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Revision 1540 by gezelter, Mon Jan 17 21:34:36 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
135 –    std::cerr << "nGA = " << nGlobalAtoms_ << "\n";
136 –    std::cerr << "nCA = " << nCutoffAtoms << "\n";
137 –    std::cerr << "nG = " << nGroups << "\n";
132  
133      nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
140 –
141 –    std::cerr << "nGCG = " << nGlobalCutoffGroups_ << "\n";
134      
135      //every free atom (atom does not belong to rigid bodies) is an
136      //integrable object therefore the total number of integrable objects
# Line 233 | 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)) {
245 –      for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
246 –           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          }
257 –            
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 281 | 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)) {
297 –      for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
298 –           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 360 | 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;
367 <         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 378 | 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 513 | 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;
520 <         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 531 | 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 687 | 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 706 | Line 732 | namespace OpenMD {
732      // count_local holds the number of found types on this processor
733      int count_local = foundTypes.size();
734  
735 <    // count holds the total number of found types on all processors
710 <    // (some will be redundant with the ones found locally):
711 <    int count;
712 <    MPI::COMM_WORLD.Allreduce(&count_local, &count, 1, MPI::INT, MPI::SUM);
735 >    int nproc = MPI::COMM_WORLD.Get_size();
736  
737 <    // create a vector to hold the globally found types, and resize it:
738 <    vector<int> ftGlobal;
739 <    ftGlobal.resize(count);
740 <    vector<int> counts;
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 <    int nproc = MPI::COMM_WORLD.Get_size();
743 <    counts.resize(nproc);
744 <    vector<int> disps;
745 <    disps.resize(nproc);
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 <    // now spray out the foundTypes to all the other processors:
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 752 | 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_;
784 <    fInfo_.SIM_requires_SelfCorrection = usesElectrostaticAtoms_;
785 <    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
801 –    vector<RealType> mfact;
881      SimInfo::MoleculeIterator mi;
882      Molecule* mol;
883      Molecule::CutoffGroupIterator ci;
# Line 807 | 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
828 <    //AtomType, it is so confusing !!!)
829 <    vector<int> identArray;
915 >    // Build the identArray_
916  
917 <    //to avoid memory reallocation, reserve enough space identArray
918 <    identArray.reserve(getNAtoms());
833 <    
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      }    
839 –
840 –    //fill molMembershipArray
841 –    //molMembershipArray is filled by SimCreator    
842 –    vector<int> molMembershipArray(nGlobalAtoms_);
843 –    for (int i = 0; i < nGlobalAtoms_; i++) {
844 –      molMembershipArray[i] = globalMolMembership_[i] + 1;
845 –    }
924      
925 <    //setup fortran simulation
925 >    //scan topology
926  
927      nExclude = excludedInteractions_.getSize();
928      nOneTwo = oneTwoInteractions_.getSize();
# Line 856 | Line 934 | namespace OpenMD {
934      int* oneThreeList = oneThreeInteractions_.getPairList();
935      int* oneFourList = oneFourInteractions_.getPairList();
936  
937 <    setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
860 <                   &nExclude, excludeList,
861 <                   &nOneTwo, oneTwoList,
862 <                   &nOneThree, oneThreeList,
863 <                   &nOneFour, oneFourList,
864 <                   &molMembershipArray[0], &mfact[0], &nCutoffGroups_,
865 <                   &fortranGlobalGroupMembership[0], &isError);
866 <    
867 <    if( isError ){
868 <      
869 <      sprintf( painCave.errMsg,
870 <               "There was an error setting the simulation information in fortran.\n" );
871 <      painCave.isFatal = 1;
872 <      painCave.severity = OPENMD_ERROR;
873 <      simError();
874 <    }
875 <    
876 <    
877 <    sprintf( checkPointMsg,
878 <             "succesfully sent the simulation information to fortran.\n");
879 <    
880 <    errorCheckPoint();
881 <    
882 <    // Setup number of neighbors in neighbor list if present
883 <    if (simParams_->haveNeighborListNeighbors()) {
884 <      int nlistNeighbors = simParams_->getNeighborListNeighbors();
885 <      setNeighbors(&nlistNeighbors);
886 <    }
887 <  
888 < #ifdef IS_MPI    
889 <    //SimInfo is responsible for creating localToGlobalAtomIndex and
890 <    //localToGlobalGroupIndex
891 <    vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
892 <    vector<int> localToGlobalCutoffGroupIndex;
893 <    mpiSimData parallelData;
894 <
895 <    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
896 <
897 <      //local index(index in DataStorge) of atom is important
898 <      for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
899 <        localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
900 <      }
901 <
902 <      //local index of cutoff group is trivial, it only depends on the order of travesing
903 <      for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
904 <        localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
905 <      }        
906 <        
907 <    }
908 <
909 <    //fill up mpiSimData struct
910 <    parallelData.nMolGlobal = getNGlobalMolecules();
911 <    parallelData.nMolLocal = getNMolecules();
912 <    parallelData.nAtomsGlobal = getNGlobalAtoms();
913 <    parallelData.nAtomsLocal = getNAtoms();
914 <    parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
915 <    parallelData.nGroupsLocal = getNCutoffGroups();
916 <    parallelData.myNode = worldRank;
917 <    MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
918 <
919 <    //pass mpiSimData struct and index arrays to fortran
920 <    setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
921 <                    &localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
922 <                    &localToGlobalCutoffGroupIndex[0], &isError);
923 <
924 <    if (isError) {
925 <      sprintf(painCave.errMsg,
926 <              "mpiRefresh errror: fortran didn't like something we gave it.\n");
927 <      painCave.isFatal = 1;
928 <      simError();
929 <    }
930 <
931 <    sprintf(checkPointMsg, " mpiRefresh successful.\n");
932 <    errorCheckPoint();
933 < #endif
934 <
935 <    initFortranFF(&isError);
936 <    if (isError) {
937 <      sprintf(painCave.errMsg,
938 <              "initFortranFF errror: fortran didn't like something we gave it.\n");
939 <      painCave.isFatal = 1;
940 <      simError();
941 <    }
942 <    fortranInitialized_ = true;
937 >    topologyDone_ = true;
938    }
939  
940    void SimInfo::addProperty(GenericData* genData) {
# Line 999 | Line 994 | namespace OpenMD {
994      
995    }
996  
1002 –  Vector3d SimInfo::getComVel(){
1003 –    SimInfo::MoleculeIterator i;
1004 –    Molecule* mol;
997  
1006 –    Vector3d comVel(0.0);
1007 –    RealType totalMass = 0.0;
1008 –    
1009 –
1010 –    for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1011 –      RealType mass = mol->getMass();
1012 –      totalMass += mass;
1013 –      comVel += mass * mol->getComVel();
1014 –    }  
1015 –
1016 – #ifdef IS_MPI
1017 –    RealType tmpMass = totalMass;
1018 –    Vector3d tmpComVel(comVel);    
1019 –    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1020 –    MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1021 – #endif
1022 –
1023 –    comVel /= totalMass;
1024 –
1025 –    return comVel;
1026 –  }
1027 –
1028 –  Vector3d SimInfo::getCom(){
1029 –    SimInfo::MoleculeIterator i;
1030 –    Molecule* mol;
1031 –
1032 –    Vector3d com(0.0);
1033 –    RealType totalMass = 0.0;
1034 –    
1035 –    for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1036 –      RealType mass = mol->getMass();
1037 –      totalMass += mass;
1038 –      com += mass * mol->getCom();
1039 –    }  
1040 –
1041 – #ifdef IS_MPI
1042 –    RealType tmpMass = totalMass;
1043 –    Vector3d tmpCom(com);    
1044 –    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1045 –    MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1046 – #endif
1047 –
1048 –    com /= totalMass;
1049 –
1050 –    return com;
1051 –
1052 –  }        
1053 –
998    ostream& operator <<(ostream& o, SimInfo& info) {
999  
1000      return o;
1001    }
1002    
1003 <  
1060 <   /*
1061 <   Returns center of mass and center of mass velocity in one function call.
1062 <   */
1063 <  
1064 <   void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1065 <      SimInfo::MoleculeIterator i;
1066 <      Molecule* mol;
1067 <      
1068 <    
1069 <      RealType totalMass = 0.0;
1070 <    
1071 <
1072 <      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1073 <         RealType mass = mol->getMass();
1074 <         totalMass += mass;
1075 <         com += mass * mol->getCom();
1076 <         comVel += mass * mol->getComVel();          
1077 <      }  
1078 <      
1079 < #ifdef IS_MPI
1080 <      RealType tmpMass = totalMass;
1081 <      Vector3d tmpCom(com);  
1082 <      Vector3d tmpComVel(comVel);
1083 <      MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1084 <      MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1085 <      MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1086 < #endif
1087 <      
1088 <      com /= totalMass;
1089 <      comVel /= totalMass;
1090 <   }        
1091 <  
1092 <   /*
1093 <   Return intertia tensor for entire system and angular momentum Vector.
1094 <
1095 <
1096 <       [  Ixx -Ixy  -Ixz ]
1097 <    J =| -Iyx  Iyy  -Iyz |
1098 <       [ -Izx -Iyz   Izz ]
1099 <    */
1100 <
1101 <   void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1102 <      
1103 <
1104 <      RealType xx = 0.0;
1105 <      RealType yy = 0.0;
1106 <      RealType zz = 0.0;
1107 <      RealType xy = 0.0;
1108 <      RealType xz = 0.0;
1109 <      RealType yz = 0.0;
1110 <      Vector3d com(0.0);
1111 <      Vector3d comVel(0.0);
1112 <      
1113 <      getComAll(com, comVel);
1114 <      
1115 <      SimInfo::MoleculeIterator i;
1116 <      Molecule* mol;
1117 <      
1118 <      Vector3d thisq(0.0);
1119 <      Vector3d thisv(0.0);
1120 <
1121 <      RealType thisMass = 0.0;
1122 <    
1123 <      
1124 <      
1125 <  
1126 <      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1127 <        
1128 <         thisq = mol->getCom()-com;
1129 <         thisv = mol->getComVel()-comVel;
1130 <         thisMass = mol->getMass();
1131 <         // Compute moment of intertia coefficients.
1132 <         xx += thisq[0]*thisq[0]*thisMass;
1133 <         yy += thisq[1]*thisq[1]*thisMass;
1134 <         zz += thisq[2]*thisq[2]*thisMass;
1135 <        
1136 <         // compute products of intertia
1137 <         xy += thisq[0]*thisq[1]*thisMass;
1138 <         xz += thisq[0]*thisq[2]*thisMass;
1139 <         yz += thisq[1]*thisq[2]*thisMass;
1140 <            
1141 <         angularMomentum += cross( thisq, thisv ) * thisMass;
1142 <            
1143 <      }  
1144 <      
1145 <      
1146 <      inertiaTensor(0,0) = yy + zz;
1147 <      inertiaTensor(0,1) = -xy;
1148 <      inertiaTensor(0,2) = -xz;
1149 <      inertiaTensor(1,0) = -xy;
1150 <      inertiaTensor(1,1) = xx + zz;
1151 <      inertiaTensor(1,2) = -yz;
1152 <      inertiaTensor(2,0) = -xz;
1153 <      inertiaTensor(2,1) = -yz;
1154 <      inertiaTensor(2,2) = xx + yy;
1155 <      
1156 < #ifdef IS_MPI
1157 <      Mat3x3d tmpI(inertiaTensor);
1158 <      Vector3d tmpAngMom;
1159 <      MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1160 <      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1161 < #endif
1162 <              
1163 <      return;
1164 <   }
1165 <
1166 <   //Returns the angular momentum of the system
1167 <   Vector3d SimInfo::getAngularMomentum(){
1168 <      
1169 <      Vector3d com(0.0);
1170 <      Vector3d comVel(0.0);
1171 <      Vector3d angularMomentum(0.0);
1172 <      
1173 <      getComAll(com,comVel);
1174 <      
1175 <      SimInfo::MoleculeIterator i;
1176 <      Molecule* mol;
1177 <      
1178 <      Vector3d thisr(0.0);
1179 <      Vector3d thisp(0.0);
1180 <      
1181 <      RealType thisMass;
1182 <      
1183 <      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {        
1184 <        thisMass = mol->getMass();
1185 <        thisr = mol->getCom()-com;
1186 <        thisp = (mol->getComVel()-comVel)*thisMass;
1187 <        
1188 <        angularMomentum += cross( thisr, thisp );
1189 <        
1190 <      }  
1191 <      
1192 < #ifdef IS_MPI
1193 <      Vector3d tmpAngMom;
1194 <      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1195 < #endif
1196 <      
1197 <      return angularMomentum;
1198 <   }
1199 <  
1003 >  
1004    StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1005      return IOIndexToIntegrableObject.at(index);
1006    }
# Line 1204 | Line 1008 | namespace OpenMD {
1008    void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1009      IOIndexToIntegrableObject= v;
1010    }
1207 –
1208 –  /* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1209 –     based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1210 –     where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1211 –     V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1212 –  */
1213 –  void SimInfo::getGyrationalVolume(RealType &volume){
1214 –    Mat3x3d intTensor;
1215 –    RealType det;
1216 –    Vector3d dummyAngMom;
1217 –    RealType sysconstants;
1218 –    RealType geomCnst;
1219 –
1220 –    geomCnst = 3.0/2.0;
1221 –    /* Get the inertial tensor and angular momentum for free*/
1222 –    getInertiaTensor(intTensor,dummyAngMom);
1223 –    
1224 –    det = intTensor.determinant();
1225 –    sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1226 –    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1227 –    return;
1228 –  }
1229 –
1230 –  void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1231 –    Mat3x3d intTensor;
1232 –    Vector3d dummyAngMom;
1233 –    RealType sysconstants;
1234 –    RealType geomCnst;
1235 –
1236 –    geomCnst = 3.0/2.0;
1237 –    /* Get the inertial tensor and angular momentum for free*/
1238 –    getInertiaTensor(intTensor,dummyAngMom);
1239 –    
1240 –    detI = intTensor.determinant();
1241 –    sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1242 –    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1243 –    return;
1244 –  }
1011   /*
1012     void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1013        assert( v.size() == nAtoms_ + nRigidBodies_);

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