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root/group/trunk/OOPSE/libmdtools/SimSetup.cpp
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Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 378 by mmeineke, Fri Mar 21 17:42:12 2003 UTC vs.
Revision 431 by mmeineke, Thu Mar 27 22:16:27 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 248 | Line 246 | void SimSetup::createSim( void ){
246    
247    int localMol, allMol;
248    int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
249 +
250 +  int* mol2proc = mpiSim->getMolToProcMap();
251 +  int* molCompType = mpiSim->getMolComponentType();
252    
253    allMol = 0;
254    localMol = 0;
# Line 259 | Line 260 | void SimSetup::createSim( void ){
260  
261      for( j=0; j<components_nmol[i]; j++ ){
262        
263 <      if( mpiSim->getMyMolStart() <= allMol &&
263 <          allMol <= mpiSim->getMyMolEnd() ){
263 >      if( mol2proc[j] == worldRank ){
264          
265          local_atoms +=    comp_stamps[i]->getNAtoms();
266          local_bonds +=    comp_stamps[i]->getNBonds();
# Line 279 | Line 279 | void SimSetup::createSim( void ){
279    if( local_atoms != simnfo->n_atoms ){
280      sprintf( painCave.errMsg,
281               "SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
282 <             " localAtom (%d) are note equal.\n",
282 >             " localAtom (%d) are not equal.\n",
283               simnfo->n_atoms,
284               local_atoms );
285      painCave.isFatal = 1;
# Line 304 | Line 304 | void SimSetup::createSim( void ){
304    Atom::createArrays(simnfo->n_atoms);
305    the_atoms = new Atom*[simnfo->n_atoms];
306    the_molecules = new Molecule[simnfo->n_mol];
307 +  int molIndex;
308 +
309 +  // initialize the molecule's stampID's
310 +
311 + #ifdef IS_MPI
312 +  
313 +
314 +  molIndex = 0;
315 +  for(i=0; i<mpiSim->getTotNmol(); i++){
316 +    
317 +    if(mol2proc[i] == worldRank ){
318 +      the_molecules[molIndex].setStampID( molCompType[i] );
319 +      molIndex++;
320 +    }
321 +  }
322  
323 + #else // is_mpi
324 +  
325 +  molIndex = 0;
326 +  for(i=0; i<n_components; i++){
327 +    for(j=0; j<components_nmol[i]; j++ ){
328 +      the_molecules[molIndex].setStampID( i );
329 +      molIndex++;
330 +    }
331 +  }
332 +    
333  
334 + #endif // is_mpi
335 +
336 +
337    if( simnfo->n_SRI ){
338 <    the_sris = new SRI*[simnfo->n_SRI];
339 <    the_excludes = new int[2 * 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;
346    }
347    else{
348      
349 <    the_excludes = new int[2];
350 <    the_excludes[0] = 0;
351 <    the_excludes[1] = 0;
349 >    Exclude::createArray( 1 );
350 >    the_excludes = new Exclude*;
351 >    the_excludes[0] = new Exclude(0);
352 >    the_excludes[0]->setPair( 0,0 );
353      simnfo->globalExcludes = new int;
354      simnfo->globalExcludes[0] = 0;
355 <
323 <    simnfo->n_exclude = 1;
355 >    simnfo->n_exclude = 0;
356    }
357  
358    // set the arrays into the SimInfo object
359  
360    simnfo->atoms = the_atoms;
361 <  simnfo->sr_interactions = the_sris;
361 >  simnfo->molecules = the_molecules;
362    simnfo->nGlobalExcludes = 0;
363    simnfo->excludes = the_excludes;
364  
365  
366    // get some of the tricky things that may still be in the globals
367  
336 –  if( simnfo->n_dipoles ){
337 –
338 –    if( !the_globals->haveRRF() ){
339 –      sprintf( painCave.errMsg,
340 –               "SimSetup Error, system has dipoles, but no rRF was set.\n");
341 –      painCave.isFatal = 1;
342 –      simError();
343 –    }
344 –    if( !the_globals->haveDielectric() ){
345 –      sprintf( painCave.errMsg,
346 –               "SimSetup Error, system has dipoles, but no"
347 –               " dielectric was set.\n" );
348 –      painCave.isFatal = 1;
349 –      simError();
350 –    }
351 –
352 –    simnfo->rRF        = the_globals->getRRF();
353 –    simnfo->dielectric = the_globals->getDielectric();
354 –  }
355 –
356 – #ifdef IS_MPI
357 –  strcpy( checkPointMsg, "rRf and dielectric check out" );
358 –  MPIcheckPoint();
359 – #endif // is_mpi
368    
369    if( the_globals->haveBox() ){
370      simnfo->box_x = the_globals->getBox();
# Line 407 | Line 415 | void SimSetup::createSim( void ){
415  
416    the_ff->setSimInfo( simnfo );
417  
418 <  makeAtoms();
418 >  makeMolecules();
419    simnfo->identArray = new int[simnfo->n_atoms];
420    for(i=0; i<simnfo->n_atoms; i++){
421      simnfo->identArray[i] = the_atoms[i]->getIdent();
422    }
423    
424 <  if( tot_bonds ){
425 <    makeBonds();
426 <  }
427 <
428 <  if( tot_bends ){
429 <    makeBends();
430 <  }
431 <
432 <  if( tot_torsions ){
433 <    makeTorsions();
434 <  }
424 >  if (the_globals->getUseRF() ) {
425 >    simnfo->useReactionField = 1;
426 >  
427 >    if( !the_globals->haveECR() ){
428 >      sprintf( painCave.errMsg,
429 >               "SimSetup Warning: using default value of 1/2 the smallest "
430 >               "box length for the electrostaticCutoffRadius.\n"
431 >               "I hope you have a very fast processor!\n");
432 >      painCave.isFatal = 0;
433 >      simError();
434 >      double smallest;
435 >      smallest = simnfo->box_x;
436 >      if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
437 >      if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
438 >      simnfo->ecr = 0.5 * smallest;
439 >    } else {
440 >      simnfo->ecr        = the_globals->getECR();
441 >    }
442  
443 +    if( !the_globals->haveEST() ){
444 +      sprintf( painCave.errMsg,
445 +               "SimSetup Warning: using default value of 0.05 * the "
446 +               "electrostaticCutoffRadius for the electrostaticSkinThickness\n"
447 +               );
448 +      painCave.isFatal = 0;
449 +      simError();
450 +      simnfo->est = 0.05 * simnfo->ecr;
451 +    } else {
452 +      simnfo->est        = the_globals->getEST();
453 +    }
454 +    
455 +    if(!the_globals->haveDielectric() ){
456 +      sprintf( painCave.errMsg,
457 +               "SimSetup Error: You are trying to use Reaction Field without"
458 +               "setting a dielectric constant!\n"
459 +               );
460 +      painCave.isFatal = 1;
461 +      simError();
462 +    }
463 +    simnfo->dielectric = the_globals->getDielectric();  
464 +  } else {
465 +    if (simnfo->n_dipoles) {
466 +      
467 +      if( !the_globals->haveECR() ){
468 +        sprintf( painCave.errMsg,
469 +                 "SimSetup Warning: using default value of 1/2 the smallest"
470 +                 "box length for the electrostaticCutoffRadius.\n"
471 +                 "I hope you have a very fast processor!\n");
472 +        painCave.isFatal = 0;
473 +        simError();
474 +        double smallest;
475 +        smallest = simnfo->box_x;
476 +        if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
477 +        if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
478 +        simnfo->ecr = 0.5 * smallest;
479 +      } else {
480 +        simnfo->ecr        = the_globals->getECR();
481 +      }
482 +      
483 +      if( !the_globals->haveEST() ){
484 +        sprintf( painCave.errMsg,
485 +                 "SimSetup Warning: using default value of 5% of the"
486 +                 "electrostaticCutoffRadius for the "
487 +                 "electrostaticSkinThickness\n"
488 +                 );
489 +        painCave.isFatal = 0;
490 +        simError();
491 +        simnfo->est = 0.05 * simnfo->ecr;
492 +      } else {
493 +        simnfo->est        = the_globals->getEST();
494 +      }
495 +    }
496 +  }  
497  
498 + #ifdef IS_MPI
499 +  strcpy( checkPointMsg, "electrostatic parameters check out" );
500 +  MPIcheckPoint();
501 + #endif // is_mpi
502  
430 –
431 –
432 –
503   if( the_globals->haveInitialConfig() ){
504  
505       InitializeFromFile* fileInit;
# Line 587 | Line 657 | void SimSetup::createSim( void ){
657  
658   //   new AllLong( simnfo );
659  
590 –  if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff );
591 –  if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff );
660    if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff );
661    if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff );
662  
# Line 620 | Line 688 | void SimSetup::makeAtoms( void ){
688   #endif // is_mpi
689   }
690  
623 – void SimSetup::makeAtoms( void ){
691  
692 <  int i, j, k, index;
626 <  double ux, uy, uz, uSqr, u;
627 <  AtomStamp* current_atom;
692 > void SimSetup::makeMolecules( void ){
693  
694 +  int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
695 +  molInit info;
696    DirectionalAtom* dAtom;
697 <  int molIndex, molStart, molEnd, nMemb, lMolIndex;
697 >  LinkedAssign* extras;
698 >  LinkedAssign* current_extra;
699 >  AtomStamp* currentAtom;
700 >  BondStamp* currentBond;
701 >  BendStamp* currentBend;
702 >  TorsionStamp* currentTorsion;
703  
704 <  lMolIndex = 0;
705 <  molIndex = 0;
706 <  index = 0;
635 <  for( i=0; i<n_components; i++ ){
704 >  bond_pair* theBonds;
705 >  bend_set* theBends;
706 >  torsion_set* theTorsions;
707  
708 <    for( j=0; j<components_nmol[i]; j++ ){
708 >  
709 >  //init the forceField paramters
710  
711 < #ifdef IS_MPI
640 <      if( mpiSim->getMyMolStart() <= molIndex &&
641 <          molIndex <= mpiSim->getMyMolEnd() ){
642 < #endif // is_mpi        
711 >  the_ff->readParams();
712  
713 <        molStart = index;
714 <        nMemb = comp_stamps[i]->getNAtoms();
646 <        for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){
647 <          
648 <          current_atom = comp_stamps[i]->getAtom( k );
649 <          if( current_atom->haveOrientation() ){
650 <            
651 <            dAtom = new DirectionalAtom(index);
652 <            simnfo->n_oriented++;
653 <            the_atoms[index] = dAtom;
654 <            
655 <            ux = current_atom->getOrntX();
656 <            uy = current_atom->getOrntY();
657 <            uz = current_atom->getOrntZ();
658 <            
659 <            uSqr = (ux * ux) + (uy * uy) + (uz * uz);
660 <            
661 <            u = sqrt( uSqr );
662 <            ux = ux / u;
663 <            uy = uy / u;
664 <            uz = uz / u;
665 <            
666 <            dAtom->setSUx( ux );
667 <            dAtom->setSUy( uy );
668 <            dAtom->setSUz( uz );
669 <          }
670 <          else{
671 <            the_atoms[index] = new GeneralAtom(index);
672 <          }
673 <          the_atoms[index]->setType( current_atom->getType() );
674 <          the_atoms[index]->setIndex( index );
675 <          
676 <          // increment the index and repeat;
677 <          index++;
678 <        }
679 <        
680 <        molEnd = index -1;
681 <        the_molecules[lMolIndex].setNMembers( nMemb );
682 <        the_molecules[lMolIndex].setStartAtom( molStart );
683 <        the_molecules[lMolIndex].setEndAtom( molEnd );
684 <        the_molecules[lMolIndex].setStampID( i );
685 <        lMolIndex++;
713 >  
714 >  // init the atoms
715  
716 < #ifdef IS_MPI
717 <      }
718 < #endif //is_mpi
719 <      
720 <      molIndex++;
692 <    }
693 <  }
694 <
695 < #ifdef IS_MPI
696 <    for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] );
716 >  double ux, uy, uz, u, uSqr;
717 >  
718 >  atomOffset = 0;
719 >  excludeOffset = 0;
720 >  for(i=0; i<simnfo->n_mol; i++){
721      
722 <    delete[] globalIndex;
722 >    stampID = the_molecules[i].getStampID();
723  
724 <    mpiSim->mpiRefresh();
725 < #endif //IS_MPI
726 <          
727 <  the_ff->initializeAtoms();
728 < }
724 >    info.nAtoms    = comp_stamps[stampID]->getNAtoms();
725 >    info.nBonds    = comp_stamps[stampID]->getNBonds();
726 >    info.nBends    = comp_stamps[stampID]->getNBends();
727 >    info.nTorsions = comp_stamps[stampID]->getNTorsions();
728 >    info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
729  
730 < void SimSetup::makeBonds( void ){
730 >    info.myAtoms = &the_atoms[atomOffset];
731 >    info.myExcludes = &the_excludes[excludeOffset];
732 >    info.myBonds = new Bond*[info.nBonds];
733 >    info.myBends = new Bend*[info.nBends];
734 >    info.myTorsions = new Torsion*[info.nTorsions];
735  
736 <  int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
737 <  bond_pair* the_bonds;
738 <  BondStamp* current_bond;
739 <
740 <  the_bonds = new bond_pair[tot_bonds];
741 <  index = 0;
742 <  offset = 0;
743 <  molIndex = 0;
744 <
745 <  for( i=0; i<n_components; i++ ){
718 <
719 <    for( j=0; j<components_nmol[i]; j++ ){
720 <
721 < #ifdef IS_MPI
722 <      if( mpiSim->getMyMolStart() <= molIndex &&
723 <          molIndex <= mpiSim->getMyMolEnd() ){
724 < #endif // is_mpi        
736 >    theBonds = new bond_pair[info.nBonds];
737 >    theBends = new bend_set[info.nBends];
738 >    theTorsions = new torsion_set[info.nTorsions];
739 >    
740 >    // make the Atoms
741 >    
742 >    for(j=0; j<info.nAtoms; j++){
743 >      
744 >      currentAtom = comp_stamps[stampID]->getAtom( j );
745 >      if( currentAtom->haveOrientation() ){
746          
747 <        for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){
748 <          
749 <          current_bond = comp_stamps[i]->getBond( k );
750 <          the_bonds[index].a = current_bond->getA() + offset;
751 <          the_bonds[index].b = current_bond->getB() + offset;
752 <
753 <          exI = the_bonds[index].a;
754 <          exJ = the_bonds[index].b;
755 <
756 <          // exclude_I must always be the smaller of the pair
757 <          if( exI > exJ ){
758 <            tempEx = exI;
759 <            exI = exJ;
760 <            exJ = tempEx;
761 <          }
762 <
763 <          
747 >        dAtom = new DirectionalAtom(j + atomOffset);
748 >        simnfo->n_oriented++;
749 >        info.myAtoms[j] = dAtom;
750 >        
751 >        ux = currentAtom->getOrntX();
752 >        uy = currentAtom->getOrntY();
753 >        uz = currentAtom->getOrntZ();
754 >        
755 >        uSqr = (ux * ux) + (uy * uy) + (uz * uz);
756 >        
757 >        u = sqrt( uSqr );
758 >        ux = ux / u;
759 >        uy = uy / u;
760 >        uz = uz / u;
761 >        
762 >        dAtom->setSUx( ux );
763 >        dAtom->setSUy( uy );
764 >        dAtom->setSUz( uz );
765 >      }
766 >      else{
767 >        info.myAtoms[j] = new GeneralAtom(j + atomOffset);
768 >      }
769 >      info.myAtoms[j]->setType( currentAtom->getType() );
770 >    
771   #ifdef IS_MPI
772 <
773 <          the_excludes[index*2] =    
746 <            the_atoms[exI]->getGlobalIndex() + 1;
747 <          the_excludes[index*2 + 1] =
748 <            the_atoms[exJ]->getGlobalIndex() + 1;
749 <
750 < #else  // isn't MPI
751 <          
752 <          the_excludes[index*2] =     exI + 1;
753 <          the_excludes[index*2 + 1] = exJ + 1;
754 <          // fortran index from 1 (hence the +1 in the indexing)
755 < #endif  //is_mpi
756 <          
757 <          // increment the index and repeat;
758 <          index++;
759 <        }
760 <        offset += comp_stamps[i]->getNAtoms();
761 <        
762 < #ifdef IS_MPI
763 <      }
764 < #endif //is_mpi
772 >      
773 >      info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
774        
775 <      molIndex++;
776 <    }      
777 <  }
775 > #endif // is_mpi
776 >    }
777 >    
778 >    // make the bonds
779 >    for(j=0; j<info.nBonds; j++){
780 >      
781 >      currentBond = comp_stamps[stampID]->getBond( j );
782 >      theBonds[j].a = currentBond->getA() + atomOffset;
783 >      theBonds[j].b = currentBond->getB() + atomOffset;
784  
785 <  the_ff->initializeBonds( the_bonds );
786 < }
785 >      exI = theBonds[i].a;
786 >      exJ = theBonds[i].b;
787  
788 < void SimSetup::makeBends( void ){
789 <
790 <  int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
791 <  bend_set* the_bends;
792 <  BendStamp* current_bend;
793 <  LinkedAssign* extras;
779 <  LinkedAssign* current_extra;
780 <  
781 <
782 <  the_bends = new bend_set[tot_bends];
783 <  index = 0;
784 <  offset = 0;
785 <  molIndex = 0;
786 <  for( i=0; i<n_components; i++ ){
787 <
788 <    for( j=0; j<components_nmol[i]; j++ ){
789 <
788 >      // exclude_I must always be the smaller of the pair
789 >      if( exI > exJ ){
790 >        tempEx = exI;
791 >        exI = exJ;
792 >        exJ = tempEx;
793 >      }
794   #ifdef IS_MPI
795 <      if( mpiSim->getMyMolStart() <= molIndex &&
796 <          molIndex <= mpiSim->getMyMolEnd() ){
797 < #endif // is_mpi        
795 >      tempEx = exI;
796 >      exI = the_atoms[tempEx]->getGlobalIndex() + 1;
797 >      tempEx = exJ;
798 >      exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
799 >      
800 >      the_excludes[j+excludeOffset]->setPair( exI, exJ );
801 > #else  // isn't MPI
802 >      the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
803 > #endif  //is_mpi
804 >    }
805 >    excludeOffset += info.nBonds;
806  
807 <        for( k=0; k<comp_stamps[i]->getNBends(); k++ ){
807 >    //make the bends
808 >    for(j=0; j<info.nBends; j++){
809 >      
810 >      currentBend = comp_stamps[stampID]->getBend( j );
811 >      theBends[j].a = currentBend->getA() + atomOffset;
812 >      theBends[j].b = currentBend->getB() + atomOffset;
813 >      theBends[j].c = currentBend->getC() + atomOffset;
814            
815 <          current_bend = comp_stamps[i]->getBend( k );
798 <          the_bends[index].a = current_bend->getA() + offset;
799 <          the_bends[index].b = current_bend->getB() + offset;
800 <          the_bends[index].c = current_bend->getC() + offset;
801 <          
802 <          if( current_bend->haveExtras() ){
815 >      if( currentBend->haveExtras() ){
816              
817 <            extras = current_bend->getExtras();
818 <            current_extra = extras;
817 >        extras = currentBend->getExtras();
818 >        current_extra = extras;
819              
820 <            while( current_extra != NULL ){
821 <              if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
820 >        while( current_extra != NULL ){
821 >          if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
822                  
823 <                switch( current_extra->getType() ){
823 >            switch( current_extra->getType() ){
824 >              
825 >            case 0:
826 >              theBends[j].ghost =
827 >                current_extra->getInt() + atomOffset;
828 >              theBends[j].isGhost = 1;
829 >              break;
830                    
831 <                case 0:
832 <                  the_bends[index].ghost =
833 <                    current_extra->getInt() + offset;
834 <                  the_bends[index].isGhost = 1;
835 <                  break;
817 <                  
818 <                case 1:
819 <                  the_bends[index].ghost =
820 <                    (int)current_extra->getDouble() + offset;
821 <                  the_bends[index].isGhost = 1;
822 <                  break;
823 <                  
824 <                default:
825 <                  sprintf( painCave.errMsg,
826 <                           "SimSetup Error: ghostVectorSource was neiter a "
827 <                           "double nor an int.\n"
828 <                           "-->Bend[%d] in %s\n",
829 <                           k, comp_stamps[i]->getID() );
830 <                  painCave.isFatal = 1;
831 <                  simError();
832 <                }
833 <              }
831 >            case 1:
832 >              theBends[j].ghost =
833 >                (int)current_extra->getDouble() + atomOffset;
834 >              theBends[j].isGhost = 1;
835 >              break;
836                
837 <              else{
838 <                
839 <                sprintf( painCave.errMsg,
840 <                         "SimSetup Error: unhandled bend assignment:\n"
841 <                         "    -->%s in Bend[%d] in %s\n",
842 <                         current_extra->getlhs(),
843 <                         k, comp_stamps[i]->getID() );
844 <                painCave.isFatal = 1;
843 <                simError();
844 <              }
845 <              
846 <              current_extra = current_extra->getNext();
837 >            default:
838 >              sprintf( painCave.errMsg,
839 >                       "SimSetup Error: ghostVectorSource was neiter a "
840 >                       "double nor an int.\n"
841 >                       "-->Bend[%d] in %s\n",
842 >                       j, comp_stamps[stampID]->getID() );
843 >              painCave.isFatal = 1;
844 >              simError();
845              }
846            }
847            
850 –          if( !the_bends[index].isGhost ){
851 –            
852 –            exI = the_bends[index].a;
853 –            exJ = the_bends[index].c;
854 –          }
848            else{
849              
850 <            exI = the_bends[index].a;
851 <            exJ = the_bends[index].b;
850 >            sprintf( painCave.errMsg,
851 >                     "SimSetup Error: unhandled bend assignment:\n"
852 >                     "    -->%s in Bend[%d] in %s\n",
853 >                     current_extra->getlhs(),
854 >                     j, comp_stamps[stampID]->getID() );
855 >            painCave.isFatal = 1;
856 >            simError();
857            }
858            
859 <          // exclude_I must always be the smaller of the pair
860 <          if( exI > exJ ){
861 <            tempEx = exI;
862 <            exI = exJ;
863 <            exJ = tempEx;
864 <          }
859 >          current_extra = current_extra->getNext();
860 >        }
861 >      }
862 >          
863 >      if( !theBends[j].isGhost ){
864 >            
865 >        exI = theBends[j].a;
866 >        exJ = theBends[j].c;
867 >      }
868 >      else{
869 >        
870 >        exI = theBends[j].a;
871 >        exJ = theBends[j].b;
872 >      }
873 >      
874 >      // exclude_I must always be the smaller of the pair
875 >      if( exI > exJ ){
876 >        tempEx = exI;
877 >        exI = exJ;
878 >        exJ = tempEx;
879 >      }
880 > #ifdef IS_MPI
881 >      tempEx = exI;
882 >      exI = the_atoms[tempEx]->getGlobalIndex() + 1;
883 >      tempEx = exJ;
884 >      exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
885 >      
886 >      the_excludes[j+excludeOffset]->setPair( exI, exJ );
887 > #else  // isn't MPI
888 >      the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
889 > #endif  //is_mpi
890 >    }
891 >    excludeOffset += info.nBends;
892  
893 +    for(j=0; j<info.nTorsions; j++){
894 +      
895 +      currentTorsion = comp_stamps[stampID]->getTorsion( j );
896 +      theTorsions[j].a = currentTorsion->getA() + atomOffset;
897 +      theTorsions[j].b = currentTorsion->getB() + atomOffset;
898 +      theTorsions[j].c = currentTorsion->getC() + atomOffset;
899 +      theTorsions[j].d = currentTorsion->getD() + atomOffset;
900 +      
901 +      exI = theTorsions[j].a;
902 +      exJ = theTorsions[j].d;
903  
904 +      // exclude_I must always be the smaller of the pair
905 +      if( exI > exJ ){
906 +        tempEx = exI;
907 +        exI = exJ;
908 +        exJ = tempEx;
909 +      }
910   #ifdef IS_MPI
911 <
912 <          the_excludes[(index + tot_bonds)*2] =    
913 <            the_atoms[exI]->getGlobalIndex() + 1;
914 <          the_excludes[(index + tot_bonds)*2 + 1] =
915 <            the_atoms[exJ]->getGlobalIndex() + 1;
916 <          
911 >      tempEx = exI;
912 >      exI = the_atoms[tempEx]->getGlobalIndex() + 1;
913 >      tempEx = exJ;
914 >      exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
915 >      
916 >      the_excludes[j+excludeOffset]->setPair( exI, exJ );
917   #else  // isn't MPI
918 <          
878 <          the_excludes[(index + tot_bonds)*2] =     exI + 1;
879 <          the_excludes[(index + tot_bonds)*2 + 1] = exJ + 1;
880 <          // fortran index from 1 (hence the +1 in the indexing)
918 >      the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
919   #endif  //is_mpi
882 –          
883 –          
884 –          // increment the index and repeat;
885 –          index++;
886 –        }
887 –        offset += comp_stamps[i]->getNAtoms();
888 –        
889 – #ifdef IS_MPI
890 –      }
891 – #endif //is_mpi
892 –
893 –      molIndex++;
920      }
921 <  }
921 >    excludeOffset += info.nTorsions;
922  
923 < #ifdef IS_MPI
924 <  sprintf( checkPointMsg,
899 <           "Successfully created the bends list.\n" );
900 <  MPIcheckPoint();
901 < #endif // is_mpi
902 <  
923 >    
924 >    // send the arrays off to the forceField for init.
925  
926 <  the_ff->initializeBends( the_bends );
927 < }
926 >    the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
927 >    the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
928 >    the_ff->initializeBends( info.nBends, info.myBends, theBends );
929 >    the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
930  
907 – void SimSetup::makeTorsions( void ){
931  
932 <  int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
933 <  torsion_set* the_torsions;
934 <  TorsionStamp* current_torsion;
935 <
936 <  the_torsions = new torsion_set[tot_torsions];
914 <  index = 0;
915 <  offset = 0;
916 <  molIndex = 0;
917 <  for( i=0; i<n_components; i++ ){
918 <
919 <    for( j=0; j<components_nmol[i]; j++ ){
920 <
921 < #ifdef IS_MPI
922 <      if( mpiSim->getMyMolStart() <= molIndex &&
923 <          molIndex <= mpiSim->getMyMolEnd() ){
924 < #endif // is_mpi        
925 <
926 <      for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){
927 <
928 <        current_torsion = comp_stamps[i]->getTorsion( k );
929 <        the_torsions[index].a = current_torsion->getA() + offset;
930 <        the_torsions[index].b = current_torsion->getB() + offset;
931 <        the_torsions[index].c = current_torsion->getC() + offset;
932 <        the_torsions[index].d = current_torsion->getD() + offset;
933 <
934 <        exI = the_torsions[index].a;
935 <        exJ = the_torsions[index].d;
936 <
937 <        
938 <        // exclude_I must always be the smaller of the pair
939 <        if( exI > exJ ){
940 <          tempEx = exI;
941 <          exI = exJ;
942 <          exJ = tempEx;
943 <        }
944 <
945 <
946 < #ifdef IS_MPI
947 <        
948 <        the_excludes[(index + tot_bonds + tot_bends)*2] =    
949 <          the_atoms[exI]->getGlobalIndex() + 1;
950 <        the_excludes[(index + tot_bonds + tot_bends)*2 + 1] =
951 <          the_atoms[exJ]->getGlobalIndex() + 1;
952 <        
953 < #else  // isn't MPI
954 <        
955 <        the_excludes[(index + tot_bonds + tot_bends)*2] =     exI + 1;
956 <        the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = exJ + 1;
957 <        // fortran indexes from 1 (hence the +1 in the indexing)
958 < #endif  //is_mpi
959 <        
960 <
961 <        // increment the index and repeat;
962 <        index++;
963 <      }
964 <      offset += comp_stamps[i]->getNAtoms();
965 <
966 < #ifdef IS_MPI
967 <      }
968 < #endif //is_mpi      
969 <
970 <      molIndex++;
971 <    }
932 >    the_molecules[i].initialize( info );
933 >    atomOffset += info.nAtoms;
934 >    delete[] theBonds;
935 >    delete[] theBends;
936 >    delete[] theTorsions;
937    }
938  
939 <  the_ff->initializeTorsions( the_torsions );
939 >  // clean up the forcefield
940 >  the_ff->calcRcut();
941 >  the_ff->cleanMe();
942   }
943  
944   void SimSetup::initFromBass( void ){

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