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root/group/trunk/OOPSE/libmdtools/SimSetup.cpp
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Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 432 by chuckv, Thu Mar 27 23:33:40 2003 UTC vs.
Revision 438 by chuckv, Mon Mar 31 21:50:59 2003 UTC

# Line 314 | Line 314 | void SimSetup::createSim( void ){
314      
315      if(mol2proc[i] == worldRank ){
316        the_molecules[molIndex].setStampID( molCompType[i] );
317 +      the_molecules[molIndex].setMyIndex( molIndex );
318        molIndex++;
319      }
320    }
# Line 324 | Line 325 | void SimSetup::createSim( void ){
325    for(i=0; i<n_components; i++){
326      for(j=0; j<components_nmol[i]; j++ ){
327        the_molecules[molIndex].setStampID( i );
328 +      the_molecules[molIndex].setMyIndex( molIndex );
329        molIndex++;
330      }
331    }
# Line 340 | Line 342 | void SimSetup::createSim( void ){
342      the_excludes = new Exclude*[simnfo->n_SRI];
343      for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
344      simnfo->globalExcludes = new int;
345 <    simnfo->n_exclude = tot_SRI;
345 >    simnfo->n_exclude = simnfo->n_SRI;
346    }
347    else{
348      
# Line 783 | Line 785 | void SimSetup::makeMolecules( void ){
785        theBonds[j].a = currentBond->getA() + atomOffset;
786        theBonds[j].b = currentBond->getB() + atomOffset;
787  
788 <      exI = theBonds[i].a;
789 <      exJ = theBonds[i].b;
788 >      exI = theBonds[j].a;
789 >      exJ = theBonds[j].b;
790  
791        // exclude_I must always be the smaller of the pair
792        if( exI > exJ ){
# Line 800 | Line 802 | void SimSetup::makeMolecules( void ){
802        
803        the_excludes[j+excludeOffset]->setPair( exI, exJ );
804   #else  // isn't MPI
805 +
806        the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
807   #endif  //is_mpi
808      }
# Line 837 | Line 840 | void SimSetup::makeMolecules( void ){
840                
841              default:
842                sprintf( painCave.errMsg,
843 <                       "SimSetup Error: ghostVectorSource was neiter a "
843 >                       "SimSetup Error: ghostVectorSource was neither a "
844                         "double nor an int.\n"
845                         "-->Bend[%d] in %s\n",
846                         j, comp_stamps[stampID]->getID() );
# Line 931 | Line 934 | void SimSetup::makeMolecules( void ){
934  
935  
936      the_molecules[i].initialize( info );
937 +
938 +
939      atomOffset += info.nAtoms;
940      delete[] theBonds;
941      delete[] theBends;
942      delete[] theTorsions;
943    }
944  
945 + #ifdef IS_MPI
946 +  sprintf( checkPointMsg, "all molecules initialized succesfully" );
947 +  MPIcheckPoint();
948 + #endif // is_mpi
949 +
950    // clean up the forcefield
951    the_ff->calcRcut();
952    the_ff->cleanMe();
953 +
954   }
955  
956   void SimSetup::initFromBass( void ){

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