;
1050 <      Molecule* mol;
1051 <      
1052 <      Vector3d thisq(0.0);
1053 <      Vector3d thisv(0.0);
1054 <
1055 <      RealType thisMass = 0.0;
1056 <    
1057 <      
1058 <      
1059 <  
1060 <      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1061 <        
1062 <         thisq = mol->getCom()-com;
1063 <         thisv = mol->getComVel()-comVel;
1064 <         thisMass = mol->getMass();
1065 <         // Compute moment of intertia coefficients.
1066 <         xx += thisq[0]*thisq[0]*thisMass;
1067 <         yy += thisq[1]*thisq[1]*thisMass;
1068 <         zz += thisq[2]*thisq[2]*thisMass;
1069 <        
1070 <         // compute products of intertia
1071 <         xy += thisq[0]*thisq[1]*thisMass;
1072 <         xz += thisq[0]*thisq[2]*thisMass;
1073 <         yz += thisq[1]*thisq[2]*thisMass;
1074 <            
1075 <         angularMomentum += cross( thisq, thisv ) * thisMass;
1076 <            
1077 <      }  
1078 <      
1079 <      
1080 <      inertiaTensor(0,0) = yy + zz;
1081 <      inertiaTensor(0,1) = -xy;
1082 <      inertiaTensor(0,2) = -xz;
1083 <      inertiaTensor(1,0) = -xy;
1084 <      inertiaTensor(1,1) = xx + zz;
1085 <      inertiaTensor(1,2) = -yz;
1086 <      inertiaTensor(2,0) = -xz;
1087 <      inertiaTensor(2,1) = -yz;
1088 <      inertiaTensor(2,2) = xx + yy;
1089 <      
1090 < #ifdef IS_MPI
1091 <      Mat3x3d tmpI(inertiaTensor);
1092 <      Vector3d tmpAngMom;
1093 <      MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1094 <      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1095 < #endif
1096 <              
1097 <      return;
1098 <   }
1099 <
1100 <   //Returns the angular momentum of the system
1101 <   Vector3d SimInfo::getAngularMomentum(){
1102 <      
1103 <      Vector3d com(0.0);
1104 <      Vector3d comVel(0.0);
1105 <      Vector3d angularMomentum(0.0);
1106 <      
1107 <      getComAll(com,comVel);
1108 <      
1109 <      SimInfo::MoleculeIterator i;
1110 <      Molecule* mol;
1111 <      
1112 <      Vector3d thisr(0.0);
1113 <      Vector3d thisp(0.0);
1114 <      
1115 <      RealType thisMass;
1116 <      
1117 <      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {        
1118 <        thisMass = mol->getMass();
1119 <        thisr = mol->getCom()-com;
1120 <        thisp = (mol->getComVel()-comVel)*thisMass;
1121 <        
1122 <        angularMomentum += cross( thisr, thisp );
1123 <        
1124 <      }  
1125 <      
1126 < #ifdef IS_MPI
1127 <      Vector3d tmpAngMom;
1128 <      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1129 < #endif
1130 <      
1131 <      return angularMomentum;
1132 <   }
1133 <  
1008 >  
1009    StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1010 <    return IOIndexToIntegrableObject.at(index);
1010 >    if (index >= IOIndexToIntegrableObject.size()) {
1011 >      sprintf(painCave.errMsg,
1012 >              "SimInfo::getIOIndexToIntegrableObject Error: Integrable Object\n"
1013 >              "\tindex exceeds number of known objects!\n");
1014 >      painCave.isFatal = 1;
1015 >      simError();
1016 >      return NULL;
1017 >    } else
1018 >      return IOIndexToIntegrableObject.at(index);
1019    }
1020    
1021    void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1022      IOIndexToIntegrableObject= v;
1023    }
1024  
1142 –  /* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1143 –     based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1144 –     where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1145 –     V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1146 –  */
1147 –  void SimInfo::getGyrationalVolume(RealType &volume){
1148 –    Mat3x3d intTensor;
1149 –    RealType det;
1150 –    Vector3d dummyAngMom;
1151 –    RealType sysconstants;
1152 –    RealType geomCnst;
1153 –
1154 –    geomCnst = 3.0/2.0;
1155 –    /* Get the inertial tensor and angular momentum for free*/
1156 –    getInertiaTensor(intTensor,dummyAngMom);
1157 –    
1158 –    det = intTensor.determinant();
1159 –    sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1160 –    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1161 –    return;
1162 –  }
1163 –
1164 –  void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1165 –    Mat3x3d intTensor;
1166 –    Vector3d dummyAngMom;
1167 –    RealType sysconstants;
1168 –    RealType geomCnst;
1169 –
1170 –    geomCnst = 3.0/2.0;
1171 –    /* Get the inertial tensor and angular momentum for free*/
1172 –    getInertiaTensor(intTensor,dummyAngMom);
1173 –    
1174 –    detI = intTensor.determinant();
1175 –    sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1176 –    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1177 –    return;
1178 –  }
1179 – /*
1180 –   void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1181 –      assert( v.size() == nAtoms_ + nRigidBodies_);
1182 –      sdByGlobalIndex_ = v;
1183 –    }
1184 –
1185 –    StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1186 –      //assert(index < nAtoms_ + nRigidBodies_);
1187 –      return sdByGlobalIndex_.at(index);
1188 –    }  
1189 – */  
1025    int SimInfo::getNGlobalConstraints() {
1026      int nGlobalConstraints;
1027   #ifdef IS_MPI

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