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root/group/trunk/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 443 by mmeineke, Wed Apr 2 22:19:03 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      Exclude::createArray(simnfo->n_SRI);
340      the_excludes = new Exclude*[simnfo->n_SRI];
341 +    for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
342      simnfo->globalExcludes = new int;
343 <    simnfo->n_exclude = tot_SRI;
343 >    simnfo->n_exclude = simnfo->n_SRI;
344    }
345    else{
346      
# Line 354 | Line 356 | void SimSetup::createSim( void ){
356    // set the arrays into the SimInfo object
357  
358    simnfo->atoms = the_atoms;
359 +  simnfo->molecules = the_molecules;
360    simnfo->nGlobalExcludes = 0;
361    simnfo->excludes = the_excludes;
362  
# Line 654 | Line 657 | void SimSetup::createSim( void ){
657  
658    if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff );
659    if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff );
657 –
660  
661 + #ifdef IS_MPI
662 +  mpiSim->mpiRefresh();
663 + #endif
664  
665    // initialize the Fortran
666 <  
666 >
667 >
668    simnfo->refreshSim();
669    
670    if( !strcmp( simnfo->mixingRule, "standard") ){
# Line 695 | Line 701 | void SimSetup::makeMolecules( void ){
701    BondStamp* currentBond;
702    BendStamp* currentBend;
703    TorsionStamp* currentTorsion;
704 +
705 +  bond_pair* theBonds;
706 +  bend_set* theBends;
707 +  torsion_set* theTorsions;
708 +
709    
710    //init the forceField paramters
711  
712    the_ff->readParams();
713  
714    
715 <  // init the molecules
715 >  // init the atoms
716  
717 +  double ux, uy, uz, u, uSqr;
718 +  
719    atomOffset = 0;
720    excludeOffset = 0;
721    for(i=0; i<simnfo->n_mol; i++){
# Line 719 | Line 732 | void SimSetup::makeMolecules( void ){
732      info.myExcludes = &the_excludes[excludeOffset];
733      info.myBonds = new Bond*[info.nBonds];
734      info.myBends = new Bend*[info.nBends];
735 <    info.myTorsions = new Torsions*[info.nTorsions];
735 >    info.myTorsions = new Torsion*[info.nTorsions];
736  
737      theBonds = new bond_pair[info.nBonds];
738      theBends = new bend_set[info.nBends];
# Line 729 | Line 742 | void SimSetup::makeMolecules( void ){
742      
743      for(j=0; j<info.nAtoms; j++){
744        
745 <      currentAtom = theComponents[stampID]->getAtom( j );
745 >      currentAtom = comp_stamps[stampID]->getAtom( j );
746        if( currentAtom->haveOrientation() ){
747          
748          dAtom = new DirectionalAtom(j + atomOffset);
# Line 770 | Line 783 | void SimSetup::makeMolecules( void ){
783        theBonds[j].a = currentBond->getA() + atomOffset;
784        theBonds[j].b = currentBond->getB() + atomOffset;
785  
786 <      exI = theBonds[i].a;
787 <      exJ = theBonds[i].b;
786 >      exI = theBonds[j].a;
787 >      exJ = theBonds[j].b;
788  
789        // exclude_I must always be the smaller of the pair
790        if( exI > exJ ){
# Line 787 | Line 800 | void SimSetup::makeMolecules( void ){
800        
801        the_excludes[j+excludeOffset]->setPair( exI, exJ );
802   #else  // isn't MPI
803 +
804        the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
805   #endif  //is_mpi
806      }
# Line 802 | Line 816 | void SimSetup::makeMolecules( void ){
816            
817        if( currentBend->haveExtras() ){
818              
819 <        extras = current_bend->getExtras();
819 >        extras = currentBend->getExtras();
820          current_extra = extras;
821              
822          while( current_extra != NULL ){
# Line 824 | Line 838 | void SimSetup::makeMolecules( void ){
838                
839              default:
840                sprintf( painCave.errMsg,
841 <                       "SimSetup Error: ghostVectorSource was neiter a "
841 >                       "SimSetup Error: ghostVectorSource was neither a "
842                         "double nor an int.\n"
843                         "-->Bend[%d] in %s\n",
844                         j, comp_stamps[stampID]->getID() );
# Line 918 | Line 932 | void SimSetup::makeMolecules( void ){
932  
933  
934      the_molecules[i].initialize( info );
935 +
936 +
937      atomOffset += info.nAtoms;
938 +    delete[] theBonds;
939 +    delete[] theBends;
940 +    delete[] theTorsions;
941    }
942  
943 + #ifdef IS_MPI
944 +  sprintf( checkPointMsg, "all molecules initialized succesfully" );
945 +  MPIcheckPoint();
946 + #endif // is_mpi
947 +
948    // clean up the forcefield
949    the_ff->calcRcut();
950    the_ff->cleanMe();
951 +
952   }
953  
954   void SimSetup::initFromBass( void ){

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