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Comparing branches/development/src/brains/SimInfo.cpp (file contents):
Revision 1528 by gezelter, Fri Dec 17 20:11:05 2010 UTC vs.
Revision 1764 by gezelter, Tue Jul 3 18:32:27 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/fCutoffPolicy.h"
58 – #include "UseTheForce/DarkSide/fSwitchingFunctionType.h"
59 – #include "UseTheForce/doForces_interface.h"
60 – #include "UseTheForce/DarkSide/neighborLists_interface.h"
61 – #include "UseTheForce/DarkSide/switcheroo_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"
63 < #include "nonbonded/InteractionManager.hpp"
68 <
69 <
62 > #include "brains/ForceField.hpp"
63 > #include "nonbonded/SwitchingFunction.hpp"
64   #ifdef IS_MPI
65 < #include "UseTheForce/mpiComponentPlan.h"
66 < #include "UseTheForce/DarkSide/simParallel_interface.h"
73 < #endif
65 > #include <mpi.h>
66 > #endif
67  
68   using namespace std;
69   namespace OpenMD {
# Line 79 | 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 136 | 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 231 | 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;
235 +    Atom* atom;
236  
237      ndf_local = 0;
238 +    nfq_local = 0;
239      
240      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
241        for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
# Line 252 | Line 250 | namespace OpenMD {
250              ndf_local += 3;
251            }
252          }
255 –            
253        }
254 +      for (atom = mol->beginFluctuatingCharge(k); atom != NULL;
255 +           atom = mol->nextFluctuatingCharge(k)) {
256 +        if (atom->isFluctuatingCharge()) {
257 +          nfq_local++;
258 +        }
259 +      }
260      }
261      
262 +    ndfLocal_ = ndf_local;
263 +
264      // n_constraints is local, so subtract them on each processor
265      ndf_local -= nConstraints_;
266  
267   #ifdef IS_MPI
268      MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
269 +    MPI_Allreduce(&nfq_local,&nGlobalFluctuatingCharges_,1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
270   #else
271      ndf_ = ndf_local;
272 +    nGlobalFluctuatingCharges_ = nfq_local;
273   #endif
274  
275      // nZconstraints_ is global, as are the 3 COM translations for the
# Line 279 | Line 286 | namespace OpenMD {
286   #endif
287      return fdf_;
288    }
289 +  
290 +  unsigned int SimInfo::getNLocalCutoffGroups(){
291 +    int nLocalCutoffAtoms = 0;
292 +    Molecule* mol;
293 +    MoleculeIterator mi;
294 +    CutoffGroup* cg;
295 +    Molecule::CutoffGroupIterator ci;
296      
297 +    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
298 +      
299 +      for (cg = mol->beginCutoffGroup(ci); cg != NULL;
300 +           cg = mol->nextCutoffGroup(ci)) {
301 +        nLocalCutoffAtoms += cg->getNumAtom();
302 +        
303 +      }        
304 +    }
305 +    
306 +    return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_;
307 +  }
308 +    
309    void SimInfo::calcNdfRaw() {
310      int ndfRaw_local;
311  
# Line 656 | Line 682 | namespace OpenMD {
682      molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
683    }
684  
659 –  void SimInfo::update() {
685  
686 <    setupSimType();
687 <    setupCutoffRadius();
688 <    setupSwitchingRadius();
689 <    setupCutoffMethod();
690 <    setupSkinThickness();
691 <    setupSwitchingFunction();
692 <    setupAccumulateBoxDipole();
693 <
694 < #ifdef IS_MPI
670 <    setupFortranParallel();
671 < #endif
672 <    setupFortranSim();
673 <    fortranInitialized_ = true;
674 <
686 >  /**
687 >   * update
688 >   *
689 >   *  Performs the global checks and variable settings after the
690 >   *  objects have been created.
691 >   *
692 >   */
693 >  void SimInfo::update() {  
694 >    setupSimVariables();
695      calcNdf();
696      calcNdfRaw();
697      calcNdfTrans();
698    }
699    
700 +  /**
701 +   * getSimulatedAtomTypes
702 +   *
703 +   * Returns an STL set of AtomType* that are actually present in this
704 +   * simulation.  Must query all processors to assemble this information.
705 +   *
706 +   */
707    set<AtomType*> SimInfo::getSimulatedAtomTypes() {
708      SimInfo::MoleculeIterator mi;
709      Molecule* mol;
# Line 685 | Line 712 | namespace OpenMD {
712      set<AtomType*> atomTypes;
713      
714      for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
715 <      
716 <      for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
715 >      for(atom = mol->beginAtom(ai); atom != NULL;
716 >          atom = mol->nextAtom(ai)) {
717          atomTypes.insert(atom->getAtomType());
718 <      }
719 <      
720 <    }
721 <    
695 <    return atomTypes;        
696 <  }
718 >      }      
719 >    }    
720 >    
721 > #ifdef IS_MPI
722  
723 <  /**
724 <   * setupCutoffRadius
700 <   *
701 <   *  If the cutoffRadius was explicitly set, use that value.
702 <   *  If the cutoffRadius was not explicitly set:
703 <   *      Are there electrostatic atoms?  Use 12.0 Angstroms.
704 <   *      No electrostatic atoms?  Poll the atom types present in the
705 <   *      simulation for suggested cutoff values (e.g. 2.5 * sigma).
706 <   *      Use the maximum suggested value that was found.
707 <   */
708 <  void SimInfo::setupCutoffRadius() {
723 >    // loop over the found atom types on this processor, and add their
724 >    // numerical idents to a vector:
725      
726 <    if (simParams_->haveCutoffRadius()) {
727 <      cutoffRadius_ = simParams_->getCutoffRadius();
728 <    } else {      
729 <      if (usesElectrostaticAtoms_) {
714 <        sprintf(painCave.errMsg,
715 <                "SimInfo Warning: No value was set for the cutoffRadius.\n"
716 <                "\tOpenMD will use a default value of 12.0 angstroms"
717 <                "\tfor the cutoffRadius.\n");
718 <        painCave.isFatal = 0;
719 <        simError();
720 <        cutoffRadius_ = 12.0;
721 <      } else {
722 <        RealType thisCut;
723 <        set<AtomType*>::iterator i;
724 <        set<AtomType*> atomTypes;
725 <        atomTypes = getSimulatedAtomTypes();        
726 <        for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
727 <          thisCut = InteractionManager::Instance()->getSuggestedCutoffRadius((*i));
728 <          cutoffRadius_ = max(thisCut, cutoffRadius_);
729 <        }
730 <        sprintf(painCave.errMsg,
731 <                "SimInfo Warning: No value was set for the cutoffRadius.\n"
732 <                "\tOpenMD will use %lf angstroms.\n",
733 <                cutoffRadius_);
734 <        painCave.isFatal = 0;
735 <        simError();
736 <      }            
737 <    }
726 >    vector<int> foundTypes;
727 >    set<AtomType*>::iterator i;
728 >    for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
729 >      foundTypes.push_back( (*i)->getIdent() );
730  
731 <    InteractionManager::Instance()->setCutoffRadius(cutoffRadius_);
732 <  }
731 >    // count_local holds the number of found types on this processor
732 >    int count_local = foundTypes.size();
733 >
734 >    int nproc = MPI::COMM_WORLD.Get_size();
735 >
736 >    // we need arrays to hold the counts and displacement vectors for
737 >    // all processors
738 >    vector<int> counts(nproc, 0);
739 >    vector<int> disps(nproc, 0);
740 >
741 >    // fill the counts array
742 >    MPI::COMM_WORLD.Allgather(&count_local, 1, MPI::INT, &counts[0],
743 >                              1, MPI::INT);
744    
745 <  /**
746 <   * setupSwitchingRadius
747 <   *
748 <   *  If the switchingRadius was explicitly set, use that value (but check it)
749 <   *  If the switchingRadius was not explicitly set: use 0.85 * cutoffRadius_
750 <   */
751 <  void SimInfo::setupSwitchingRadius() {
745 >    // use the processor counts to compute the displacement array
746 >    disps[0] = 0;    
747 >    int totalCount = counts[0];
748 >    for (int iproc = 1; iproc < nproc; iproc++) {
749 >      disps[iproc] = disps[iproc-1] + counts[iproc-1];
750 >      totalCount += counts[iproc];
751 >    }
752 >
753 >    // we need a (possibly redundant) set of all found types:
754 >    vector<int> ftGlobal(totalCount);
755      
756 <    if (simParams_->haveSwitchingRadius()) {
757 <      switchingRadius_ = simParams_->getSwitchingRadius();
758 <      if (switchingRadius_ > cutoffRadius_) {        
759 <        sprintf(painCave.errMsg,
754 <                "SimInfo Error: switchingRadius (%f) is larger than cutoffRadius(%f)\n",
755 <                switchingRadius_, cutoffRadius_);
756 <        painCave.isFatal = 1;
757 <        simError();
756 >    // now spray out the foundTypes to all the other processors:    
757 >    MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
758 >                               &ftGlobal[0], &counts[0], &disps[0],
759 >                               MPI::INT);
760  
761 <      }
760 <    } else {      
761 <      switchingRadius_ = 0.85 * cutoffRadius_;
762 <      sprintf(painCave.errMsg,
763 <              "SimInfo Warning: No value was set for the switchingRadius.\n"
764 <              "\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
765 <              "\tswitchingRadius = %f. for this simulation\n", switchingRadius_);
766 <      painCave.isFatal = 0;
767 <      simError();
768 <    }            
769 <    InteractionManager::Instance()->setSwitchingRadius(switchingRadius_);
770 <  }
761 >    vector<int>::iterator j;
762  
763 <  /**
764 <   * setupSkinThickness
765 <   *
766 <   *  If the skinThickness was explicitly set, use that value (but check it)
767 <   *  If the skinThickness was not explicitly set: use 1.0 angstroms
768 <   */
769 <  void SimInfo::setupSkinThickness() {    
770 <    if (simParams_->haveSkinThickness()) {
771 <      skinThickness_ = simParams_->getSkinThickness();
772 <    } else {      
773 <      skinThickness_ = 1.0;
774 <      sprintf(painCave.errMsg,
775 <              "SimInfo Warning: No value was set for the skinThickness.\n"
776 <              "\tOpenMD will use a default value of %f Angstroms\n"
777 <              "\tfor this simulation\n", skinThickness_);
778 <      painCave.isFatal = 0;
788 <      simError();
789 <    }            
763 >    // foundIdents is a stl set, so inserting an already found ident
764 >    // will have no effect.
765 >    set<int> foundIdents;
766 >
767 >    for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
768 >      foundIdents.insert((*j));
769 >    
770 >    // now iterate over the foundIdents and get the actual atom types
771 >    // that correspond to these:
772 >    set<int>::iterator it;
773 >    for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
774 >      atomTypes.insert( forceField_->getAtomType((*it)) );
775 >
776 > #endif
777 >
778 >    return atomTypes;        
779    }
780  
781 <  void SimInfo::setupSimType() {
781 >  void SimInfo::setupSimVariables() {
782 >    useAtomicVirial_ = simParams_->getUseAtomicVirial();
783 >    // we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
784 >    calcBoxDipole_ = false;
785 >    if ( simParams_->haveAccumulateBoxDipole() )
786 >      if ( simParams_->getAccumulateBoxDipole() ) {
787 >        calcBoxDipole_ = true;      
788 >      }
789 >    
790      set<AtomType*>::iterator i;
791      set<AtomType*> atomTypes;
792 <    atomTypes = getSimulatedAtomTypes();
796 <
797 <    useAtomicVirial_ = simParams_->getUseAtomicVirial();
798 <
792 >    atomTypes = getSimulatedAtomTypes();    
793      int usesElectrostatic = 0;
794      int usesMetallic = 0;
795      int usesDirectional = 0;
796 +    int usesFluctuatingCharges =  0;
797      //loop over all of the atom types
798      for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
799        usesElectrostatic |= (*i)->isElectrostatic();
800        usesMetallic |= (*i)->isMetal();
801        usesDirectional |= (*i)->isDirectional();
802 +      usesFluctuatingCharges |= (*i)->isFluctuatingCharge();
803      }
804  
805   #ifdef IS_MPI    
806      int temp;
807      temp = usesDirectional;
808      MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
809 <
809 >    
810      temp = usesMetallic;
811      MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
812 <
812 >    
813      temp = usesElectrostatic;
814      MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
815 +
816 +    temp = usesFluctuatingCharges;
817 +    MPI_Allreduce(&temp, &usesFluctuatingCharges_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
818 + #else
819 +
820 +    usesDirectionalAtoms_ = usesDirectional;
821 +    usesMetallicAtoms_ = usesMetallic;
822 +    usesElectrostaticAtoms_ = usesElectrostatic;
823 +    usesFluctuatingCharges_ = usesFluctuatingCharges;
824 +
825   #endif
826 <    fInfo_.SIM_uses_PBC = usesPeriodicBoundaries_;    
827 <    fInfo_.SIM_uses_DirectionalAtoms = usesDirectionalAtoms_;
828 <    fInfo_.SIM_uses_MetallicAtoms = usesMetallicAtoms_;
829 <    fInfo_.SIM_requires_SkipCorrection = usesElectrostaticAtoms_;
824 <    fInfo_.SIM_requires_SelfCorrection = usesElectrostaticAtoms_;
825 <    fInfo_.SIM_uses_AtomicVirial = usesAtomicVirial_;
826 >    
827 >    requiresPrepair_ = usesMetallicAtoms_ ? true : false;
828 >    requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
829 >    requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;    
830    }
831  
832 <  void SimInfo::setupFortranSim() {
833 <    int isError;
834 <    int nExclude, nOneTwo, nOneThree, nOneFour;
835 <    vector<int> fortranGlobalGroupMembership;
832 >
833 >  vector<int> SimInfo::getGlobalAtomIndices() {
834 >    SimInfo::MoleculeIterator mi;
835 >    Molecule* mol;
836 >    Molecule::AtomIterator ai;
837 >    Atom* atom;
838 >
839 >    vector<int> GlobalAtomIndices(getNAtoms(), 0);
840      
841 <    notifyFortranSkinThickness(&skinThickness_);
841 >    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
842 >      
843 >      for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
844 >        GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
845 >      }
846 >    }
847 >    return GlobalAtomIndices;
848 >  }
849  
835 –    int ljsp = cutoffMethod_ == SHIFTED_POTENTIAL ? 1 : 0;
836 –    int ljsf = cutoffMethod_ == SHIFTED_FORCE ? 1 : 0;
837 –    notifyFortranCutoffs(&cutoffRadius_, &switchingRadius_, &ljsp, &ljsf);
850  
851 <    isError = 0;
851 >  vector<int> SimInfo::getGlobalGroupIndices() {
852 >    SimInfo::MoleculeIterator mi;
853 >    Molecule* mol;
854 >    Molecule::CutoffGroupIterator ci;
855 >    CutoffGroup* cg;
856  
857 <    //globalGroupMembership_ is filled by SimCreator    
858 <    for (int i = 0; i < nGlobalAtoms_; i++) {
859 <      fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
857 >    vector<int> GlobalGroupIndices;
858 >    
859 >    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
860 >      
861 >      //local index of cutoff group is trivial, it only depends on the
862 >      //order of travesing
863 >      for (cg = mol->beginCutoffGroup(ci); cg != NULL;
864 >           cg = mol->nextCutoffGroup(ci)) {
865 >        GlobalGroupIndices.push_back(cg->getGlobalIndex());
866 >      }        
867      }
868 +    return GlobalGroupIndices;
869 +  }
870  
871 +
872 +  void SimInfo::prepareTopology() {
873 +    int nExclude, nOneTwo, nOneThree, nOneFour;
874 +
875      //calculate mass ratio of cutoff group
847 –    vector<RealType> mfact;
876      SimInfo::MoleculeIterator mi;
877      Molecule* mol;
878      Molecule::CutoffGroupIterator ci;
# Line 853 | Line 881 | namespace OpenMD {
881      Atom* atom;
882      RealType totalMass;
883  
884 <    //to avoid memory reallocation, reserve enough space for mfact
885 <    mfact.reserve(getNCutoffGroups());
884 >    /**
885 >     * The mass factor is the relative mass of an atom to the total
886 >     * mass of the cutoff group it belongs to.  By default, all atoms
887 >     * are their own cutoff groups, and therefore have mass factors of
888 >     * 1.  We need some special handling for massless atoms, which
889 >     * will be treated as carrying the entire mass of the cutoff
890 >     * group.
891 >     */
892 >    massFactors_.clear();
893 >    massFactors_.resize(getNAtoms(), 1.0);
894      
895      for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {        
896 <      for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
896 >      for (cg = mol->beginCutoffGroup(ci); cg != NULL;
897 >           cg = mol->nextCutoffGroup(ci)) {
898  
899          totalMass = cg->getMass();
900          for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
901            // Check for massless groups - set mfact to 1 if true
902 <          if (totalMass != 0)
903 <            mfact.push_back(atom->getMass()/totalMass);
902 >          if (totalMass != 0)
903 >            massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
904            else
905 <            mfact.push_back( 1.0 );
905 >            massFactors_[atom->getLocalIndex()] = 1.0;
906          }
907        }      
908      }
909  
910 <    //fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
874 <    vector<int> identArray;
910 >    // Build the identArray_
911  
912 <    //to avoid memory reallocation, reserve enough space identArray
913 <    identArray.reserve(getNAtoms());
878 <    
912 >    identArray_.clear();
913 >    identArray_.reserve(getNAtoms());    
914      for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {        
915        for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
916 <        identArray.push_back(atom->getIdent());
916 >        identArray_.push_back(atom->getIdent());
917        }
918      }    
919 <
920 <    //fill molMembershipArray
886 <    //molMembershipArray is filled by SimCreator    
887 <    vector<int> molMembershipArray(nGlobalAtoms_);
888 <    for (int i = 0; i < nGlobalAtoms_; i++) {
889 <      molMembershipArray[i] = globalMolMembership_[i] + 1;
890 <    }
891 <    
892 <    //setup fortran simulation
919 >    
920 >    //scan topology
921  
922      nExclude = excludedInteractions_.getSize();
923      nOneTwo = oneTwoInteractions_.getSize();
# Line 901 | Line 929 | namespace OpenMD {
929      int* oneThreeList = oneThreeInteractions_.getPairList();
930      int* oneFourList = oneFourInteractions_.getPairList();
931  
932 <    setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
905 <                   &nExclude, excludeList,
906 <                   &nOneTwo, oneTwoList,
907 <                   &nOneThree, oneThreeList,
908 <                   &nOneFour, oneFourList,
909 <                   &molMembershipArray[0], &mfact[0], &nCutoffGroups_,
910 <                   &fortranGlobalGroupMembership[0], &isError);
911 <    
912 <    if( isError ){
913 <      
914 <      sprintf( painCave.errMsg,
915 <               "There was an error setting the simulation information in fortran.\n" );
916 <      painCave.isFatal = 1;
917 <      painCave.severity = OPENMD_ERROR;
918 <      simError();
919 <    }
920 <    
921 <    
922 <    sprintf( checkPointMsg,
923 <             "succesfully sent the simulation information to fortran.\n");
924 <    
925 <    errorCheckPoint();
926 <    
927 <    // Setup number of neighbors in neighbor list if present
928 <    if (simParams_->haveNeighborListNeighbors()) {
929 <      int nlistNeighbors = simParams_->getNeighborListNeighbors();
930 <      setNeighbors(&nlistNeighbors);
931 <    }
932 <  
933 <
932 >    topologyDone_ = true;
933    }
934  
936 –
937 –  void SimInfo::setupFortranParallel() {
938 – #ifdef IS_MPI    
939 –    //SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
940 –    vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
941 –    vector<int> localToGlobalCutoffGroupIndex;
942 –    SimInfo::MoleculeIterator mi;
943 –    Molecule::AtomIterator ai;
944 –    Molecule::CutoffGroupIterator ci;
945 –    Molecule* mol;
946 –    Atom* atom;
947 –    CutoffGroup* cg;
948 –    mpiSimData parallelData;
949 –    int isError;
950 –
951 –    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
952 –
953 –      //local index(index in DataStorge) of atom is important
954 –      for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
955 –        localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
956 –      }
957 –
958 –      //local index of cutoff group is trivial, it only depends on the order of travesing
959 –      for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
960 –        localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
961 –      }        
962 –        
963 –    }
964 –
965 –    //fill up mpiSimData struct
966 –    parallelData.nMolGlobal = getNGlobalMolecules();
967 –    parallelData.nMolLocal = getNMolecules();
968 –    parallelData.nAtomsGlobal = getNGlobalAtoms();
969 –    parallelData.nAtomsLocal = getNAtoms();
970 –    parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
971 –    parallelData.nGroupsLocal = getNCutoffGroups();
972 –    parallelData.myNode = worldRank;
973 –    MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
974 –
975 –    //pass mpiSimData struct and index arrays to fortran
976 –    setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
977 –                    &localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
978 –                    &localToGlobalCutoffGroupIndex[0], &isError);
979 –
980 –    if (isError) {
981 –      sprintf(painCave.errMsg,
982 –              "mpiRefresh errror: fortran didn't like something we gave it.\n");
983 –      painCave.isFatal = 1;
984 –      simError();
985 –    }
986 –
987 –    sprintf(checkPointMsg, " mpiRefresh successful.\n");
988 –    errorCheckPoint();
989 –
990 – #endif
991 –  }
992 –
993 –
994 –  void SimInfo::setupSwitchingFunction() {    
995 –    int ft = CUBIC;
996 –    
997 –    if (simParams_->haveSwitchingFunctionType()) {
998 –      string funcType = simParams_->getSwitchingFunctionType();
999 –      toUpper(funcType);
1000 –      if (funcType == "CUBIC") {
1001 –        ft = CUBIC;
1002 –      } else {
1003 –        if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1004 –          ft = FIFTH_ORDER_POLY;
1005 –        } else {
1006 –          // throw error        
1007 –          sprintf( painCave.errMsg,
1008 –                   "SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1009 –          painCave.isFatal = 1;
1010 –          simError();
1011 –        }          
1012 –      }
1013 –    }
1014 –
1015 –    // send switching function notification to switcheroo
1016 –    setFunctionType(&ft);
1017 –
1018 –  }
1019 –
1020 –  void SimInfo::setupAccumulateBoxDipole() {    
1021 –
1022 –    // we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1023 –    if ( simParams_->haveAccumulateBoxDipole() )
1024 –      if ( simParams_->getAccumulateBoxDipole() ) {
1025 –        calcBoxDipole_ = true;
1026 –      }
1027 –
1028 –  }
1029 –
935    void SimInfo::addProperty(GenericData* genData) {
936      properties_.addProperty(genData);  
937    }
# Line 1061 | Line 966 | namespace OpenMD {
966      Molecule* mol;
967      RigidBody* rb;
968      Atom* atom;
969 +    CutoffGroup* cg;
970      SimInfo::MoleculeIterator mi;
971      Molecule::RigidBodyIterator rbIter;
972 <    Molecule::AtomIterator atomIter;;
972 >    Molecule::AtomIterator atomIter;
973 >    Molecule::CutoffGroupIterator cgIter;
974  
975      for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
976          
# Line 1074 | Line 981 | namespace OpenMD {
981        for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
982          rb->setSnapshotManager(sman_);
983        }
984 +
985 +      for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
986 +        cg->setSnapshotManager(sman_);
987 +      }
988      }    
989      
990    }
991  
1081 –  Vector3d SimInfo::getComVel(){
1082 –    SimInfo::MoleculeIterator i;
1083 –    Molecule* mol;
992  
1085 –    Vector3d comVel(0.0);
1086 –    RealType totalMass = 0.0;
1087 –    
1088 –
1089 –    for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1090 –      RealType mass = mol->getMass();
1091 –      totalMass += mass;
1092 –      comVel += mass * mol->getComVel();
1093 –    }  
1094 –
1095 – #ifdef IS_MPI
1096 –    RealType tmpMass = totalMass;
1097 –    Vector3d tmpComVel(comVel);    
1098 –    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1099 –    MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1100 – #endif
1101 –
1102 –    comVel /= totalMass;
1103 –
1104 –    return comVel;
1105 –  }
1106 –
1107 –  Vector3d SimInfo::getCom(){
1108 –    SimInfo::MoleculeIterator i;
1109 –    Molecule* mol;
1110 –
1111 –    Vector3d com(0.0);
1112 –    RealType totalMass = 0.0;
1113 –    
1114 –    for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1115 –      RealType mass = mol->getMass();
1116 –      totalMass += mass;
1117 –      com += mass * mol->getCom();
1118 –    }  
1119 –
1120 – #ifdef IS_MPI
1121 –    RealType tmpMass = totalMass;
1122 –    Vector3d tmpCom(com);    
1123 –    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1124 –    MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1125 – #endif
1126 –
1127 –    com /= totalMass;
1128 –
1129 –    return com;
1130 –
1131 –  }        
1132 –
993    ostream& operator <<(ostream& o, SimInfo& info) {
994  
995      return o;
996    }
997    
998 <  
1139 <   /*
1140 <   Returns center of mass and center of mass velocity in one function call.
1141 <   */
1142 <  
1143 <   void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1144 <      SimInfo::MoleculeIterator i;
1145 <      Molecule* mol;
1146 <      
1147 <    
1148 <      RealType totalMass = 0.0;
1149 <    
1150 <
1151 <      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1152 <         RealType mass = mol->getMass();
1153 <         totalMass += mass;
1154 <         com += mass * mol->getCom();
1155 <         comVel += mass * mol->getComVel();          
1156 <      }  
1157 <      
1158 < #ifdef IS_MPI
1159 <      RealType tmpMass = totalMass;
1160 <      Vector3d tmpCom(com);  
1161 <      Vector3d tmpComVel(comVel);
1162 <      MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1163 <      MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1164 <      MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1165 < #endif
1166 <      
1167 <      com /= totalMass;
1168 <      comVel /= totalMass;
1169 <   }        
1170 <  
1171 <   /*
1172 <   Return intertia tensor for entire system and angular momentum Vector.
1173 <
1174 <
1175 <       [  Ixx -Ixy  -Ixz ]
1176 <    J =| -Iyx  Iyy  -Iyz |
1177 <       [ -Izx -Iyz   Izz ]
1178 <    */
1179 <
1180 <   void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1181 <      
1182 <
1183 <      RealType xx = 0.0;
1184 <      RealType yy = 0.0;
1185 <      RealType zz = 0.0;
1186 <      RealType xy = 0.0;
1187 <      RealType xz = 0.0;
1188 <      RealType yz = 0.0;
1189 <      Vector3d com(0.0);
1190 <      Vector3d comVel(0.0);
1191 <      
1192 <      getComAll(com, comVel);
1193 <      
1194 <      SimInfo::MoleculeIterator i;
1195 <      Molecule* mol;
1196 <      
1197 <      Vector3d thisq(0.0);
1198 <      Vector3d thisv(0.0);
1199 <
1200 <      RealType thisMass = 0.0;
1201 <    
1202 <      
1203 <      
1204 <  
1205 <      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1206 <        
1207 <         thisq = mol->getCom()-com;
1208 <         thisv = mol->getComVel()-comVel;
1209 <         thisMass = mol->getMass();
1210 <         // Compute moment of intertia coefficients.
1211 <         xx += thisq[0]*thisq[0]*thisMass;
1212 <         yy += thisq[1]*thisq[1]*thisMass;
1213 <         zz += thisq[2]*thisq[2]*thisMass;
1214 <        
1215 <         // compute products of intertia
1216 <         xy += thisq[0]*thisq[1]*thisMass;
1217 <         xz += thisq[0]*thisq[2]*thisMass;
1218 <         yz += thisq[1]*thisq[2]*thisMass;
1219 <            
1220 <         angularMomentum += cross( thisq, thisv ) * thisMass;
1221 <            
1222 <      }  
1223 <      
1224 <      
1225 <      inertiaTensor(0,0) = yy + zz;
1226 <      inertiaTensor(0,1) = -xy;
1227 <      inertiaTensor(0,2) = -xz;
1228 <      inertiaTensor(1,0) = -xy;
1229 <      inertiaTensor(1,1) = xx + zz;
1230 <      inertiaTensor(1,2) = -yz;
1231 <      inertiaTensor(2,0) = -xz;
1232 <      inertiaTensor(2,1) = -yz;
1233 <      inertiaTensor(2,2) = xx + yy;
1234 <      
1235 < #ifdef IS_MPI
1236 <      Mat3x3d tmpI(inertiaTensor);
1237 <      Vector3d tmpAngMom;
1238 <      MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1239 <      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1240 < #endif
1241 <              
1242 <      return;
1243 <   }
1244 <
1245 <   //Returns the angular momentum of the system
1246 <   Vector3d SimInfo::getAngularMomentum(){
1247 <      
1248 <      Vector3d com(0.0);
1249 <      Vector3d comVel(0.0);
1250 <      Vector3d angularMomentum(0.0);
1251 <      
1252 <      getComAll(com,comVel);
1253 <      
1254 <      SimInfo::MoleculeIterator i;
1255 <      Molecule* mol;
1256 <      
1257 <      Vector3d thisr(0.0);
1258 <      Vector3d thisp(0.0);
1259 <      
1260 <      RealType thisMass;
1261 <      
1262 <      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {        
1263 <        thisMass = mol->getMass();
1264 <        thisr = mol->getCom()-com;
1265 <        thisp = (mol->getComVel()-comVel)*thisMass;
1266 <        
1267 <        angularMomentum += cross( thisr, thisp );
1268 <        
1269 <      }  
1270 <      
1271 < #ifdef IS_MPI
1272 <      Vector3d tmpAngMom;
1273 <      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1274 < #endif
1275 <      
1276 <      return angularMomentum;
1277 <   }
1278 <  
998 >  
999    StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1000      return IOIndexToIntegrableObject.at(index);
1001    }
# Line 1283 | Line 1003 | namespace OpenMD {
1003    void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1004      IOIndexToIntegrableObject= v;
1005    }
1286 –
1287 –  /* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1288 –     based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1289 –     where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1290 –     V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1291 –  */
1292 –  void SimInfo::getGyrationalVolume(RealType &volume){
1293 –    Mat3x3d intTensor;
1294 –    RealType det;
1295 –    Vector3d dummyAngMom;
1296 –    RealType sysconstants;
1297 –    RealType geomCnst;
1298 –
1299 –    geomCnst = 3.0/2.0;
1300 –    /* Get the inertial tensor and angular momentum for free*/
1301 –    getInertiaTensor(intTensor,dummyAngMom);
1302 –    
1303 –    det = intTensor.determinant();
1304 –    sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1305 –    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1306 –    return;
1307 –  }
1308 –
1309 –  void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1310 –    Mat3x3d intTensor;
1311 –    Vector3d dummyAngMom;
1312 –    RealType sysconstants;
1313 –    RealType geomCnst;
1314 –
1315 –    geomCnst = 3.0/2.0;
1316 –    /* Get the inertial tensor and angular momentum for free*/
1317 –    getInertiaTensor(intTensor,dummyAngMom);
1318 –    
1319 –    detI = intTensor.determinant();
1320 –    sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1321 –    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1322 –    return;
1323 –  }
1006   /*
1007     void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1008        assert( v.size() == nAtoms_ + nRigidBodies_);

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