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Revision 1532 by gezelter, Wed Dec 29 19:59:21 2010 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/doForces_interface.h"
58 – #include "UseTheForce/DarkSide/neighborLists_interface.h"
58   #include "utils/MemoryUtils.hpp"
59   #include "utils/simError.h"
60   #include "selection/SelectionManager.hpp"
61   #include "io/ForceFieldOptions.hpp"
62 < #include "UseTheForce/ForceField.hpp"
62 > #include "brains/ForceField.hpp"
63   #include "nonbonded/SwitchingFunction.hpp"
65 –
66 –
64   #ifdef IS_MPI
65 < #include "UseTheForce/mpiComponentPlan.h"
66 < #include "UseTheForce/DarkSide/simParallel_interface.h"
70 < #endif
65 > #include <mpi.h>
66 > #endif
67  
68   using namespace std;
69   namespace OpenMD {
# Line 76 | 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 133 | 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 228 | 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)) {
240 –      for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
241 –           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          }
252 –            
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 276 | 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)) {
292 –      for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
293 –           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 355 | 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;
362 <         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 373 | 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 508 | 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;
515 <         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 526 | 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 657 | Line 687 | namespace OpenMD {
687    /**
688     * update
689     *
690 <   *  Performs the global checks and variable settings after the objects have been
691 <   *  created.
690 >   *  Performs the global checks and variable settings after the
691 >   *  objects have been created.
692     *
693     */
694 <  void SimInfo::update() {
665 <    
694 >  void SimInfo::update() {  
695      setupSimVariables();
667 –    setupCutoffs();
668 –    setupSwitching();
669 –    setupElectrostatics();
670 –    setupNeighborlists();
671 –
672 – #ifdef IS_MPI
673 –    setupFortranParallel();
674 – #endif
675 –    setupFortranSim();
676 –    fortranInitialized_ = true;
677 –
696      calcNdf();
697      calcNdfRaw();
698      calcNdfTrans();
699    }
700    
701 +  /**
702 +   * getSimulatedAtomTypes
703 +   *
704 +   * Returns an STL set of AtomType* that are actually present in this
705 +   * simulation.  Must query all processors to assemble this information.
706 +   *
707 +   */
708    set<AtomType*> SimInfo::getSimulatedAtomTypes() {
709      SimInfo::MoleculeIterator mi;
710      Molecule* mol;
# 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 <    return atomTypes;        
722 <  }
721 >    
722 > #ifdef IS_MPI
723  
724 <  /**
725 <   * setupCutoffs
700 <   *
701 <   * Sets the values of cutoffRadius and cutoffMethod
702 <   *
703 <   * cutoffRadius : realType
704 <   *  If the cutoffRadius was explicitly set, use that value.
705 <   *  If the cutoffRadius was not explicitly set:
706 <   *      Are there electrostatic atoms?  Use 12.0 Angstroms.
707 <   *      No electrostatic atoms?  Poll the atom types present in the
708 <   *      simulation for suggested cutoff values (e.g. 2.5 * sigma).
709 <   *      Use the maximum suggested value that was found.
710 <   *
711 <   * cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE, SHIFTED_POTENTIAL)
712 <   *      If cutoffMethod was explicitly set, use that choice.
713 <   *      If cutoffMethod was not explicitly set, use SHIFTED_FORCE
714 <   */
715 <  void SimInfo::setupCutoffs() {
724 >    // loop over the found atom types on this processor, and add their
725 >    // numerical idents to a vector:
726      
727 <    if (simParams_->haveCutoffRadius()) {
728 <      cutoffRadius_ = simParams_->getCutoffRadius();
729 <    } else {      
730 <      if (usesElectrostaticAtoms_) {
721 <        sprintf(painCave.errMsg,
722 <                "SimInfo: No value was set for the cutoffRadius.\n"
723 <                "\tOpenMD will use a default value of 12.0 angstroms"
724 <                "\tfor the cutoffRadius.\n");
725 <        painCave.isFatal = 0;
726 <        painCave.severity = OPENMD_INFO;
727 <        simError();
728 <        cutoffRadius_ = 12.0;
729 <      } else {
730 <        RealType thisCut;
731 <        set<AtomType*>::iterator i;
732 <        set<AtomType*> atomTypes;
733 <        atomTypes = getSimulatedAtomTypes();        
734 <        for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
735 <          thisCut = InteractionManager::Instance()->getSuggestedCutoffRadius((*i));
736 <          cutoffRadius_ = max(thisCut, cutoffRadius_);
737 <        }
738 <        sprintf(painCave.errMsg,
739 <                "SimInfo: No value was set for the cutoffRadius.\n"
740 <                "\tOpenMD will use %lf angstroms.\n",
741 <                cutoffRadius_);
742 <        painCave.isFatal = 0;
743 <        painCave.severity = OPENMD_INFO;
744 <        simError();
745 <      }            
746 <    }
727 >    vector<int> foundTypes;
728 >    set<AtomType*>::iterator i;
729 >    for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
730 >      foundTypes.push_back( (*i)->getIdent() );
731  
732 <    InteractionManager::Instance()->setCutoffRadius(cutoffRadius_);
732 >    // count_local holds the number of found types on this processor
733 >    int count_local = foundTypes.size();
734  
735 <    map<string, CutoffMethod> stringToCutoffMethod;
736 <    stringToCutoffMethod["HARD"] = HARD;
737 <    stringToCutoffMethod["SWITCHING_FUNCTION"] = SWITCHING_FUNCTION;
738 <    stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;    
739 <    stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
735 >    int nproc = MPI::COMM_WORLD.Get_size();
736 >
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 <    if (simParams_->haveCutoffMethod()) {
747 <      string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
748 <      map<string, CutoffMethod>::iterator i;
749 <      i = stringToCutoffMethod.find(cutMeth);
750 <      if (i == stringToCutoffMethod.end()) {
751 <        sprintf(painCave.errMsg,
762 <                "SimInfo: Could not find chosen cutoffMethod %s\n"
763 <                "\tShould be one of: "
764 <                "HARD, SWITCHING_FUNCTION, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n",
765 <                cutMeth.c_str());
766 <        painCave.isFatal = 1;
767 <        painCave.severity = OPENMD_ERROR;
768 <        simError();
769 <      } else {
770 <        cutoffMethod_ = i->second;
771 <      }
772 <    } else {
773 <      sprintf(painCave.errMsg,
774 <              "SimInfo: No value was set for the cutoffMethod.\n"
775 <              "\tOpenMD will use SHIFTED_FORCE.\n");
776 <        painCave.isFatal = 0;
777 <        painCave.severity = OPENMD_INFO;
778 <        simError();
779 <        cutoffMethod_ = SHIFTED_FORCE;        
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 <    InteractionManager::Instance()->setCutoffMethod(cutoffMethod_);
755 <  }
784 <  
785 <  /**
786 <   * setupSwitching
787 <   *
788 <   * Sets the values of switchingRadius and
789 <   *  If the switchingRadius was explicitly set, use that value (but check it)
790 <   *  If the switchingRadius was not explicitly set: use 0.85 * cutoffRadius_
791 <   */
792 <  void SimInfo::setupSwitching() {
754 >    // we need a (possibly redundant) set of all found types:
755 >    vector<int> ftGlobal(totalCount);
756      
757 <    if (simParams_->haveSwitchingRadius()) {
758 <      switchingRadius_ = simParams_->getSwitchingRadius();
759 <      if (switchingRadius_ > cutoffRadius_) {        
760 <        sprintf(painCave.errMsg,
798 <                "SimInfo: switchingRadius (%f) is larger than cutoffRadius(%f)\n",
799 <                switchingRadius_, cutoffRadius_);
800 <        painCave.isFatal = 1;
801 <        painCave.severity = OPENMD_ERROR;
802 <        simError();
803 <      }
804 <    } else {      
805 <      switchingRadius_ = 0.85 * cutoffRadius_;
806 <      sprintf(painCave.errMsg,
807 <              "SimInfo: No value was set for the switchingRadius.\n"
808 <              "\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
809 <              "\tswitchingRadius = %f. for this simulation\n", switchingRadius_);
810 <      painCave.isFatal = 0;
811 <      painCave.severity = OPENMD_WARNING;
812 <      simError();
813 <    }          
814 <  
815 <    InteractionManager::Instance()->setSwitchingRadius(switchingRadius_);
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],
760 >                               MPI::INT);
761  
762 <    SwitchingFunctionType ft;
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 >
768 >    for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
769 >      foundIdents.insert((*j));
770      
771 <    if (simParams_->haveSwitchingFunctionType()) {
772 <      string funcType = simParams_->getSwitchingFunctionType();
773 <      toUpper(funcType);
774 <      if (funcType == "CUBIC") {
775 <        ft = cubic;
776 <      } else {
777 <        if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
826 <          ft = fifth_order_poly;
827 <        } else {
828 <          // throw error        
829 <          sprintf( painCave.errMsg,
830 <                   "SimInfo : Unknown switchingFunctionType. (Input file specified %s .)\n"
831 <                   "\tswitchingFunctionType must be one of: "
832 <                   "\"cubic\" or \"fifth_order_polynomial\".",
833 <                   funcType.c_str() );
834 <          painCave.isFatal = 1;
835 <          painCave.severity = OPENMD_ERROR;
836 <          simError();
837 <        }          
838 <      }
839 <    }
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)
775 >      atomTypes.insert( forceField_->getAtomType((*it)) );
776 >
777 > #endif
778  
779 <    InteractionManager::Instance()->setSwitchingFunctionType(ft);
779 >    return atomTypes;        
780    }
781  
782 <  /**
783 <   * setupSkinThickness
784 <   *
785 <   *  If the skinThickness was explicitly set, use that value (but check it)
786 <   *  If the skinThickness was not explicitly set: use 1.0 angstroms
787 <   */
788 <  void SimInfo::setupSkinThickness() {    
789 <    if (simParams_->haveSkinThickness()) {
790 <      skinThickness_ = simParams_->getSkinThickness();
853 <    } else {      
854 <      skinThickness_ = 1.0;
855 <      sprintf(painCave.errMsg,
856 <              "SimInfo Warning: No value was set for the skinThickness.\n"
857 <              "\tOpenMD will use a default value of %f Angstroms\n"
858 <              "\tfor this simulation\n", skinThickness_);
859 <      painCave.isFatal = 0;
860 <      simError();
861 <    }            
862 <  }
863 <
864 <  void SimInfo::setupSimType() {
782 >  void SimInfo::setupSimVariables() {
783 >    useAtomicVirial_ = simParams_->getUseAtomicVirial();
784 >    // we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
785 >    calcBoxDipole_ = false;
786 >    if ( simParams_->haveAccumulateBoxDipole() )
787 >      if ( simParams_->getAccumulateBoxDipole() ) {
788 >        calcBoxDipole_ = true;      
789 >      }
790 >    
791      set<AtomType*>::iterator i;
792      set<AtomType*> atomTypes;
793 <    atomTypes = getSimulatedAtomTypes();
794 <
795 <    useAtomicVirial_ = simParams_->getUseAtomicVirial();
796 <
797 <    int usesElectrostatic = 0;
872 <    int usesMetallic = 0;
873 <    int usesDirectional = 0;
793 >    atomTypes = getSimulatedAtomTypes();    
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_;
896 <    fInfo_.SIM_requires_SelfCorrection = usesElectrostaticAtoms_;
897 <    fInfo_.SIM_uses_AtomicVirial = usesAtomicVirial_;
831 >    
832 >    requiresPrepair_ = usesMetallicAtoms_ ? true : false;
833 >    requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
834 >    requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;    
835    }
836  
900 –  void SimInfo::setupFortranSim() {
901 –    int isError;
902 –    int nExclude, nOneTwo, nOneThree, nOneFour;
903 –    vector<int> fortranGlobalGroupMembership;
904 –    
905 –    notifyFortranSkinThickness(&skinThickness_);
837  
838 <    int ljsp = cutoffMethod_ == SHIFTED_POTENTIAL ? 1 : 0;
839 <    int ljsf = cutoffMethod_ == SHIFTED_FORCE ? 1 : 0;
840 <    notifyFortranCutoffs(&cutoffRadius_, &switchingRadius_, &ljsp, &ljsf);
838 >  vector<int> SimInfo::getGlobalAtomIndices() {
839 >    SimInfo::MoleculeIterator mi;
840 >    Molecule* mol;
841 >    Molecule::AtomIterator ai;
842 >    Atom* atom;
843  
844 <    isError = 0;
845 <
846 <    //globalGroupMembership_ is filled by SimCreator    
847 <    for (int i = 0; i < nGlobalAtoms_; i++) {
848 <      fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
844 >    vector<int> GlobalAtomIndices(getNAtoms(), 0);
845 >    
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 +
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
919 –    vector<RealType> mfact;
881      SimInfo::MoleculeIterator mi;
882      Molecule* mol;
883      Molecule::CutoffGroupIterator ci;
# Line 925 | 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 AtomType, it is so confusing !!!)
946 <    vector<int> identArray;
915 >    // Build the identArray_
916  
917 <    //to avoid memory reallocation, reserve enough space identArray
918 <    identArray.reserve(getNAtoms());
950 <    
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      }    
956 –
957 –    //fill molMembershipArray
958 –    //molMembershipArray is filled by SimCreator    
959 –    vector<int> molMembershipArray(nGlobalAtoms_);
960 –    for (int i = 0; i < nGlobalAtoms_; i++) {
961 –      molMembershipArray[i] = globalMolMembership_[i] + 1;
962 –    }
924      
925 <    //setup fortran simulation
925 >    //scan topology
926  
927      nExclude = excludedInteractions_.getSize();
928      nOneTwo = oneTwoInteractions_.getSize();
# Line 973 | Line 934 | namespace OpenMD {
934      int* oneThreeList = oneThreeInteractions_.getPairList();
935      int* oneFourList = oneFourInteractions_.getPairList();
936  
937 <    setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
977 <                   &nExclude, excludeList,
978 <                   &nOneTwo, oneTwoList,
979 <                   &nOneThree, oneThreeList,
980 <                   &nOneFour, oneFourList,
981 <                   &molMembershipArray[0], &mfact[0], &nCutoffGroups_,
982 <                   &fortranGlobalGroupMembership[0], &isError);
983 <    
984 <    if( isError ){
985 <      
986 <      sprintf( painCave.errMsg,
987 <               "There was an error setting the simulation information in fortran.\n" );
988 <      painCave.isFatal = 1;
989 <      painCave.severity = OPENMD_ERROR;
990 <      simError();
991 <    }
992 <    
993 <    
994 <    sprintf( checkPointMsg,
995 <             "succesfully sent the simulation information to fortran.\n");
996 <    
997 <    errorCheckPoint();
998 <    
999 <    // Setup number of neighbors in neighbor list if present
1000 <    if (simParams_->haveNeighborListNeighbors()) {
1001 <      int nlistNeighbors = simParams_->getNeighborListNeighbors();
1002 <      setNeighbors(&nlistNeighbors);
1003 <    }
1004 <  
1005 <
937 >    topologyDone_ = true;
938    }
939  
1008 –
1009 –  void SimInfo::setupFortranParallel() {
1010 – #ifdef IS_MPI    
1011 –    //SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
1012 –    vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
1013 –    vector<int> localToGlobalCutoffGroupIndex;
1014 –    SimInfo::MoleculeIterator mi;
1015 –    Molecule::AtomIterator ai;
1016 –    Molecule::CutoffGroupIterator ci;
1017 –    Molecule* mol;
1018 –    Atom* atom;
1019 –    CutoffGroup* cg;
1020 –    mpiSimData parallelData;
1021 –    int isError;
1022 –
1023 –    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
1024 –
1025 –      //local index(index in DataStorge) of atom is important
1026 –      for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
1027 –        localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
1028 –      }
1029 –
1030 –      //local index of cutoff group is trivial, it only depends on the order of travesing
1031 –      for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
1032 –        localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
1033 –      }        
1034 –        
1035 –    }
1036 –
1037 –    //fill up mpiSimData struct
1038 –    parallelData.nMolGlobal = getNGlobalMolecules();
1039 –    parallelData.nMolLocal = getNMolecules();
1040 –    parallelData.nAtomsGlobal = getNGlobalAtoms();
1041 –    parallelData.nAtomsLocal = getNAtoms();
1042 –    parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
1043 –    parallelData.nGroupsLocal = getNCutoffGroups();
1044 –    parallelData.myNode = worldRank;
1045 –    MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
1046 –
1047 –    //pass mpiSimData struct and index arrays to fortran
1048 –    setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
1049 –                    &localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
1050 –                    &localToGlobalCutoffGroupIndex[0], &isError);
1051 –
1052 –    if (isError) {
1053 –      sprintf(painCave.errMsg,
1054 –              "mpiRefresh errror: fortran didn't like something we gave it.\n");
1055 –      painCave.isFatal = 1;
1056 –      simError();
1057 –    }
1058 –
1059 –    sprintf(checkPointMsg, " mpiRefresh successful.\n");
1060 –    errorCheckPoint();
1061 –
1062 – #endif
1063 –  }
1064 –
1065 –
1066 –  void SimInfo::setupSwitchingFunction() {    
1067 –
1068 –  }
1069 –
1070 –  void SimInfo::setupAccumulateBoxDipole() {    
1071 –
1072 –    // we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1073 –    if ( simParams_->haveAccumulateBoxDipole() )
1074 –      if ( simParams_->getAccumulateBoxDipole() ) {
1075 –        calcBoxDipole_ = true;
1076 –      }
1077 –
1078 –  }
1079 –
940    void SimInfo::addProperty(GenericData* genData) {
941      properties_.addProperty(genData);  
942    }
# Line 1111 | 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 1124 | 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      
1129 –  }
1130 –
1131 –  Vector3d SimInfo::getComVel(){
1132 –    SimInfo::MoleculeIterator i;
1133 –    Molecule* mol;
1134 –
1135 –    Vector3d comVel(0.0);
1136 –    RealType totalMass = 0.0;
1137 –    
1138 –
1139 –    for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1140 –      RealType mass = mol->getMass();
1141 –      totalMass += mass;
1142 –      comVel += mass * mol->getComVel();
1143 –    }  
1144 –
1145 – #ifdef IS_MPI
1146 –    RealType tmpMass = totalMass;
1147 –    Vector3d tmpComVel(comVel);    
1148 –    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1149 –    MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1150 – #endif
1151 –
1152 –    comVel /= totalMass;
1153 –
1154 –    return comVel;
995    }
996  
1157 –  Vector3d SimInfo::getCom(){
1158 –    SimInfo::MoleculeIterator i;
1159 –    Molecule* mol;
997  
1161 –    Vector3d com(0.0);
1162 –    RealType totalMass = 0.0;
1163 –    
1164 –    for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1165 –      RealType mass = mol->getMass();
1166 –      totalMass += mass;
1167 –      com += mass * mol->getCom();
1168 –    }  
1169 –
1170 – #ifdef IS_MPI
1171 –    RealType tmpMass = totalMass;
1172 –    Vector3d tmpCom(com);    
1173 –    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1174 –    MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1175 – #endif
1176 –
1177 –    com /= totalMass;
1178 –
1179 –    return com;
1180 –
1181 –  }        
1182 –
998    ostream& operator <<(ostream& o, SimInfo& info) {
999  
1000      return o;
1001    }
1002    
1003 <  
1189 <   /*
1190 <   Returns center of mass and center of mass velocity in one function call.
1191 <   */
1192 <  
1193 <   void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1194 <      SimInfo::MoleculeIterator i;
1195 <      Molecule* mol;
1196 <      
1197 <    
1198 <      RealType totalMass = 0.0;
1199 <    
1200 <
1201 <      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1202 <         RealType mass = mol->getMass();
1203 <         totalMass += mass;
1204 <         com += mass * mol->getCom();
1205 <         comVel += mass * mol->getComVel();          
1206 <      }  
1207 <      
1208 < #ifdef IS_MPI
1209 <      RealType tmpMass = totalMass;
1210 <      Vector3d tmpCom(com);  
1211 <      Vector3d tmpComVel(comVel);
1212 <      MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1213 <      MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1214 <      MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1215 < #endif
1216 <      
1217 <      com /= totalMass;
1218 <      comVel /= totalMass;
1219 <   }        
1220 <  
1221 <   /*
1222 <   Return intertia tensor for entire system and angular momentum Vector.
1223 <
1224 <
1225 <       [  Ixx -Ixy  -Ixz ]
1226 <    J =| -Iyx  Iyy  -Iyz |
1227 <       [ -Izx -Iyz   Izz ]
1228 <    */
1229 <
1230 <   void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1231 <      
1232 <
1233 <      RealType xx = 0.0;
1234 <      RealType yy = 0.0;
1235 <      RealType zz = 0.0;
1236 <      RealType xy = 0.0;
1237 <      RealType xz = 0.0;
1238 <      RealType yz = 0.0;
1239 <      Vector3d com(0.0);
1240 <      Vector3d comVel(0.0);
1241 <      
1242 <      getComAll(com, comVel);
1243 <      
1244 <      SimInfo::MoleculeIterator i;
1245 <      Molecule* mol;
1246 <      
1247 <      Vector3d thisq(0.0);
1248 <      Vector3d thisv(0.0);
1249 <
1250 <      RealType thisMass = 0.0;
1251 <    
1252 <      
1253 <      
1254 <  
1255 <      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1256 <        
1257 <         thisq = mol->getCom()-com;
1258 <         thisv = mol->getComVel()-comVel;
1259 <         thisMass = mol->getMass();
1260 <         // Compute moment of intertia coefficients.
1261 <         xx += thisq[0]*thisq[0]*thisMass;
1262 <         yy += thisq[1]*thisq[1]*thisMass;
1263 <         zz += thisq[2]*thisq[2]*thisMass;
1264 <        
1265 <         // compute products of intertia
1266 <         xy += thisq[0]*thisq[1]*thisMass;
1267 <         xz += thisq[0]*thisq[2]*thisMass;
1268 <         yz += thisq[1]*thisq[2]*thisMass;
1269 <            
1270 <         angularMomentum += cross( thisq, thisv ) * thisMass;
1271 <            
1272 <      }  
1273 <      
1274 <      
1275 <      inertiaTensor(0,0) = yy + zz;
1276 <      inertiaTensor(0,1) = -xy;
1277 <      inertiaTensor(0,2) = -xz;
1278 <      inertiaTensor(1,0) = -xy;
1279 <      inertiaTensor(1,1) = xx + zz;
1280 <      inertiaTensor(1,2) = -yz;
1281 <      inertiaTensor(2,0) = -xz;
1282 <      inertiaTensor(2,1) = -yz;
1283 <      inertiaTensor(2,2) = xx + yy;
1284 <      
1285 < #ifdef IS_MPI
1286 <      Mat3x3d tmpI(inertiaTensor);
1287 <      Vector3d tmpAngMom;
1288 <      MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1289 <      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1290 < #endif
1291 <              
1292 <      return;
1293 <   }
1294 <
1295 <   //Returns the angular momentum of the system
1296 <   Vector3d SimInfo::getAngularMomentum(){
1297 <      
1298 <      Vector3d com(0.0);
1299 <      Vector3d comVel(0.0);
1300 <      Vector3d angularMomentum(0.0);
1301 <      
1302 <      getComAll(com,comVel);
1303 <      
1304 <      SimInfo::MoleculeIterator i;
1305 <      Molecule* mol;
1306 <      
1307 <      Vector3d thisr(0.0);
1308 <      Vector3d thisp(0.0);
1309 <      
1310 <      RealType thisMass;
1311 <      
1312 <      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {        
1313 <        thisMass = mol->getMass();
1314 <        thisr = mol->getCom()-com;
1315 <        thisp = (mol->getComVel()-comVel)*thisMass;
1316 <        
1317 <        angularMomentum += cross( thisr, thisp );
1318 <        
1319 <      }  
1320 <      
1321 < #ifdef IS_MPI
1322 <      Vector3d tmpAngMom;
1323 <      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1324 < #endif
1325 <      
1326 <      return angularMomentum;
1327 <   }
1328 <  
1003 >  
1004    StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1005      return IOIndexToIntegrableObject.at(index);
1006    }
# Line 1333 | Line 1008 | namespace OpenMD {
1008    void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1009      IOIndexToIntegrableObject= v;
1010    }
1336 –
1337 –  /* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1338 –     based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1339 –     where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1340 –     V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1341 –  */
1342 –  void SimInfo::getGyrationalVolume(RealType &volume){
1343 –    Mat3x3d intTensor;
1344 –    RealType det;
1345 –    Vector3d dummyAngMom;
1346 –    RealType sysconstants;
1347 –    RealType geomCnst;
1348 –
1349 –    geomCnst = 3.0/2.0;
1350 –    /* Get the inertial tensor and angular momentum for free*/
1351 –    getInertiaTensor(intTensor,dummyAngMom);
1352 –    
1353 –    det = intTensor.determinant();
1354 –    sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1355 –    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1356 –    return;
1357 –  }
1358 –
1359 –  void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1360 –    Mat3x3d intTensor;
1361 –    Vector3d dummyAngMom;
1362 –    RealType sysconstants;
1363 –    RealType geomCnst;
1364 –
1365 –    geomCnst = 3.0/2.0;
1366 –    /* Get the inertial tensor and angular momentum for free*/
1367 –    getInertiaTensor(intTensor,dummyAngMom);
1368 –    
1369 –    detI = intTensor.determinant();
1370 –    sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1371 –    volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1372 –    return;
1373 –  }
1011   /*
1012     void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1013        assert( v.size() == nAtoms_ + nRigidBodies_);

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