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Revision 1536 by gezelter, Wed Jan 5 14:49:05 2011 UTC vs.
Revision 1769 by gezelter, Mon Jul 9 14:15:52 2012 UTC

# Line 36 | Line 36
36   * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).            
37   * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
38   * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
39 < * [4]  Vardeman & Gezelter, in progress (2009).                        
39 > * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40 > * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
42  
43   /**
# Line 54 | Line 55
55   #include "math/Vector3.hpp"
56   #include "primitives/Molecule.hpp"
57   #include "primitives/StuntDouble.hpp"
57 – #include "UseTheForce/DarkSide/neighborLists_interface.h"
58 – #include "UseTheForce/doForces_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 132 | Line 129 | namespace OpenMD {
129      //equal to the total number of atoms minus number of atoms belong to
130      //cutoff group defined in meta-data file plus the number of cutoff
131      //groups defined in meta-data file
132 +
133      nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
134      
135      //every free atom (atom does not belong to rigid bodies) is an
# Line 227 | Line 225 | namespace OpenMD {
225  
226  
227    void SimInfo::calcNdf() {
228 <    int ndf_local;
228 >    int ndf_local, nfq_local;
229      MoleculeIterator i;
230      vector<StuntDouble*>::iterator j;
231 +    vector<Atom*>::iterator k;
232 +
233      Molecule* mol;
234 <    StuntDouble* integrableObject;
234 >    StuntDouble* sd;
235 >    Atom* atom;
236  
237      ndf_local = 0;
238 +    nfq_local = 0;
239      
240      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
239 –      for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
240 –           integrableObject = mol->nextIntegrableObject(j)) {
241  
242 +      for (sd = mol->beginIntegrableObject(j); sd != NULL;
243 +           sd = mol->nextIntegrableObject(j)) {
244 +
245          ndf_local += 3;
246  
247 <        if (integrableObject->isDirectional()) {
248 <          if (integrableObject->isLinear()) {
247 >        if (sd->isDirectional()) {
248 >          if (sd->isLinear()) {
249              ndf_local += 2;
250            } else {
251              ndf_local += 3;
252            }
253          }
251 –            
254        }
255 +
256 +      for (atom = mol->beginFluctuatingCharge(k); atom != NULL;
257 +           atom = mol->nextFluctuatingCharge(k)) {
258 +        if (atom->isFluctuatingCharge()) {
259 +          nfq_local++;
260 +        }
261 +      }
262      }
263      
264 +    ndfLocal_ = ndf_local;
265 +
266      // n_constraints is local, so subtract them on each processor
267      ndf_local -= nConstraints_;
268  
269   #ifdef IS_MPI
270      MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
271 +    MPI_Allreduce(&nfq_local,&nGlobalFluctuatingCharges_,1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
272   #else
273      ndf_ = ndf_local;
274 +    nGlobalFluctuatingCharges_ = nfq_local;
275   #endif
276  
277      // nZconstraints_ is global, as are the 3 COM translations for the
# Line 275 | Line 288 | namespace OpenMD {
288   #endif
289      return fdf_;
290    }
291 +  
292 +  unsigned int SimInfo::getNLocalCutoffGroups(){
293 +    int nLocalCutoffAtoms = 0;
294 +    Molecule* mol;
295 +    MoleculeIterator mi;
296 +    CutoffGroup* cg;
297 +    Molecule::CutoffGroupIterator ci;
298      
299 +    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
300 +      
301 +      for (cg = mol->beginCutoffGroup(ci); cg != NULL;
302 +           cg = mol->nextCutoffGroup(ci)) {
303 +        nLocalCutoffAtoms += cg->getNumAtom();
304 +        
305 +      }        
306 +    }
307 +    
308 +    return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_;
309 +  }
310 +    
311    void SimInfo::calcNdfRaw() {
312      int ndfRaw_local;
313  
314      MoleculeIterator i;
315      vector<StuntDouble*>::iterator j;
316      Molecule* mol;
317 <    StuntDouble* integrableObject;
317 >    StuntDouble* sd;
318  
319      // Raw degrees of freedom that we have to set
320      ndfRaw_local = 0;
321      
322      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
291 –      for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
292 –           integrableObject = mol->nextIntegrableObject(j)) {
323  
324 +      for (sd = mol->beginIntegrableObject(j); sd != NULL;
325 +           sd = mol->nextIntegrableObject(j)) {
326 +
327          ndfRaw_local += 3;
328  
329 <        if (integrableObject->isDirectional()) {
330 <          if (integrableObject->isLinear()) {
329 >        if (sd->isDirectional()) {
330 >          if (sd->isLinear()) {
331              ndfRaw_local += 2;
332            } else {
333              ndfRaw_local += 3;
# Line 354 | Line 387 | namespace OpenMD {
387      Molecule::RigidBodyIterator rbIter;
388      RigidBody* rb;
389      Molecule::IntegrableObjectIterator ii;
390 <    StuntDouble* integrableObject;
390 >    StuntDouble* sd;
391      
392 <    for (integrableObject = mol->beginIntegrableObject(ii);
393 <         integrableObject != NULL;
361 <         integrableObject = mol->nextIntegrableObject(ii)) {
392 >    for (sd = mol->beginIntegrableObject(ii); sd != NULL;
393 >         sd = mol->nextIntegrableObject(ii)) {
394        
395 <      if (integrableObject->isRigidBody()) {
396 <        rb = static_cast<RigidBody*>(integrableObject);
395 >      if (sd->isRigidBody()) {
396 >        rb = static_cast<RigidBody*>(sd);
397          vector<Atom*> atoms = rb->getAtoms();
398          set<int> rigidAtoms;
399          for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
# Line 372 | Line 404 | namespace OpenMD {
404          }      
405        } else {
406          set<int> oneAtomSet;
407 <        oneAtomSet.insert(integrableObject->getGlobalIndex());
408 <        atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));        
407 >        oneAtomSet.insert(sd->getGlobalIndex());
408 >        atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));        
409        }
410      }  
411            
# Line 507 | Line 539 | namespace OpenMD {
539      Molecule::RigidBodyIterator rbIter;
540      RigidBody* rb;
541      Molecule::IntegrableObjectIterator ii;
542 <    StuntDouble* integrableObject;
542 >    StuntDouble* sd;
543      
544 <    for (integrableObject = mol->beginIntegrableObject(ii);
545 <         integrableObject != NULL;
514 <         integrableObject = mol->nextIntegrableObject(ii)) {
544 >    for (sd = mol->beginIntegrableObject(ii); sd != NULL;
545 >         sd = mol->nextIntegrableObject(ii)) {
546        
547 <      if (integrableObject->isRigidBody()) {
548 <        rb = static_cast<RigidBody*>(integrableObject);
547 >      if (sd->isRigidBody()) {
548 >        rb = static_cast<RigidBody*>(sd);
549          vector<Atom*> atoms = rb->getAtoms();
550          set<int> rigidAtoms;
551          for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
# Line 525 | Line 556 | namespace OpenMD {
556          }      
557        } else {
558          set<int> oneAtomSet;
559 <        oneAtomSet.insert(integrableObject->getGlobalIndex());
560 <        atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));        
559 >        oneAtomSet.insert(sd->getGlobalIndex());
560 >        atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));        
561        }
562      }  
563  
# Line 681 | Line 712 | namespace OpenMD {
712      Atom* atom;
713      set<AtomType*> atomTypes;
714      
715 <    for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {      
716 <      for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
715 >    for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
716 >      for(atom = mol->beginAtom(ai); atom != NULL;
717 >          atom = mol->nextAtom(ai)) {
718          atomTypes.insert(atom->getAtomType());
719        }      
720      }    
721 <
721 >    
722   #ifdef IS_MPI
723  
724      // loop over the found atom types on this processor, and add their
725      // numerical idents to a vector:
726 <
726 >    
727      vector<int> foundTypes;
728      set<AtomType*>::iterator i;
729      for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
# Line 700 | Line 732 | namespace OpenMD {
732      // count_local holds the number of found types on this processor
733      int count_local = foundTypes.size();
734  
703 –    // count holds the total number of found types on all processors
704 –    // (some will be redundant with the ones found locally):
705 –    int count;
706 –    MPI::COMM_WORLD.Allreduce(&count_local, &count, 1, MPI::INT, MPI::SUM);
707 –
708 –    // create a vector to hold the globally found types, and resize it:
709 –    vector<int> ftGlobal;
710 –    ftGlobal.resize(count);
711 –    vector<int> counts;
712 –
735      int nproc = MPI::COMM_WORLD.Get_size();
714 –    counts.resize(nproc);
715 –    vector<int> disps;
716 –    disps.resize(nproc);
736  
737 <    // now spray out the foundTypes to all the other processors:
737 >    // we need arrays to hold the counts and displacement vectors for
738 >    // all processors
739 >    vector<int> counts(nproc, 0);
740 >    vector<int> disps(nproc, 0);
741 >
742 >    // fill the counts array
743 >    MPI::COMM_WORLD.Allgather(&count_local, 1, MPI::INT, &counts[0],
744 >                              1, MPI::INT);
745 >  
746 >    // use the processor counts to compute the displacement array
747 >    disps[0] = 0;    
748 >    int totalCount = counts[0];
749 >    for (int iproc = 1; iproc < nproc; iproc++) {
750 >      disps[iproc] = disps[iproc-1] + counts[iproc-1];
751 >      totalCount += counts[iproc];
752 >    }
753 >
754 >    // we need a (possibly redundant) set of all found types:
755 >    vector<int> ftGlobal(totalCount);
756      
757 +    // now spray out the foundTypes to all the other processors:    
758      MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
759 <                               &ftGlobal[0], &counts[0], &disps[0], MPI::INT);
759 >                               &ftGlobal[0], &counts[0], &disps[0],
760 >                               MPI::INT);
761  
762 +    vector<int>::iterator j;
763 +
764      // foundIdents is a stl set, so inserting an already found ident
765      // will have no effect.
766      set<int> foundIdents;
767 <    vector<int>::iterator j;
767 >
768      for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
769        foundIdents.insert((*j));
770      
771      // now iterate over the foundIdents and get the actual atom types
772      // that correspond to these:
773      set<int>::iterator it;
774 <    for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
774 >    for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
775        atomTypes.insert( forceField_->getAtomType((*it)) );
776  
777   #endif
778 <    
778 >
779      return atomTypes;        
780    }
781  
# Line 746 | Line 787 | namespace OpenMD {
787        if ( simParams_->getAccumulateBoxDipole() ) {
788          calcBoxDipole_ = true;      
789        }
790 <
790 >    
791      set<AtomType*>::iterator i;
792      set<AtomType*> atomTypes;
793      atomTypes = getSimulatedAtomTypes();    
794 <    int usesElectrostatic = 0;
795 <    int usesMetallic = 0;
796 <    int usesDirectional = 0;
794 >    bool usesElectrostatic = false;
795 >    bool usesMetallic = false;
796 >    bool usesDirectional = false;
797 >    bool usesFluctuatingCharges =  false;
798      //loop over all of the atom types
799      for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
800        usesElectrostatic |= (*i)->isElectrostatic();
801        usesMetallic |= (*i)->isMetal();
802        usesDirectional |= (*i)->isDirectional();
803 +      usesFluctuatingCharges |= (*i)->isFluctuatingCharge();
804      }
805  
806 < #ifdef IS_MPI    
807 <    int temp;
806 > #ifdef IS_MPI
807 >    bool temp;
808      temp = usesDirectional;
809 <    MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
810 <
809 >    MPI::COMM_WORLD.Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI::BOOL,
810 >                              MPI::LOR);
811 >        
812      temp = usesMetallic;
813 <    MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
814 <
813 >    MPI::COMM_WORLD.Allreduce(&temp, &usesMetallicAtoms_, 1, MPI::BOOL,
814 >                              MPI::LOR);
815 >    
816      temp = usesElectrostatic;
817 <    MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
817 >    MPI::COMM_WORLD.Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI::BOOL,
818 >                              MPI::LOR);
819 >
820 >    temp = usesFluctuatingCharges;
821 >    MPI::COMM_WORLD.Allreduce(&temp, &usesFluctuatingCharges_, 1, MPI::BOOL,
822 >                              MPI::LOR);
823 > #else
824 >
825 >    usesDirectionalAtoms_ = usesDirectional;
826 >    usesMetallicAtoms_ = usesMetallic;
827 >    usesElectrostaticAtoms_ = usesElectrostatic;
828 >    usesFluctuatingCharges_ = usesFluctuatingCharges;
829 >
830   #endif
831 <    fInfo_.SIM_uses_PBC = usesPeriodicBoundaries_;    
832 <    fInfo_.SIM_uses_DirectionalAtoms = usesDirectionalAtoms_;
833 <    fInfo_.SIM_uses_MetallicAtoms = usesMetallicAtoms_;
834 <    fInfo_.SIM_requires_SkipCorrection = usesElectrostaticAtoms_;
778 <    fInfo_.SIM_requires_SelfCorrection = usesElectrostaticAtoms_;
779 <    fInfo_.SIM_uses_AtomicVirial = usesAtomicVirial_;
831 >    
832 >    requiresPrepair_ = usesMetallicAtoms_ ? true : false;
833 >    requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
834 >    requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;    
835    }
836  
837 <  void SimInfo::setupFortran() {
838 <    int isError;
839 <    int nExclude, nOneTwo, nOneThree, nOneFour;
840 <    vector<int> fortranGlobalGroupMembership;
837 >
838 >  vector<int> SimInfo::getGlobalAtomIndices() {
839 >    SimInfo::MoleculeIterator mi;
840 >    Molecule* mol;
841 >    Molecule::AtomIterator ai;
842 >    Atom* atom;
843 >
844 >    vector<int> GlobalAtomIndices(getNAtoms(), 0);
845      
846 <    isError = 0;
846 >    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
847 >      
848 >      for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
849 >        GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
850 >      }
851 >    }
852 >    return GlobalAtomIndices;
853 >  }
854  
855 <    //globalGroupMembership_ is filled by SimCreator    
856 <    for (int i = 0; i < nGlobalAtoms_; i++) {
857 <      fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
855 >
856 >  vector<int> SimInfo::getGlobalGroupIndices() {
857 >    SimInfo::MoleculeIterator mi;
858 >    Molecule* mol;
859 >    Molecule::CutoffGroupIterator ci;
860 >    CutoffGroup* cg;
861 >
862 >    vector<int> GlobalGroupIndices;
863 >    
864 >    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
865 >      
866 >      //local index of cutoff group is trivial, it only depends on the
867 >      //order of travesing
868 >      for (cg = mol->beginCutoffGroup(ci); cg != NULL;
869 >           cg = mol->nextCutoffGroup(ci)) {
870 >        GlobalGroupIndices.push_back(cg->getGlobalIndex());
871 >      }        
872      }
873 +    return GlobalGroupIndices;
874 +  }
875  
876 +
877 +  void SimInfo::prepareTopology() {
878 +    int nExclude, nOneTwo, nOneThree, nOneFour;
879 +
880      //calculate mass ratio of cutoff group
795 –    vector<RealType> mfact;
881      SimInfo::MoleculeIterator mi;
882      Molecule* mol;
883      Molecule::CutoffGroupIterator ci;
# Line 801 | Line 886 | namespace OpenMD {
886      Atom* atom;
887      RealType totalMass;
888  
889 <    //to avoid memory reallocation, reserve enough space for mfact
890 <    mfact.reserve(getNCutoffGroups());
889 >    /**
890 >     * The mass factor is the relative mass of an atom to the total
891 >     * mass of the cutoff group it belongs to.  By default, all atoms
892 >     * are their own cutoff groups, and therefore have mass factors of
893 >     * 1.  We need some special handling for massless atoms, which
894 >     * will be treated as carrying the entire mass of the cutoff
895 >     * group.
896 >     */
897 >    massFactors_.clear();
898 >    massFactors_.resize(getNAtoms(), 1.0);
899      
900      for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {        
901 <      for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
901 >      for (cg = mol->beginCutoffGroup(ci); cg != NULL;
902 >           cg = mol->nextCutoffGroup(ci)) {
903  
904          totalMass = cg->getMass();
905          for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
906            // Check for massless groups - set mfact to 1 if true
907 <          if (totalMass != 0)
908 <            mfact.push_back(atom->getMass()/totalMass);
907 >          if (totalMass != 0)
908 >            massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
909            else
910 <            mfact.push_back( 1.0 );
910 >            massFactors_[atom->getLocalIndex()] = 1.0;
911          }
912        }      
913      }
914  
915 <    //fill ident array of local atoms (it is actually ident of
822 <    //AtomType, it is so confusing !!!)
823 <    vector<int> identArray;
915 >    // Build the identArray_
916  
917 <    //to avoid memory reallocation, reserve enough space identArray
918 <    identArray.reserve(getNAtoms());
827 <    
917 >    identArray_.clear();
918 >    identArray_.reserve(getNAtoms());    
919      for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {        
920        for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
921 <        identArray.push_back(atom->getIdent());
921 >        identArray_.push_back(atom->getIdent());
922        }
923      }    
833 –
834 –    //fill molMembershipArray
835 –    //molMembershipArray is filled by SimCreator    
836 –    vector<int> molMembershipArray(nGlobalAtoms_);
837 –    for (int i = 0; i < nGlobalAtoms_; i++) {
838 –      molMembershipArray[i] = globalMolMembership_[i] + 1;
839 –    }
924      
925 <    //setup fortran simulation
925 >    //scan topology
926  
927      nExclude = excludedInteractions_.getSize();
928      nOneTwo = oneTwoInteractions_.getSize();
# Line 850 | Line 934 | namespace OpenMD {
934      int* oneThreeList = oneThreeInteractions_.getPairList();
935      int* oneFourList = oneFourInteractions_.getPairList();
936  
937 <    setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
854 <                   &nExclude, excludeList,
855 <                   &nOneTwo, oneTwoList,
856 <                   &nOneThree, oneThreeList,
857 <                   &nOneFour, oneFourList,
858 <                   &molMembershipArray[0], &mfact[0], &nCutoffGroups_,
859 <                   &fortranGlobalGroupMembership[0], &isError);
860 <    
861 <    if( isError ){
862 <      
863 <      sprintf( painCave.errMsg,
864 <               "There was an error setting the simulation information in fortran.\n" );
865 <      painCave.isFatal = 1;
866 <      painCave.severity = OPENMD_ERROR;
867 <      simError();
868 <    }
869 <    
870 <    
871 <    sprintf( checkPointMsg,
872 <             "succesfully sent the simulation information to fortran.\n");
873 <    
874 <    errorCheckPoint();
875 <    
876 <    // Setup number of neighbors in neighbor list if present
877 <    if (simParams_->haveNeighborListNeighbors()) {
878 <      int nlistNeighbors = simParams_->getNeighborListNeighbors();
879 <      setNeighbors(&nlistNeighbors);
880 <    }
881 <  
882 < #ifdef IS_MPI    
883 <    //SimInfo is responsible for creating localToGlobalAtomIndex and
884 <    //localToGlobalGroupIndex
885 <    vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
886 <    vector<int> localToGlobalCutoffGroupIndex;
887 <    mpiSimData parallelData;
888 <
889 <    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
890 <
891 <      //local index(index in DataStorge) of atom is important
892 <      for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
893 <        localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
894 <      }
895 <
896 <      //local index of cutoff group is trivial, it only depends on the order of travesing
897 <      for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
898 <        localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
899 <      }        
900 <        
901 <    }
902 <
903 <    //fill up mpiSimData struct
904 <    parallelData.nMolGlobal = getNGlobalMolecules();
905 <    parallelData.nMolLocal = getNMolecules();
906 <    parallelData.nAtomsGlobal = getNGlobalAtoms();
907 <    parallelData.nAtomsLocal = getNAtoms();
908 <    parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
909 <    parallelData.nGroupsLocal = getNCutoffGroups();
910 <    parallelData.myNode = worldRank;
911 <    MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
912 <
913 <    //pass mpiSimData struct and index arrays to fortran
914 <    setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
915 <                    &localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
916 <                    &localToGlobalCutoffGroupIndex[0], &isError);
917 <
918 <    if (isError) {
919 <      sprintf(painCave.errMsg,
920 <              "mpiRefresh errror: fortran didn't like something we gave it.\n");
921 <      painCave.isFatal = 1;
922 <      simError();
923 <    }
924 <
925 <    sprintf(checkPointMsg, " mpiRefresh successful.\n");
926 <    errorCheckPoint();
927 < #endif
928 <
929 <    initFortranFF(&isError);
930 <    if (isError) {
931 <      sprintf(painCave.errMsg,
932 <              "initFortranFF errror: fortran didn't like something we gave it.\n");
933 <      painCave.isFatal = 1;
934 <      simError();
935 <    }
936 <    fortranInitialized_ = true;
937 >    topologyDone_ = true;
938    }
939  
940    void SimInfo::addProperty(GenericData* genData) {
# Line 970 | Line 971 | namespace OpenMD {
971      Molecule* mol;
972      RigidBody* rb;
973      Atom* atom;
974 +    CutoffGroup* cg;
975      SimInfo::MoleculeIterator mi;
976      Molecule::RigidBodyIterator rbIter;
977 <    Molecule::AtomIterator atomIter;;
977 >    Molecule::AtomIterator atomIter;
978 >    Molecule::CutoffGroupIterator cgIter;
979  
980      for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
981          
# Line 983 | Line 986 | namespace OpenMD {
986        for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
987          rb->setSnapshotManager(sman_);
988        }
989 +
990 +      for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
991 +        cg->setSnapshotManager(sman_);
992 +      }
993      }    
994      
995    }
996  
990 –  Vector3d SimInfo::getComVel(){
991 –    SimInfo::MoleculeIterator i;
992 –    Molecule* mol;
997  
994 –    Vector3d comVel(0.0);
995 –    RealType totalMass = 0.0;
996 –    
997 –
998 –    for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
999 –      RealType mass = mol->getMass();
1000 –      totalMass += mass;
1001 –      comVel += mass * mol->getComVel();
1002 –    }  
1003 –
1004 – #ifdef IS_MPI
1005 –    RealType tmpMass = totalMass;
1006 –    Vector3d tmpComVel(comVel);    
1007 –    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1008 –    MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1009 – #endif
1010 –
1011 –    comVel /= totalMass;
1012 –
1013 –    return comVel;
1014 –  }
1015 –
1016 –  Vector3d SimInfo::getCom(){
1017 –    SimInfo::MoleculeIterator i;
1018 –    Molecule* mol;
1019 –
1020 –    Vector3d com(0.0);
1021 –    RealType totalMass = 0.0;
1022 –    
1023 –    for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1024 –      RealType mass = mol->getMass();
1025 –      totalMass += mass;
1026 –      com += mass * mol->getCom();
1027 –    }  
1028 –
1029 – #ifdef IS_MPI
1030 –    RealType tmpMass = totalMass;
1031 –    Vector3d tmpCom(com);    
1032 –    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1033 –    MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1034 – #endif
1035 –
1036 –    com /= totalMass;
1037 –
1038 –    return com;
1039 –
1040 –  }        
1041 –
998    ostream& operator <<(ostream& o, SimInfo& info) {
999  
1000      return o;
1001    }
1002    
1003 <  
1048 <   /*
1049 <   Returns center of mass and center of mass velocity in one function call.
1050 <   */
1051 <  
1052 <   void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1053 <      SimInfo::MoleculeIterator i;
1054 <      Molecule* mol;
1055 <      
1056 <    
1057 <      RealType totalMass = 0.0;
1058 <    
1059 <
1060 <      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1061 <         RealType mass = mol->getMass();
1062 <         totalMass += mass;
1063 <         com += mass * mol->getCom();
1064 <         comVel += mass * mol->getComVel();          
1065 <      }  
1066 <      
1067 < #ifdef IS_MPI
1068 <      RealType tmpMass = totalMass;
1069 <      Vector3d tmpCom(com);  
1070 <      Vector3d tmpComVel(comVel);
1071 <      MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1072 <      MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1073 <      MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1074 < #endif
1075 <      
1076 <      com /= totalMass;
1077 <      comVel /= totalMass;
1078 <   }        
1079 <  
1080 <   /*
1081 <   Return intertia tensor for entire system and angular momentum Vector.
1082 <
1083 <
1084 <       [  Ixx -Ixy  -Ixz ]
1085 <    J =| -Iyx  Iyy  -Iyz |
1086 <       [ -Izx -Iyz   Izz ]
1087 <    */
1088 <
1089 <   void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1090 <      
1091 <
1092 <      RealType xx = 0.0;
1093 <      RealType yy = 0.0;
1094 <      RealType zz = 0.0;
1095 <      RealType xy = 0.0;
1096 <      RealType xz = 0.0;
1097 <      RealType yz = 0.0;
1098 <      Vector3d com(0.0);
1099 <      Vector3d comVel(0.0);
1100 <      
1101 <      getComAll(com, comVel);
1102 <      
1103 <      SimInfo::MoleculeIterator i;
1104 <      Molecule* mol;
1105 <      
1106 <      Vector3d thisq(0.0);
1107 <      Vector3d thisv(0.0);
1108 <
1109 <      RealType thisMass = 0.0;
1110 <    
1111 <      
1112 <      
1113 <  
1114 <      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1115 <        
1116 <         thisq = mol->getCom()-com;
1117 <         thisv = mol->getComVel()-comVel;
1118 <         thisMass = mol->getMass();
1119 <         // Compute moment of intertia coefficients.
1120 <         xx += thisq[0]*thisq[0]*thisMass;
1121 <         yy += thisq[1]*thisq[1]*thisMass;
1122 <         zz += thisq[2]*thisq[2]*thisMass;
1123 <        
1124 <         // compute products of intertia
1125 <         xy += thisq[0]*thisq[1]*thisMass;
1126 <         xz += thisq[0]*thisq[2]*thisMass;
1127 <         yz += thisq[1]*thisq[2]*thisMass;
1128 <            
1129 <         angularMomentum += cross( thisq, thisv ) * thisMass;
1130 <            
1131 <      }  
1132 <      
1133 <      
1134 <      inertiaTensor(0,0) = yy + zz;
1135 <      inertiaTensor(0,1) = -xy;
1136 <      inertiaTensor(0,2) = -xz;
1137 <      inertiaTensor(1,0) = -xy;
1138 <      inertiaTensor(1,1) = xx + zz;
1139 <      inertiaTensor(1,2) = -yz;
1140 <      inertiaTensor(2,0) = -xz;
1141 <      inertiaTensor(2,1) = -yz;
1142 <      inertiaTensor(2,2) = xx + yy;
1143 <      
1144 < #ifdef IS_MPI
1145 <      Mat3x3d tmpI(inertiaTensor);
1146 <      Vector3d tmpAngMom;
1147 <      MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1148 <      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1149 < #endif
1150 <              
1151 <      return;
1152 <   }
1153 <
1154 <   //Returns the angular momentum of the system
1155 <   Vector3d SimInfo::getAngularMomentum(){
1156 <      
1157 <      Vector3d com(0.0);
1158 <      Vector3d comVel(0.0);
1159 <      Vector3d angularMomentum(0.0);
1160 <      
1161 <      getComAll(com,comVel);
1162 <      
1163 <      SimInfo::MoleculeIterator i;
1164 <      Molecule* mol;
1165 <      
1166 <      Vector3d thisr(0.0);
1167 <      Vector3d thisp(0.0);
1168 <      
1169 <      RealType thisMass;
1170 <      
1171 <      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {        
1172 <        thisMass = mol->getMass();
1173 <        thisr = mol->getCom()-com;
1174 <        thisp = (mol->getComVel()-comVel)*thisMass;
1175 <        
1176 <        angularMomentum += cross( thisr, thisp );
1177 <        
1178 <      }  
1179 <      
1180 < #ifdef IS_MPI
1181 <      Vector3d tmpAngMom;
1182 <      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1183 < #endif
1184 <      
1185 <      return angularMomentum;
1186 <   }
1187 <  
1003 >  
1004    StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1005      return IOIndexToIntegrableObject.at(index);
1006    }
# Line 1192 | Line 1008 | namespace OpenMD {
1008    void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1009      IOIndexToIntegrableObject= v;
1010    }
1195 –
1196 –  /* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1197 –     based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1198 –     where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1199 –     V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1200 –  */
1201 –  void SimInfo::getGyrationalVolume(RealType &volume){
1202 –    Mat3x3d intTensor;
1203 –    RealType det;
1204 –    Vector3d dummyAngMom;
1205 –    RealType sysconstants;
1206 –    RealType geomCnst;
1207 –
1208 –    geomCnst = 3.0/2.0;
1209 –    /* Get the inertial tensor and angular momentum for free*/
1210 –    getInertiaTensor(intTensor,dummyAngMom);
1211 –    
1212 –    det = intTensor.determinant();
1213 –    sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1214 –    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1215 –    return;
1216 –  }
1217 –
1218 –  void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1219 –    Mat3x3d intTensor;
1220 –    Vector3d dummyAngMom;
1221 –    RealType sysconstants;
1222 –    RealType geomCnst;
1223 –
1224 –    geomCnst = 3.0/2.0;
1225 –    /* Get the inertial tensor and angular momentum for free*/
1226 –    getInertiaTensor(intTensor,dummyAngMom);
1227 –    
1228 –    detI = intTensor.determinant();
1229 –    sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1230 –    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1231 –    return;
1232 –  }
1011   /*
1012     void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1013        assert( v.size() == nAtoms_ + nRigidBodies_);

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