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Revision 1767 by gezelter, Fri Jul 6 22:01:58 2012 UTC vs.
Revision 1874 by gezelter, Wed May 15 15:09:35 2013 UTC

# Line 35 | Line 35
35   *                                                                      
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).          
38 > * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
39   * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40   * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
# Line 88 | Line 88 | namespace OpenMD {
88      
89      vector<Component*> components = simParams->getComponents();
90      
91 <    for (vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
91 >    for (vector<Component*>::iterator i = components.begin();
92 >         i !=components.end(); ++i) {
93        molStamp = (*i)->getMoleculeStamp();
94        nMolWithSameStamp = (*i)->getNMol();
95        
# Line 231 | Line 232 | namespace OpenMD {
232      vector<Atom*>::iterator k;
233  
234      Molecule* mol;
235 <    StuntDouble* integrableObject;
235 >    StuntDouble* sd;
236      Atom* atom;
237  
238      ndf_local = 0;
239      nfq_local = 0;
240      
241      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
242 <      for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
243 <           integrableObject = mol->nextIntegrableObject(j)) {
242 >
243 >      for (sd = mol->beginIntegrableObject(j); sd != NULL;
244 >           sd = mol->nextIntegrableObject(j)) {
245  
246          ndf_local += 3;
247  
248 <        if (integrableObject->isDirectional()) {
249 <          if (integrableObject->isLinear()) {
248 >        if (sd->isDirectional()) {
249 >          if (sd->isLinear()) {
250              ndf_local += 2;
251            } else {
252              ndf_local += 3;
253            }
254          }
255        }
256 +
257        for (atom = mol->beginFluctuatingCharge(k); atom != NULL;
258             atom = mol->nextFluctuatingCharge(k)) {
259          if (atom->isFluctuatingCharge()) {
# Line 265 | Line 268 | namespace OpenMD {
268      ndf_local -= nConstraints_;
269  
270   #ifdef IS_MPI
271 <    MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
272 <    MPI_Allreduce(&nfq_local,&nGlobalFluctuatingCharges_,1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
271 >    MPI::COMM_WORLD.Allreduce(&ndf_local, &ndf_, 1, MPI::INT,MPI::SUM);
272 >    MPI::COMM_WORLD.Allreduce(&nfq_local, &nGlobalFluctuatingCharges_, 1,
273 >                              MPI::INT, MPI::SUM);
274   #else
275      ndf_ = ndf_local;
276      nGlobalFluctuatingCharges_ = nfq_local;
# Line 280 | Line 284 | namespace OpenMD {
284  
285    int SimInfo::getFdf() {
286   #ifdef IS_MPI
287 <    MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
287 >    MPI::COMM_WORLD.Allreduce(&fdf_local, &fdf_, 1, MPI::INT, MPI::SUM);
288   #else
289      fdf_ = fdf_local;
290   #endif
# Line 312 | Line 316 | namespace OpenMD {
316      MoleculeIterator i;
317      vector<StuntDouble*>::iterator j;
318      Molecule* mol;
319 <    StuntDouble* integrableObject;
319 >    StuntDouble* sd;
320  
321      // Raw degrees of freedom that we have to set
322      ndfRaw_local = 0;
323      
324      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
321 –      for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
322 –           integrableObject = mol->nextIntegrableObject(j)) {
325  
326 +      for (sd = mol->beginIntegrableObject(j); sd != NULL;
327 +           sd = mol->nextIntegrableObject(j)) {
328 +
329          ndfRaw_local += 3;
330  
331 <        if (integrableObject->isDirectional()) {
332 <          if (integrableObject->isLinear()) {
331 >        if (sd->isDirectional()) {
332 >          if (sd->isLinear()) {
333              ndfRaw_local += 2;
334            } else {
335              ndfRaw_local += 3;
# Line 335 | Line 340 | namespace OpenMD {
340      }
341      
342   #ifdef IS_MPI
343 <    MPI_Allreduce(&ndfRaw_local,&ndfRaw_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
343 >    MPI::COMM_WORLD.Allreduce(&ndfRaw_local, &ndfRaw_, 1, MPI::INT, MPI::SUM);
344   #else
345      ndfRaw_ = ndfRaw_local;
346   #endif
# Line 348 | Line 353 | namespace OpenMD {
353  
354  
355   #ifdef IS_MPI
356 <    MPI_Allreduce(&ndfTrans_local,&ndfTrans_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
356 >    MPI::COMM_WORLD.Allreduce(&ndfTrans_local, &ndfTrans_, 1,
357 >                              MPI::INT, MPI::SUM);
358   #else
359      ndfTrans_ = ndfTrans_local;
360   #endif
# Line 384 | Line 390 | namespace OpenMD {
390      Molecule::RigidBodyIterator rbIter;
391      RigidBody* rb;
392      Molecule::IntegrableObjectIterator ii;
393 <    StuntDouble* integrableObject;
393 >    StuntDouble* sd;
394      
395 <    for (integrableObject = mol->beginIntegrableObject(ii);
396 <         integrableObject != NULL;
391 <         integrableObject = mol->nextIntegrableObject(ii)) {
395 >    for (sd = mol->beginIntegrableObject(ii); sd != NULL;
396 >         sd = mol->nextIntegrableObject(ii)) {
397        
398 <      if (integrableObject->isRigidBody()) {
399 <        rb = static_cast<RigidBody*>(integrableObject);
398 >      if (sd->isRigidBody()) {
399 >        rb = static_cast<RigidBody*>(sd);
400          vector<Atom*> atoms = rb->getAtoms();
401          set<int> rigidAtoms;
402          for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
# Line 402 | Line 407 | namespace OpenMD {
407          }      
408        } else {
409          set<int> oneAtomSet;
410 <        oneAtomSet.insert(integrableObject->getGlobalIndex());
411 <        atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));        
410 >        oneAtomSet.insert(sd->getGlobalIndex());
411 >        atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));        
412        }
413      }  
414            
# Line 537 | Line 542 | namespace OpenMD {
542      Molecule::RigidBodyIterator rbIter;
543      RigidBody* rb;
544      Molecule::IntegrableObjectIterator ii;
545 <    StuntDouble* integrableObject;
545 >    StuntDouble* sd;
546      
547 <    for (integrableObject = mol->beginIntegrableObject(ii);
548 <         integrableObject != NULL;
544 <         integrableObject = mol->nextIntegrableObject(ii)) {
547 >    for (sd = mol->beginIntegrableObject(ii); sd != NULL;
548 >         sd = mol->nextIntegrableObject(ii)) {
549        
550 <      if (integrableObject->isRigidBody()) {
551 <        rb = static_cast<RigidBody*>(integrableObject);
550 >      if (sd->isRigidBody()) {
551 >        rb = static_cast<RigidBody*>(sd);
552          vector<Atom*> atoms = rb->getAtoms();
553          set<int> rigidAtoms;
554          for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
# Line 555 | Line 559 | namespace OpenMD {
559          }      
560        } else {
561          set<int> oneAtomSet;
562 <        oneAtomSet.insert(integrableObject->getGlobalIndex());
563 <        atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));        
562 >        oneAtomSet.insert(sd->getGlobalIndex());
563 >        atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));        
564        }
565      }  
566  
# Line 776 | Line 780 | namespace OpenMD {
780   #endif
781  
782      return atomTypes;        
783 +  }
784 +
785 +
786 +  int getGlobalCountOfType(AtomType* atype) {
787 +    /*
788 +    set<AtomType*> atypes = getSimulatedAtomTypes();
789 +    map<AtomType*, int> counts_;
790 +
791 +    for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
792 +      for(atom = mol->beginAtom(ai); atom != NULL;
793 +          atom = mol->nextAtom(ai)) {
794 +        atom->getAtomType();
795 +      }      
796 +    }    
797 +    */
798 +    return 0;
799    }
800  
801    void SimInfo::setupSimVariables() {
802      useAtomicVirial_ = simParams_->getUseAtomicVirial();
803 <    // we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
803 >    // we only call setAccumulateBoxDipole if the accumulateBoxDipole
804 >    // parameter is true
805      calcBoxDipole_ = false;
806      if ( simParams_->haveAccumulateBoxDipole() )
807        if ( simParams_->getAccumulateBoxDipole() ) {
# Line 874 | Line 895 | namespace OpenMD {
895  
896  
897    void SimInfo::prepareTopology() {
877 –    int nExclude, nOneTwo, nOneThree, nOneFour;
898  
899      //calculate mass ratio of cutoff group
900      SimInfo::MoleculeIterator mi;
# Line 921 | Line 941 | namespace OpenMD {
941        }
942      }    
943      
924 –    //scan topology
925 –
926 –    nExclude = excludedInteractions_.getSize();
927 –    nOneTwo = oneTwoInteractions_.getSize();
928 –    nOneThree = oneThreeInteractions_.getSize();
929 –    nOneFour = oneFourInteractions_.getSize();
930 –
931 –    int* excludeList = excludedInteractions_.getPairList();
932 –    int* oneTwoList = oneTwoInteractions_.getPairList();
933 –    int* oneThreeList = oneThreeInteractions_.getPairList();
934 –    int* oneFourList = oneFourInteractions_.getPairList();
935 –
944      topologyDone_ = true;
945    }
946  
# Line 978 | Line 986 | namespace OpenMD {
986  
987      for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
988          
989 <      for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
989 >      for (atom = mol->beginAtom(atomIter); atom != NULL;
990 >           atom = mol->nextAtom(atomIter)) {
991          atom->setSnapshotManager(sman_);
992        }
993          
994 <      for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
994 >      for (rb = mol->beginRigidBody(rbIter); rb != NULL;
995 >           rb = mol->nextRigidBody(rbIter)) {
996          rb->setSnapshotManager(sman_);
997        }
998  
999 <      for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
999 >      for (cg = mol->beginCutoffGroup(cgIter); cg != NULL;
1000 >           cg = mol->nextCutoffGroup(cgIter)) {
1001          cg->setSnapshotManager(sman_);
1002        }
1003      }    
# Line 1001 | Line 1012 | namespace OpenMD {
1012    
1013    
1014    StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1015 <    return IOIndexToIntegrableObject.at(index);
1015 >    if (index >= int(IOIndexToIntegrableObject.size())) {
1016 >      sprintf(painCave.errMsg,
1017 >              "SimInfo::getIOIndexToIntegrableObject Error: Integrable Object\n"
1018 >              "\tindex exceeds number of known objects!\n");
1019 >      painCave.isFatal = 1;
1020 >      simError();
1021 >      return NULL;
1022 >    } else
1023 >      return IOIndexToIntegrableObject.at(index);
1024    }
1025    
1026    void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1027      IOIndexToIntegrableObject= v;
1028    }
1010 – /*
1011 –   void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1012 –      assert( v.size() == nAtoms_ + nRigidBodies_);
1013 –      sdByGlobalIndex_ = v;
1014 –    }
1029  
1016 –    StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1017 –      //assert(index < nAtoms_ + nRigidBodies_);
1018 –      return sdByGlobalIndex_.at(index);
1019 –    }  
1020 – */  
1030    int SimInfo::getNGlobalConstraints() {
1031      int nGlobalConstraints;
1032   #ifdef IS_MPI
1033 <    MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1034 <                  MPI_COMM_WORLD);    
1033 >    MPI::COMM_WORLD.Allreduce(&nConstraints_, &nGlobalConstraints, 1,
1034 >                              MPI::INT, MPI::SUM);
1035   #else
1036      nGlobalConstraints =  nConstraints_;
1037   #endif

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