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root/OpenMD/trunk/src/brains/SimInfo.cpp
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Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 1793 by gezelter, Fri Aug 31 21:16:10 2012 UTC vs.
Revision 1929 by gezelter, Mon Aug 19 13:12:00 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 91 | Line 91 | namespace OpenMD {
91      for (vector<Component*>::iterator i = components.begin();
92           i !=components.end(); ++i) {
93        molStamp = (*i)->getMoleculeStamp();
94 +      if ( (*i)->haveRegion() ) {        
95 +        molStamp->setRegion( (*i)->getRegion() );
96 +      } else {
97 +        // set the region to a disallowed value:
98 +        molStamp->setRegion( -1 );
99 +      }
100 +
101        nMolWithSameStamp = (*i)->getNMol();
102        
103        addMoleculeStamp(molStamp, nMolWithSameStamp);
# Line 268 | Line 275 | namespace OpenMD {
275      ndf_local -= nConstraints_;
276  
277   #ifdef IS_MPI
278 <    MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
279 <    MPI_Allreduce(&nfq_local,&nGlobalFluctuatingCharges_,1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
278 >    MPI::COMM_WORLD.Allreduce(&ndf_local, &ndf_, 1, MPI::INT,MPI::SUM);
279 >    MPI::COMM_WORLD.Allreduce(&nfq_local, &nGlobalFluctuatingCharges_, 1,
280 >                              MPI::INT, MPI::SUM);
281   #else
282      ndf_ = ndf_local;
283      nGlobalFluctuatingCharges_ = nfq_local;
# Line 283 | Line 291 | namespace OpenMD {
291  
292    int SimInfo::getFdf() {
293   #ifdef IS_MPI
294 <    MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
294 >    MPI::COMM_WORLD.Allreduce(&fdf_local, &fdf_, 1, MPI::INT, MPI::SUM);
295   #else
296      fdf_ = fdf_local;
297   #endif
# Line 339 | Line 347 | namespace OpenMD {
347      }
348      
349   #ifdef IS_MPI
350 <    MPI_Allreduce(&ndfRaw_local,&ndfRaw_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
350 >    MPI::COMM_WORLD.Allreduce(&ndfRaw_local, &ndfRaw_, 1, MPI::INT, MPI::SUM);
351   #else
352      ndfRaw_ = ndfRaw_local;
353   #endif
# Line 352 | Line 360 | namespace OpenMD {
360  
361  
362   #ifdef IS_MPI
363 <    MPI_Allreduce(&ndfTrans_local,&ndfTrans_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
363 >    MPI::COMM_WORLD.Allreduce(&ndfTrans_local, &ndfTrans_, 1,
364 >                              MPI::INT, MPI::SUM);
365   #else
366      ndfTrans_ = ndfTrans_local;
367   #endif
# Line 780 | Line 789 | namespace OpenMD {
789      return atomTypes;        
790    }
791  
792 +
793 +  int getGlobalCountOfType(AtomType* atype) {
794 +    /*
795 +    set<AtomType*> atypes = getSimulatedAtomTypes();
796 +    map<AtomType*, int> counts_;
797 +
798 +    for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
799 +      for(atom = mol->beginAtom(ai); atom != NULL;
800 +          atom = mol->nextAtom(ai)) {
801 +        atom->getAtomType();
802 +      }      
803 +    }    
804 +    */
805 +    return 0;
806 +  }
807 +
808    void SimInfo::setupSimVariables() {
809      useAtomicVirial_ = simParams_->getUseAtomicVirial();
810      // we only call setAccumulateBoxDipole if the accumulateBoxDipole
# Line 913 | Line 938 | namespace OpenMD {
938        }      
939      }
940  
941 <    // Build the identArray_
941 >    // Build the identArray_ and regions_
942  
943      identArray_.clear();
944 <    identArray_.reserve(getNAtoms());    
945 <    for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {        
944 >    identArray_.reserve(getNAtoms());  
945 >    regions_.clear();
946 >    regions_.reserve(getNAtoms());
947 >
948 >    for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {      
949 >      int reg = mol->getRegion();      
950        for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
951          identArray_.push_back(atom->getIdent());
952 +        regions_.push_back(reg);
953        }
954      }    
955 <    
926 <    //scan topology
927 <
928 <    int* excludeList = excludedInteractions_.getPairList();
929 <    int* oneTwoList = oneTwoInteractions_.getPairList();
930 <    int* oneThreeList = oneThreeInteractions_.getPairList();
931 <    int* oneFourList = oneFourInteractions_.getPairList();
932 <
955 >      
956      topologyDone_ = true;
957    }
958  
# Line 1001 | Line 1024 | namespace OpenMD {
1024    
1025    
1026    StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1027 <    if (index >= IOIndexToIntegrableObject.size()) {
1027 >    if (index >= int(IOIndexToIntegrableObject.size())) {
1028        sprintf(painCave.errMsg,
1029                "SimInfo::getIOIndexToIntegrableObject Error: Integrable Object\n"
1030                "\tindex exceeds number of known objects!\n");
# Line 1019 | Line 1042 | namespace OpenMD {
1042    int SimInfo::getNGlobalConstraints() {
1043      int nGlobalConstraints;
1044   #ifdef IS_MPI
1045 <    MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1046 <                  MPI_COMM_WORLD);    
1045 >    MPI::COMM_WORLD.Allreduce(&nConstraints_, &nGlobalConstraints, 1,
1046 >                              MPI::INT, MPI::SUM);
1047   #else
1048      nGlobalConstraints =  nConstraints_;
1049   #endif

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