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root/OpenMD/branches/development/src/brains/SimInfo.cpp
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Comparing branches/development/src/brains/SimInfo.cpp (file contents):
Revision 1769 by gezelter, Mon Jul 9 14:15:52 2012 UTC vs.
Revision 1830 by gezelter, Wed Jan 9 22:02:30 2013 UTC

# 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 267 | 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 282 | 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 338 | 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 351 | 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 781 | Line 784 | namespace OpenMD {
784  
785    void SimInfo::setupSimVariables() {
786      useAtomicVirial_ = simParams_->getUseAtomicVirial();
787 <    // we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
787 >    // we only call setAccumulateBoxDipole if the accumulateBoxDipole
788 >    // parameter is true
789      calcBoxDipole_ = false;
790      if ( simParams_->haveAccumulateBoxDipole() )
791        if ( simParams_->getAccumulateBoxDipole() ) {
# Line 875 | Line 879 | namespace OpenMD {
879  
880  
881    void SimInfo::prepareTopology() {
878 –    int nExclude, nOneTwo, nOneThree, nOneFour;
882  
883      //calculate mass ratio of cutoff group
884      SimInfo::MoleculeIterator mi;
# Line 924 | Line 927 | namespace OpenMD {
927      
928      //scan topology
929  
927 –    nExclude = excludedInteractions_.getSize();
928 –    nOneTwo = oneTwoInteractions_.getSize();
929 –    nOneThree = oneThreeInteractions_.getSize();
930 –    nOneFour = oneFourInteractions_.getSize();
931 –
930      int* excludeList = excludedInteractions_.getPairList();
931      int* oneTwoList = oneTwoInteractions_.getPairList();
932      int* oneThreeList = oneThreeInteractions_.getPairList();
# Line 979 | Line 977 | namespace OpenMD {
977  
978      for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
979          
980 <      for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
980 >      for (atom = mol->beginAtom(atomIter); atom != NULL;
981 >           atom = mol->nextAtom(atomIter)) {
982          atom->setSnapshotManager(sman_);
983        }
984          
985 <      for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
985 >      for (rb = mol->beginRigidBody(rbIter); rb != NULL;
986 >           rb = mol->nextRigidBody(rbIter)) {
987          rb->setSnapshotManager(sman_);
988        }
989  
990 <      for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
990 >      for (cg = mol->beginCutoffGroup(cgIter); cg != NULL;
991 >           cg = mol->nextCutoffGroup(cgIter)) {
992          cg->setSnapshotManager(sman_);
993        }
994      }    
# Line 1002 | Line 1003 | namespace OpenMD {
1003    
1004    
1005    StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1006 <    return IOIndexToIntegrableObject.at(index);
1006 >    if (index >= int(IOIndexToIntegrableObject.size())) {
1007 >      sprintf(painCave.errMsg,
1008 >              "SimInfo::getIOIndexToIntegrableObject Error: Integrable Object\n"
1009 >              "\tindex exceeds number of known objects!\n");
1010 >      painCave.isFatal = 1;
1011 >      simError();
1012 >      return NULL;
1013 >    } else
1014 >      return IOIndexToIntegrableObject.at(index);
1015    }
1016    
1017    void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1018      IOIndexToIntegrableObject= v;
1019    }
1011 – /*
1012 –   void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1013 –      assert( v.size() == nAtoms_ + nRigidBodies_);
1014 –      sdByGlobalIndex_ = v;
1015 –    }
1020  
1017 –    StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1018 –      //assert(index < nAtoms_ + nRigidBodies_);
1019 –      return sdByGlobalIndex_.at(index);
1020 –    }  
1021 – */  
1021    int SimInfo::getNGlobalConstraints() {
1022      int nGlobalConstraints;
1023   #ifdef IS_MPI
1024 <    MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1025 <                  MPI_COMM_WORLD);    
1024 >    MPI::COMM_WORLD.Allreduce(&nConstraints_, &nGlobalConstraints, 1,
1025 >                              MPI::INT, MPI::SUM);
1026   #else
1027      nGlobalConstraints =  nConstraints_;
1028   #endif

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