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root/group/trunk/OOPSE/libmdtools/SimSetup.cpp
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Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 422 by mmeineke, Thu Mar 27 19:21:42 2003 UTC vs.
Revision 435 by mmeineke, Fri Mar 28 19:33:37 2003 UTC

# Line 88 | Line 88 | void SimSetup::createSim( void ){
88            
89  
90  
91 <  if( !strcmp( force_field, "TraPPE" ) ) the_ff = new TraPPEFF();
92 <  else if( !strcmp( force_field, "DipoleTest" ) ) the_ff = new DipoleTestFF();
93 <  else if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF();
91 >  if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF();
92    else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
93    else{
94      sprintf( painCave.errMsg,
# Line 242 | Line 240 | void SimSetup::createSim( void ){
240  
241    globalIndex = mpiSim->divideLabor();
242  
245 –
246 –
243    // set up the local variables
244    
245    int localMol, allMol;
# Line 337 | Line 333 | void SimSetup::createSim( void ){
333  
334  
335    if( simnfo->n_SRI ){
336 +    
337 +    std::cerr << "n_SRI = " << simnfo->n_SRI << "\n";
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;
344    }
# Line 356 | 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 655 | void SimSetup::createSim( void ){
655  
656   //   new AllLong( simnfo );
657  
657 –  if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff );
658 –  if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff );
658    if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff );
659    if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff );
660  
661 + #ifdef IS_MPI
662 +  mpiSim->mpiRefresh();
663 + #endif
664  
663 –
665    // initialize the Fortran
666 <  
666 >
667 >
668    simnfo->refreshSim();
669    
670    if( !strcmp( simnfo->mixingRule, "standard") ){
# Line 699 | 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 723 | 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 733 | 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 774 | 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 791 | 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 806 | 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 828 | 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 923 | Line 933 | void SimSetup::makeMolecules( void ){
933  
934      the_molecules[i].initialize( info );
935      atomOffset += info.nAtoms;
936 +    delete[] theBonds;
937 +    delete[] theBends;
938 +    delete[] theTorsions;
939    }
940  
941 + #ifdef IS_MPI
942 +  sprintf( checkPointMsg, "all molecules initialized succesfully" );
943 +  MPIcheckPoint();
944 + #endif // is_mpi
945 +
946    // clean up the forcefield
947    the_ff->calcRcut();
948    the_ff->cleanMe();
949 +
950   }
951  
952   void SimSetup::initFromBass( void ){

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