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root/OpenMD/trunk/src/brains/SimInfo.cpp
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Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 1782 by gezelter, Wed Aug 22 02:28:28 2012 UTC vs.
Revision 1930 by gezelter, Mon Aug 19 13:51:04 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 363 | Line 372 | namespace OpenMD {
372  
373    void SimInfo::addInteractionPairs(Molecule* mol) {
374      ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
375 +    vector<Atom*>::iterator atomIter;
376      vector<Bond*>::iterator bondIter;
377      vector<Bend*>::iterator bendIter;
378      vector<Torsion*>::iterator torsionIter;
379      vector<Inversion*>::iterator inversionIter;
380 +    Atom* atom;
381      Bond* bond;
382      Bend* bend;
383      Torsion* torsion;
# Line 409 | Line 420 | namespace OpenMD {
420          atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));        
421        }
422      }  
423 +
424            
425      for (bond= mol->beginBond(bondIter); bond != NULL;
426           bond = mol->nextBond(bondIter)) {
# Line 778 | Line 790 | namespace OpenMD {
790   #endif
791  
792      return atomTypes;        
793 +  }
794 +
795 +
796 +  int getGlobalCountOfType(AtomType* atype) {
797 +    /*
798 +    set<AtomType*> atypes = getSimulatedAtomTypes();
799 +    map<AtomType*, int> counts_;
800 +
801 +    for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
802 +      for(atom = mol->beginAtom(ai); atom != NULL;
803 +          atom = mol->nextAtom(ai)) {
804 +        atom->getAtomType();
805 +      }      
806 +    }    
807 +    */
808 +    return 0;
809    }
810  
811    void SimInfo::setupSimVariables() {
# Line 877 | Line 905 | namespace OpenMD {
905  
906  
907    void SimInfo::prepareTopology() {
880 –    int nExclude, nOneTwo, nOneThree, nOneFour;
908  
909      //calculate mass ratio of cutoff group
910      SimInfo::MoleculeIterator mi;
# Line 914 | Line 941 | namespace OpenMD {
941        }      
942      }
943  
944 <    // Build the identArray_
944 >    // Build the identArray_ and regions_
945  
946      identArray_.clear();
947 <    identArray_.reserve(getNAtoms());    
948 <    for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {        
947 >    identArray_.reserve(getNAtoms());  
948 >    regions_.clear();
949 >    regions_.reserve(getNAtoms());
950 >
951 >    for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {      
952 >      int reg = mol->getRegion();      
953        for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
954          identArray_.push_back(atom->getIdent());
955 +        regions_.push_back(reg);
956        }
957      }    
958 <    
927 <    //scan topology
928 <
929 <    nExclude = excludedInteractions_.getSize();
930 <    nOneTwo = oneTwoInteractions_.getSize();
931 <    nOneThree = oneThreeInteractions_.getSize();
932 <    nOneFour = oneFourInteractions_.getSize();
933 <
934 <    int* excludeList = excludedInteractions_.getPairList();
935 <    int* oneTwoList = oneTwoInteractions_.getPairList();
936 <    int* oneThreeList = oneThreeInteractions_.getPairList();
937 <    int* oneFourList = oneFourInteractions_.getPairList();
938 <
958 >      
959      topologyDone_ = true;
960    }
961  
# Line 1007 | Line 1027 | namespace OpenMD {
1027    
1028    
1029    StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1030 <    if (index >= IOIndexToIntegrableObject.size()) {
1030 >    if (index >= int(IOIndexToIntegrableObject.size())) {
1031        sprintf(painCave.errMsg,
1032                "SimInfo::getIOIndexToIntegrableObject Error: Integrable Object\n"
1033                "\tindex exceeds number of known objects!\n");
# Line 1025 | Line 1045 | namespace OpenMD {
1045    int SimInfo::getNGlobalConstraints() {
1046      int nGlobalConstraints;
1047   #ifdef IS_MPI
1048 <    MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1049 <                  MPI_COMM_WORLD);    
1048 >    MPI::COMM_WORLD.Allreduce(&nConstraints_, &nGlobalConstraints, 1,
1049 >                              MPI::INT, MPI::SUM);
1050   #else
1051      nGlobalConstraints =  nConstraints_;
1052   #endif

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