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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 429 by mmeineke, Thu Mar 27 21:52:21 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 >    Exclude::createArray(simnfo->n_SRI);
339 >    the_excludes = new Exclude*[simnfo->n_SRI];
340      simnfo->globalExcludes = new int;
341      simnfo->n_exclude = tot_SRI;
342    }
343    else{
344      
345 <    the_excludes = new int[2];
346 <    the_excludes[0] = 0;
347 <    the_excludes[1] = 0;
345 >    Exclude::createArray( 1 );
346 >    the_excludes = new Exclude*;
347 >    the_excludes[0] = new Exclude(0);
348 >    the_excludes[0]->setPair( 0,0 );
349      simnfo->globalExcludes = new int;
350      simnfo->globalExcludes[0] = 0;
351 <
323 <    simnfo->n_exclude = 1;
351 >    simnfo->n_exclude = 0;
352    }
353  
354    // set the arrays into the SimInfo object
355  
356    simnfo->atoms = the_atoms;
357 <  simnfo->sr_interactions = the_sris;
357 >  simnfo->molecules = the_molecules;
358    simnfo->nGlobalExcludes = 0;
359    simnfo->excludes = the_excludes;
360  
361  
362    // get some of the tricky things that may still be in the globals
363  
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
364    
365    if( the_globals->haveBox() ){
366      simnfo->box_x = the_globals->getBox();
# Line 407 | Line 411 | void SimSetup::createSim( void ){
411  
412    the_ff->setSimInfo( simnfo );
413  
414 <  makeAtoms();
414 >  makeMolecules();
415    simnfo->identArray = new int[simnfo->n_atoms];
416    for(i=0; i<simnfo->n_atoms; i++){
417      simnfo->identArray[i] = the_atoms[i]->getIdent();
418    }
419    
420 <  if( tot_bonds ){
421 <    makeBonds();
422 <  }
423 <
424 <  if( tot_bends ){
425 <    makeBends();
426 <  }
427 <
428 <  if( tot_torsions ){
429 <    makeTorsions();
430 <  }
431 <
420 >  if (the_globals->getUseRF() ) {
421 >    simnfo->useReactionField = 1;
422 >  
423 >    if( !the_globals->haveECR() ){
424 >      sprintf( painCave.errMsg,
425 >               "SimSetup Warning: using default value of 1/2 the smallest "
426 >               "box length for the electrostaticCutoffRadius.\n"
427 >               "I hope you have a very fast processor!\n");
428 >      painCave.isFatal = 0;
429 >      simError();
430 >      double smallest;
431 >      smallest = simnfo->box_x;
432 >      if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
433 >      if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
434 >      simnfo->ecr = 0.5 * smallest;
435 >    } else {
436 >      simnfo->ecr        = the_globals->getECR();
437 >    }
438  
439 +    if( !the_globals->haveEST() ){
440 +      sprintf( painCave.errMsg,
441 +               "SimSetup Warning: using default value of 0.05 * the "
442 +               "electrostaticCutoffRadius for the electrostaticSkinThickness\n"
443 +               );
444 +      painCave.isFatal = 0;
445 +      simError();
446 +      simnfo->est = 0.05 * simnfo->ecr;
447 +    } else {
448 +      simnfo->est        = the_globals->getEST();
449 +    }
450 +    
451 +    if(!the_globals->haveDielectric() ){
452 +      sprintf( painCave.errMsg,
453 +               "SimSetup Error: You are trying to use Reaction Field without"
454 +               "setting a dielectric constant!\n"
455 +               );
456 +      painCave.isFatal = 1;
457 +      simError();
458 +    }
459 +    simnfo->dielectric = the_globals->getDielectric();  
460 +  } else {
461 +    if (simnfo->n_dipoles) {
462 +      
463 +      if( !the_globals->haveECR() ){
464 +        sprintf( painCave.errMsg,
465 +                 "SimSetup Warning: using default value of 1/2 the smallest"
466 +                 "box length for the electrostaticCutoffRadius.\n"
467 +                 "I hope you have a very fast processor!\n");
468 +        painCave.isFatal = 0;
469 +        simError();
470 +        double smallest;
471 +        smallest = simnfo->box_x;
472 +        if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
473 +        if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
474 +        simnfo->ecr = 0.5 * smallest;
475 +      } else {
476 +        simnfo->ecr        = the_globals->getECR();
477 +      }
478 +      
479 +      if( !the_globals->haveEST() ){
480 +        sprintf( painCave.errMsg,
481 +                 "SimSetup Warning: using default value of 5% of the"
482 +                 "electrostaticCutoffRadius for the "
483 +                 "electrostaticSkinThickness\n"
484 +                 );
485 +        painCave.isFatal = 0;
486 +        simError();
487 +        simnfo->est = 0.05 * simnfo->ecr;
488 +      } else {
489 +        simnfo->est        = the_globals->getEST();
490 +      }
491 +    }
492 +  }  
493  
494 + #ifdef IS_MPI
495 +  strcpy( checkPointMsg, "electrostatic parameters check out" );
496 +  MPIcheckPoint();
497 + #endif // is_mpi
498  
431 –
432 –
499   if( the_globals->haveInitialConfig() ){
500  
501       InitializeFromFile* fileInit;
# Line 587 | Line 653 | void SimSetup::createSim( void ){
653  
654   //   new AllLong( simnfo );
655  
590 –  if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff );
591 –  if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff );
656    if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff );
657    if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff );
658  
# Line 620 | Line 684 | void SimSetup::makeAtoms( void ){
684   #endif // is_mpi
685   }
686  
623 – void SimSetup::makeAtoms( void ){
687  
688 <  int i, j, k, index;
626 <  double ux, uy, uz, uSqr, u;
627 <  AtomStamp* current_atom;
688 > void SimSetup::makeMolecules( void ){
689  
690 +  int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
691 +  molInit info;
692    DirectionalAtom* dAtom;
693 <  int molIndex, molStart, molEnd, nMemb, lMolIndex;
693 >  LinkedAssign* extras;
694 >  LinkedAssign* current_extra;
695 >  AtomStamp* currentAtom;
696 >  BondStamp* currentBond;
697 >  BendStamp* currentBend;
698 >  TorsionStamp* currentTorsion;
699  
700 <  lMolIndex = 0;
701 <  molIndex = 0;
702 <  index = 0;
635 <  for( i=0; i<n_components; i++ ){
700 >  bond_pair* theBonds;
701 >  bend_set* theBends;
702 >  torsion_set* theTorsions;
703  
704 <    for( j=0; j<components_nmol[i]; j++ ){
704 >  
705 >  //init the forceField paramters
706  
707 < #ifdef IS_MPI
640 <      if( mpiSim->getMyMolStart() <= molIndex &&
641 <          molIndex <= mpiSim->getMyMolEnd() ){
642 < #endif // is_mpi        
707 >  the_ff->readParams();
708  
709 <        molStart = index;
710 <        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++;
709 >  
710 >  // init the atoms
711  
712 < #ifdef IS_MPI
713 <      }
714 < #endif //is_mpi
715 <      
716 <      molIndex++;
692 <    }
693 <  }
694 <
695 < #ifdef IS_MPI
696 <    for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] );
712 >  double ux, uy, uz, u, uSqr;
713 >  
714 >  atomOffset = 0;
715 >  excludeOffset = 0;
716 >  for(i=0; i<simnfo->n_mol; i++){
717      
718 <    delete[] globalIndex;
718 >    stampID = the_molecules[i].getStampID();
719  
720 <    mpiSim->mpiRefresh();
721 < #endif //IS_MPI
722 <          
723 <  the_ff->initializeAtoms();
724 < }
720 >    info.nAtoms    = comp_stamps[stampID]->getNAtoms();
721 >    info.nBonds    = comp_stamps[stampID]->getNBonds();
722 >    info.nBends    = comp_stamps[stampID]->getNBends();
723 >    info.nTorsions = comp_stamps[stampID]->getNTorsions();
724 >    info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
725  
726 < void SimSetup::makeBonds( void ){
726 >    info.myAtoms = &the_atoms[atomOffset];
727 >    info.myExcludes = &the_excludes[excludeOffset];
728 >    info.myBonds = new Bond*[info.nBonds];
729 >    info.myBends = new Bend*[info.nBends];
730 >    info.myTorsions = new Torsion*[info.nTorsions];
731  
732 <  int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
733 <  bond_pair* the_bonds;
734 <  BondStamp* current_bond;
735 <
736 <  the_bonds = new bond_pair[tot_bonds];
737 <  index = 0;
738 <  offset = 0;
739 <  molIndex = 0;
740 <
741 <  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        
732 >    theBonds = new bond_pair[info.nBonds];
733 >    theBends = new bend_set[info.nBends];
734 >    theTorsions = new torsion_set[info.nTorsions];
735 >    
736 >    // make the Atoms
737 >    
738 >    for(j=0; j<info.nAtoms; j++){
739 >      
740 >      currentAtom = comp_stamps[stampID]->getAtom( j );
741 >      if( currentAtom->haveOrientation() ){
742          
743 <        for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){
744 <          
745 <          current_bond = comp_stamps[i]->getBond( k );
746 <          the_bonds[index].a = current_bond->getA() + offset;
747 <          the_bonds[index].b = current_bond->getB() + offset;
748 <
749 <          exI = the_bonds[index].a;
750 <          exJ = the_bonds[index].b;
751 <
752 <          // exclude_I must always be the smaller of the pair
753 <          if( exI > exJ ){
754 <            tempEx = exI;
755 <            exI = exJ;
756 <            exJ = tempEx;
757 <          }
758 <
759 <          
743 >        dAtom = new DirectionalAtom(j + atomOffset);
744 >        simnfo->n_oriented++;
745 >        info.myAtoms[j] = dAtom;
746 >        
747 >        ux = currentAtom->getOrntX();
748 >        uy = currentAtom->getOrntY();
749 >        uz = currentAtom->getOrntZ();
750 >        
751 >        uSqr = (ux * ux) + (uy * uy) + (uz * uz);
752 >        
753 >        u = sqrt( uSqr );
754 >        ux = ux / u;
755 >        uy = uy / u;
756 >        uz = uz / u;
757 >        
758 >        dAtom->setSUx( ux );
759 >        dAtom->setSUy( uy );
760 >        dAtom->setSUz( uz );
761 >      }
762 >      else{
763 >        info.myAtoms[j] = new GeneralAtom(j + atomOffset);
764 >      }
765 >      info.myAtoms[j]->setType( currentAtom->getType() );
766 >    
767   #ifdef IS_MPI
768 <
769 <          the_excludes[index*2] =    
770 <            the_atoms[exI]->getGlobalIndex() + 1;
771 <          the_excludes[index*2 + 1] =
772 <            the_atoms[exJ]->getGlobalIndex() + 1;
773 <
774 < #else  // isn't MPI
775 <          
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
768 >      
769 >      info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
770 >      
771 > #endif // is_mpi
772 >    }
773 >    
774 >    // make the bonds
775 >    for(j=0; j<info.nBonds; j++){
776        
777 <      molIndex++;
778 <    }      
779 <  }
777 >      currentBond = comp_stamps[stampID]->getBond( j );
778 >      theBonds[j].a = currentBond->getA() + atomOffset;
779 >      theBonds[j].b = currentBond->getB() + atomOffset;
780  
781 <  the_ff->initializeBonds( the_bonds );
782 < }
781 >      exI = theBonds[i].a;
782 >      exJ = theBonds[i].b;
783  
784 < void SimSetup::makeBends( void ){
785 <
786 <  int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
787 <  bend_set* the_bends;
788 <  BendStamp* current_bend;
789 <  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 <
784 >      // exclude_I must always be the smaller of the pair
785 >      if( exI > exJ ){
786 >        tempEx = exI;
787 >        exI = exJ;
788 >        exJ = tempEx;
789 >      }
790   #ifdef IS_MPI
791 <      if( mpiSim->getMyMolStart() <= molIndex &&
792 <          molIndex <= mpiSim->getMyMolEnd() ){
793 < #endif // is_mpi        
791 >      tempEx = exI;
792 >      exI = the_atoms[tempEx]->getGlobalIndex() + 1;
793 >      tempEx = exJ;
794 >      exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
795 >      
796 >      the_excludes[j+excludeOffset]->setPair( exI, exJ );
797 > #else  // isn't MPI
798 >      the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
799 > #endif  //is_mpi
800 >    }
801 >    excludeOffset += info.nBonds;
802  
803 <        for( k=0; k<comp_stamps[i]->getNBends(); k++ ){
803 >    //make the bends
804 >    for(j=0; j<info.nBends; j++){
805 >      
806 >      currentBend = comp_stamps[stampID]->getBend( j );
807 >      theBends[j].a = currentBend->getA() + atomOffset;
808 >      theBends[j].b = currentBend->getB() + atomOffset;
809 >      theBends[j].c = currentBend->getC() + atomOffset;
810            
811 <          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() ){
811 >      if( currentBend->haveExtras() ){
812              
813 <            extras = current_bend->getExtras();
814 <            current_extra = extras;
813 >        extras = currentBend->getExtras();
814 >        current_extra = extras;
815              
816 <            while( current_extra != NULL ){
817 <              if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
816 >        while( current_extra != NULL ){
817 >          if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
818                  
819 <                switch( current_extra->getType() ){
819 >            switch( current_extra->getType() ){
820 >              
821 >            case 0:
822 >              theBends[j].ghost =
823 >                current_extra->getInt() + atomOffset;
824 >              theBends[j].isGhost = 1;
825 >              break;
826                    
827 <                case 0:
828 <                  the_bends[index].ghost =
829 <                    current_extra->getInt() + offset;
830 <                  the_bends[index].isGhost = 1;
831 <                  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 <              }
827 >            case 1:
828 >              theBends[j].ghost =
829 >                (int)current_extra->getDouble() + atomOffset;
830 >              theBends[j].isGhost = 1;
831 >              break;
832                
833 <              else{
834 <                
835 <                sprintf( painCave.errMsg,
836 <                         "SimSetup Error: unhandled bend assignment:\n"
837 <                         "    -->%s in Bend[%d] in %s\n",
838 <                         current_extra->getlhs(),
839 <                         k, comp_stamps[i]->getID() );
840 <                painCave.isFatal = 1;
843 <                simError();
844 <              }
845 <              
846 <              current_extra = current_extra->getNext();
833 >            default:
834 >              sprintf( painCave.errMsg,
835 >                       "SimSetup Error: ghostVectorSource was neiter a "
836 >                       "double nor an int.\n"
837 >                       "-->Bend[%d] in %s\n",
838 >                       j, comp_stamps[stampID]->getID() );
839 >              painCave.isFatal = 1;
840 >              simError();
841              }
842            }
843            
850 –          if( !the_bends[index].isGhost ){
851 –            
852 –            exI = the_bends[index].a;
853 –            exJ = the_bends[index].c;
854 –          }
844            else{
845              
846 <            exI = the_bends[index].a;
847 <            exJ = the_bends[index].b;
846 >            sprintf( painCave.errMsg,
847 >                     "SimSetup Error: unhandled bend assignment:\n"
848 >                     "    -->%s in Bend[%d] in %s\n",
849 >                     current_extra->getlhs(),
850 >                     j, comp_stamps[stampID]->getID() );
851 >            painCave.isFatal = 1;
852 >            simError();
853            }
854            
855 <          // exclude_I must always be the smaller of the pair
856 <          if( exI > exJ ){
857 <            tempEx = exI;
858 <            exI = exJ;
859 <            exJ = tempEx;
860 <          }
855 >          current_extra = current_extra->getNext();
856 >        }
857 >      }
858 >          
859 >      if( !theBends[j].isGhost ){
860 >            
861 >        exI = theBends[j].a;
862 >        exJ = theBends[j].c;
863 >      }
864 >      else{
865 >        
866 >        exI = theBends[j].a;
867 >        exJ = theBends[j].b;
868 >      }
869 >      
870 >      // exclude_I must always be the smaller of the pair
871 >      if( exI > exJ ){
872 >        tempEx = exI;
873 >        exI = exJ;
874 >        exJ = tempEx;
875 >      }
876 > #ifdef IS_MPI
877 >      tempEx = exI;
878 >      exI = the_atoms[tempEx]->getGlobalIndex() + 1;
879 >      tempEx = exJ;
880 >      exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
881 >      
882 >      the_excludes[j+excludeOffset]->setPair( exI, exJ );
883 > #else  // isn't MPI
884 >      the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
885 > #endif  //is_mpi
886 >    }
887 >    excludeOffset += info.nBends;
888  
889 +    for(j=0; j<info.nTorsions; j++){
890 +      
891 +      currentTorsion = comp_stamps[stampID]->getTorsion( j );
892 +      theTorsions[j].a = currentTorsion->getA() + atomOffset;
893 +      theTorsions[j].b = currentTorsion->getB() + atomOffset;
894 +      theTorsions[j].c = currentTorsion->getC() + atomOffset;
895 +      theTorsions[j].d = currentTorsion->getD() + atomOffset;
896 +      
897 +      exI = theTorsions[j].a;
898 +      exJ = theTorsions[j].d;
899  
900 +      // exclude_I must always be the smaller of the pair
901 +      if( exI > exJ ){
902 +        tempEx = exI;
903 +        exI = exJ;
904 +        exJ = tempEx;
905 +      }
906   #ifdef IS_MPI
907 <
908 <          the_excludes[(index + tot_bonds)*2] =    
909 <            the_atoms[exI]->getGlobalIndex() + 1;
910 <          the_excludes[(index + tot_bonds)*2 + 1] =
911 <            the_atoms[exJ]->getGlobalIndex() + 1;
912 <          
907 >      tempEx = exI;
908 >      exI = the_atoms[tempEx]->getGlobalIndex() + 1;
909 >      tempEx = exJ;
910 >      exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
911 >      
912 >      the_excludes[j+excludeOffset]->setPair( exI, exJ );
913   #else  // isn't MPI
914 <          
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)
914 >      the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
915   #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++;
916      }
917 <  }
917 >    excludeOffset += info.nTorsions;
918  
919 < #ifdef IS_MPI
920 <  sprintf( checkPointMsg,
899 <           "Successfully created the bends list.\n" );
900 <  MPIcheckPoint();
901 < #endif // is_mpi
902 <  
919 >    
920 >    // send the arrays off to the forceField for init.
921  
922 <  the_ff->initializeBends( the_bends );
923 < }
922 >    the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
923 >    the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
924 >    the_ff->initializeBends( info.nBends, info.myBends, theBends );
925 >    the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
926  
907 – void SimSetup::makeTorsions( void ){
927  
928 <  int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
929 <  torsion_set* the_torsions;
930 <  TorsionStamp* current_torsion;
931 <
932 <  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 <    }
928 >    the_molecules[i].initialize( info );
929 >    atomOffset += info.nAtoms;
930 >    delete[] theBonds;
931 >    delete[] theBends;
932 >    delete[] theTorsions;
933    }
934  
935 <  the_ff->initializeTorsions( the_torsions );
935 >  // clean up the forcefield
936 >  the_ff->calcRcut();
937 >  the_ff->cleanMe();
938   }
939  
940   void SimSetup::initFromBass( void ){

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