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root/group/branches/no-template-branch/OOPSE/libmdtools/SimSetup.cpp
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Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 424 by mmeineke, Thu Mar 27 20:36:16 2003 UTC vs.
Revision 438 by chuckv, Mon Mar 31 21:50:59 2003 UTC

# Line 240 | Line 240 | void SimSetup::createSim( void ){
240  
241    globalIndex = mpiSim->divideLabor();
242  
243 –
244 –
243    // set up the local variables
244    
245    int localMol, allMol;
# Line 316 | 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 326 | 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 335 | Line 335 | void SimSetup::createSim( void ){
335  
336  
337    if( simnfo->n_SRI ){
338 +    
339 +    std::cerr << "n_SRI = " << simnfo->n_SRI << "\n";
340 +    
341      Exclude::createArray(simnfo->n_SRI);
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 354 | Line 358 | void SimSetup::createSim( void ){
358    // set the arrays into the SimInfo object
359  
360    simnfo->atoms = the_atoms;
361 +  simnfo->molecules = the_molecules;
362    simnfo->nGlobalExcludes = 0;
363    simnfo->excludes = the_excludes;
364  
# Line 655 | Line 660 | void SimSetup::createSim( void ){
660    if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff );
661    if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff );
662  
663 <
663 > #ifdef IS_MPI
664 >  mpiSim->mpiRefresh();
665 > #endif
666  
667    // initialize the Fortran
668 <  
668 >
669 >
670    simnfo->refreshSim();
671    
672    if( !strcmp( simnfo->mixingRule, "standard") ){
# Line 695 | Line 703 | void SimSetup::makeMolecules( void ){
703    BondStamp* currentBond;
704    BendStamp* currentBend;
705    TorsionStamp* currentTorsion;
706 +
707 +  bond_pair* theBonds;
708 +  bend_set* theBends;
709 +  torsion_set* theTorsions;
710 +
711    
712    //init the forceField paramters
713  
714    the_ff->readParams();
715  
716    
717 <  // init the molecules
717 >  // init the atoms
718  
719 +  double ux, uy, uz, u, uSqr;
720 +  
721    atomOffset = 0;
722    excludeOffset = 0;
723    for(i=0; i<simnfo->n_mol; i++){
# Line 719 | Line 734 | void SimSetup::makeMolecules( void ){
734      info.myExcludes = &the_excludes[excludeOffset];
735      info.myBonds = new Bond*[info.nBonds];
736      info.myBends = new Bend*[info.nBends];
737 <    info.myTorsions = new Torsions*[info.nTorsions];
737 >    info.myTorsions = new Torsion*[info.nTorsions];
738  
739      theBonds = new bond_pair[info.nBonds];
740      theBends = new bend_set[info.nBends];
# Line 729 | Line 744 | void SimSetup::makeMolecules( void ){
744      
745      for(j=0; j<info.nAtoms; j++){
746        
747 <      currentAtom = theComponents[stampID]->getAtom( j );
747 >      currentAtom = comp_stamps[stampID]->getAtom( j );
748        if( currentAtom->haveOrientation() ){
749          
750          dAtom = new DirectionalAtom(j + atomOffset);
# Line 770 | 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 787 | 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 802 | Line 818 | void SimSetup::makeMolecules( void ){
818            
819        if( currentBend->haveExtras() ){
820              
821 <        extras = current_bend->getExtras();
821 >        extras = currentBend->getExtras();
822          current_extra = extras;
823              
824          while( current_extra != NULL ){
# Line 824 | 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 918 | 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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