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root/group/trunk/OOPSE/libmdtools/SimSetup.cpp
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Comparing:
branches/mmeineke/OOPSE/libmdtools/SimSetup.cpp (file contents), Revision 377 by mmeineke, Fri Mar 21 17:42:12 2003 UTC vs.
trunk/OOPSE/libmdtools/SimSetup.cpp (file contents), Revision 424 by mmeineke, Thu Mar 27 20:36:16 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;
329 –  simnfo->sr_interactions = the_sris;
357    simnfo->nGlobalExcludes = 0;
358    simnfo->excludes = the_excludes;
359  
360  
361    // get some of the tricky things that may still be in the globals
362  
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
363    
364    if( the_globals->haveBox() ){
365      simnfo->box_x = the_globals->getBox();
# Line 407 | Line 410 | void SimSetup::createSim( void ){
410  
411    the_ff->setSimInfo( simnfo );
412  
413 <  makeAtoms();
413 >  makeMolecules();
414    simnfo->identArray = new int[simnfo->n_atoms];
415    for(i=0; i<simnfo->n_atoms; i++){
416      simnfo->identArray[i] = the_atoms[i]->getIdent();
417    }
418    
419 <  if( tot_bonds ){
420 <    makeBonds();
421 <  }
422 <
423 <  if( tot_bends ){
424 <    makeBends();
425 <  }
426 <
427 <  if( tot_torsions ){
428 <    makeTorsions();
429 <  }
419 >  if (the_globals->getUseRF() ) {
420 >    simnfo->useReactionField = 1;
421 >  
422 >    if( !the_globals->haveECR() ){
423 >      sprintf( painCave.errMsg,
424 >               "SimSetup Warning: using default value of 1/2 the smallest "
425 >               "box length for the electrostaticCutoffRadius.\n"
426 >               "I hope you have a very fast processor!\n");
427 >      painCave.isFatal = 0;
428 >      simError();
429 >      double smallest;
430 >      smallest = simnfo->box_x;
431 >      if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
432 >      if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
433 >      simnfo->ecr = 0.5 * smallest;
434 >    } else {
435 >      simnfo->ecr        = the_globals->getECR();
436 >    }
437  
438 +    if( !the_globals->haveEST() ){
439 +      sprintf( painCave.errMsg,
440 +               "SimSetup Warning: using default value of 0.05 * the "
441 +               "electrostaticCutoffRadius for the electrostaticSkinThickness\n"
442 +               );
443 +      painCave.isFatal = 0;
444 +      simError();
445 +      simnfo->est = 0.05 * simnfo->ecr;
446 +    } else {
447 +      simnfo->est        = the_globals->getEST();
448 +    }
449 +    
450 +    if(!the_globals->haveDielectric() ){
451 +      sprintf( painCave.errMsg,
452 +               "SimSetup Error: You are trying to use Reaction Field without"
453 +               "setting a dielectric constant!\n"
454 +               );
455 +      painCave.isFatal = 1;
456 +      simError();
457 +    }
458 +    simnfo->dielectric = the_globals->getDielectric();  
459 +  } else {
460 +    if (simnfo->n_dipoles) {
461 +      
462 +      if( !the_globals->haveECR() ){
463 +        sprintf( painCave.errMsg,
464 +                 "SimSetup Warning: using default value of 1/2 the smallest"
465 +                 "box length for the electrostaticCutoffRadius.\n"
466 +                 "I hope you have a very fast processor!\n");
467 +        painCave.isFatal = 0;
468 +        simError();
469 +        double smallest;
470 +        smallest = simnfo->box_x;
471 +        if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
472 +        if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
473 +        simnfo->ecr = 0.5 * smallest;
474 +      } else {
475 +        simnfo->ecr        = the_globals->getECR();
476 +      }
477 +      
478 +      if( !the_globals->haveEST() ){
479 +        sprintf( painCave.errMsg,
480 +                 "SimSetup Warning: using default value of 5% of the"
481 +                 "electrostaticCutoffRadius for the "
482 +                 "electrostaticSkinThickness\n"
483 +                 );
484 +        painCave.isFatal = 0;
485 +        simError();
486 +        simnfo->est = 0.05 * simnfo->ecr;
487 +      } else {
488 +        simnfo->est        = the_globals->getEST();
489 +      }
490 +    }
491 +  }  
492  
493 + #ifdef IS_MPI
494 +  strcpy( checkPointMsg, "electrostatic parameters check out" );
495 +  MPIcheckPoint();
496 + #endif // is_mpi
497  
430 –
431 –
432 –
498   if( the_globals->haveInitialConfig() ){
499  
500       InitializeFromFile* fileInit;
# Line 587 | Line 652 | void SimSetup::createSim( void ){
652  
653   //   new AllLong( simnfo );
654  
590 –  if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff );
591 –  if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff );
655    if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff );
656    if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff );
657  
# Line 620 | Line 683 | void SimSetup::createSim( void ){
683   #endif // is_mpi
684   }
685  
623 – void SimSetup::makeAtoms( void ){
686  
687 <  int i, j, k, index;
626 <  double ux, uy, uz, uSqr, u;
627 <  AtomStamp* current_atom;
687 > void SimSetup::makeMolecules( void ){
688  
689 +  int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
690 +  molInit info;
691    DirectionalAtom* dAtom;
692 <  int molIndex, molStart, molEnd, nMemb, lMolIndex;
692 >  LinkedAssign* extras;
693 >  LinkedAssign* current_extra;
694 >  AtomStamp* currentAtom;
695 >  BondStamp* currentBond;
696 >  BendStamp* currentBend;
697 >  TorsionStamp* currentTorsion;
698 >  
699 >  //init the forceField paramters
700  
701 <  lMolIndex = 0;
633 <  molIndex = 0;
634 <  index = 0;
635 <  for( i=0; i<n_components; i++ ){
701 >  the_ff->readParams();
702  
703 <    for( j=0; j<components_nmol[i]; j++ ){
703 >  
704 >  // init the molecules
705  
706 < #ifdef IS_MPI
707 <      if( mpiSim->getMyMolStart() <= molIndex &&
708 <          molIndex <= mpiSim->getMyMolEnd() ){
642 < #endif // is_mpi        
643 <
644 <        molStart = index;
645 <        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++;
686 <
687 < #ifdef IS_MPI
688 <      }
689 < #endif //is_mpi
690 <      
691 <      molIndex++;
692 <    }
693 <  }
694 <
695 < #ifdef IS_MPI
696 <    for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] );
706 >  atomOffset = 0;
707 >  excludeOffset = 0;
708 >  for(i=0; i<simnfo->n_mol; i++){
709      
710 <    delete[] globalIndex;
710 >    stampID = the_molecules[i].getStampID();
711  
712 <    mpiSim->mpiRefresh();
713 < #endif //IS_MPI
714 <          
715 <  the_ff->initializeAtoms();
716 < }
712 >    info.nAtoms    = comp_stamps[stampID]->getNAtoms();
713 >    info.nBonds    = comp_stamps[stampID]->getNBonds();
714 >    info.nBends    = comp_stamps[stampID]->getNBends();
715 >    info.nTorsions = comp_stamps[stampID]->getNTorsions();
716 >    info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
717  
718 < void SimSetup::makeBonds( void ){
718 >    info.myAtoms = &the_atoms[atomOffset];
719 >    info.myExcludes = &the_excludes[excludeOffset];
720 >    info.myBonds = new Bond*[info.nBonds];
721 >    info.myBends = new Bend*[info.nBends];
722 >    info.myTorsions = new Torsions*[info.nTorsions];
723  
724 <  int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
725 <  bond_pair* the_bonds;
726 <  BondStamp* current_bond;
727 <
728 <  the_bonds = new bond_pair[tot_bonds];
729 <  index = 0;
730 <  offset = 0;
731 <  molIndex = 0;
732 <
733 <  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        
724 >    theBonds = new bond_pair[info.nBonds];
725 >    theBends = new bend_set[info.nBends];
726 >    theTorsions = new torsion_set[info.nTorsions];
727 >    
728 >    // make the Atoms
729 >    
730 >    for(j=0; j<info.nAtoms; j++){
731 >      
732 >      currentAtom = theComponents[stampID]->getAtom( j );
733 >      if( currentAtom->haveOrientation() ){
734          
735 <        for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){
736 <          
737 <          current_bond = comp_stamps[i]->getBond( k );
738 <          the_bonds[index].a = current_bond->getA() + offset;
739 <          the_bonds[index].b = current_bond->getB() + offset;
740 <
741 <          exI = the_bonds[index].a;
742 <          exJ = the_bonds[index].b;
743 <
744 <          // exclude_I must always be the smaller of the pair
745 <          if( exI > exJ ){
746 <            tempEx = exI;
747 <            exI = exJ;
748 <            exJ = tempEx;
749 <          }
750 <
751 <          
735 >        dAtom = new DirectionalAtom(j + atomOffset);
736 >        simnfo->n_oriented++;
737 >        info.myAtoms[j] = dAtom;
738 >        
739 >        ux = currentAtom->getOrntX();
740 >        uy = currentAtom->getOrntY();
741 >        uz = currentAtom->getOrntZ();
742 >        
743 >        uSqr = (ux * ux) + (uy * uy) + (uz * uz);
744 >        
745 >        u = sqrt( uSqr );
746 >        ux = ux / u;
747 >        uy = uy / u;
748 >        uz = uz / u;
749 >        
750 >        dAtom->setSUx( ux );
751 >        dAtom->setSUy( uy );
752 >        dAtom->setSUz( uz );
753 >      }
754 >      else{
755 >        info.myAtoms[j] = new GeneralAtom(j + atomOffset);
756 >      }
757 >      info.myAtoms[j]->setType( currentAtom->getType() );
758 >    
759   #ifdef IS_MPI
760 <
761 <          the_excludes[index*2] =    
762 <            the_atoms[exI]->getGlobalIndex() + 1;
763 <          the_excludes[index*2 + 1] =
764 <            the_atoms[exJ]->getGlobalIndex() + 1;
765 <
766 < #else  // isn't MPI
767 <          
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
760 >      
761 >      info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
762 >      
763 > #endif // is_mpi
764 >    }
765 >    
766 >    // make the bonds
767 >    for(j=0; j<info.nBonds; j++){
768        
769 <      molIndex++;
770 <    }      
771 <  }
769 >      currentBond = comp_stamps[stampID]->getBond( j );
770 >      theBonds[j].a = currentBond->getA() + atomOffset;
771 >      theBonds[j].b = currentBond->getB() + atomOffset;
772  
773 <  the_ff->initializeBonds( the_bonds );
774 < }
773 >      exI = theBonds[i].a;
774 >      exJ = theBonds[i].b;
775  
776 < void SimSetup::makeBends( void ){
777 <
778 <  int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
779 <  bend_set* the_bends;
780 <  BendStamp* current_bend;
781 <  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 <
776 >      // exclude_I must always be the smaller of the pair
777 >      if( exI > exJ ){
778 >        tempEx = exI;
779 >        exI = exJ;
780 >        exJ = tempEx;
781 >      }
782   #ifdef IS_MPI
783 <      if( mpiSim->getMyMolStart() <= molIndex &&
784 <          molIndex <= mpiSim->getMyMolEnd() ){
785 < #endif // is_mpi        
783 >      tempEx = exI;
784 >      exI = the_atoms[tempEx]->getGlobalIndex() + 1;
785 >      tempEx = exJ;
786 >      exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
787 >      
788 >      the_excludes[j+excludeOffset]->setPair( exI, exJ );
789 > #else  // isn't MPI
790 >      the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
791 > #endif  //is_mpi
792 >    }
793 >    excludeOffset += info.nBonds;
794  
795 <        for( k=0; k<comp_stamps[i]->getNBends(); k++ ){
795 >    //make the bends
796 >    for(j=0; j<info.nBends; j++){
797 >      
798 >      currentBend = comp_stamps[stampID]->getBend( j );
799 >      theBends[j].a = currentBend->getA() + atomOffset;
800 >      theBends[j].b = currentBend->getB() + atomOffset;
801 >      theBends[j].c = currentBend->getC() + atomOffset;
802            
803 <          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() ){
803 >      if( currentBend->haveExtras() ){
804              
805 <            extras = current_bend->getExtras();
806 <            current_extra = extras;
805 >        extras = current_bend->getExtras();
806 >        current_extra = extras;
807              
808 <            while( current_extra != NULL ){
809 <              if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
808 >        while( current_extra != NULL ){
809 >          if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
810                  
811 <                switch( current_extra->getType() ){
811 >            switch( current_extra->getType() ){
812 >              
813 >            case 0:
814 >              theBends[j].ghost =
815 >                current_extra->getInt() + atomOffset;
816 >              theBends[j].isGhost = 1;
817 >              break;
818                    
819 <                case 0:
820 <                  the_bends[index].ghost =
821 <                    current_extra->getInt() + offset;
822 <                  the_bends[index].isGhost = 1;
823 <                  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 <              }
819 >            case 1:
820 >              theBends[j].ghost =
821 >                (int)current_extra->getDouble() + atomOffset;
822 >              theBends[j].isGhost = 1;
823 >              break;
824                
825 <              else{
826 <                
827 <                sprintf( painCave.errMsg,
828 <                         "SimSetup Error: unhandled bend assignment:\n"
829 <                         "    -->%s in Bend[%d] in %s\n",
830 <                         current_extra->getlhs(),
831 <                         k, comp_stamps[i]->getID() );
832 <                painCave.isFatal = 1;
843 <                simError();
844 <              }
845 <              
846 <              current_extra = current_extra->getNext();
825 >            default:
826 >              sprintf( painCave.errMsg,
827 >                       "SimSetup Error: ghostVectorSource was neiter a "
828 >                       "double nor an int.\n"
829 >                       "-->Bend[%d] in %s\n",
830 >                       j, comp_stamps[stampID]->getID() );
831 >              painCave.isFatal = 1;
832 >              simError();
833              }
834            }
835            
850 –          if( !the_bends[index].isGhost ){
851 –            
852 –            exI = the_bends[index].a;
853 –            exJ = the_bends[index].c;
854 –          }
836            else{
837              
838 <            exI = the_bends[index].a;
839 <            exJ = the_bends[index].b;
838 >            sprintf( painCave.errMsg,
839 >                     "SimSetup Error: unhandled bend assignment:\n"
840 >                     "    -->%s in Bend[%d] in %s\n",
841 >                     current_extra->getlhs(),
842 >                     j, comp_stamps[stampID]->getID() );
843 >            painCave.isFatal = 1;
844 >            simError();
845            }
846            
847 <          // exclude_I must always be the smaller of the pair
848 <          if( exI > exJ ){
849 <            tempEx = exI;
850 <            exI = exJ;
851 <            exJ = tempEx;
852 <          }
853 <
854 <
847 >          current_extra = current_extra->getNext();
848 >        }
849 >      }
850 >          
851 >      if( !theBends[j].isGhost ){
852 >            
853 >        exI = theBends[j].a;
854 >        exJ = theBends[j].c;
855 >      }
856 >      else{
857 >        
858 >        exI = theBends[j].a;
859 >        exJ = theBends[j].b;
860 >      }
861 >      
862 >      // exclude_I must always be the smaller of the pair
863 >      if( exI > exJ ){
864 >        tempEx = exI;
865 >        exI = exJ;
866 >        exJ = tempEx;
867 >      }
868   #ifdef IS_MPI
869 <
870 <          the_excludes[(index + tot_bonds)*2] =    
871 <            the_atoms[exI]->getGlobalIndex() + 1;
872 <          the_excludes[(index + tot_bonds)*2 + 1] =
873 <            the_atoms[exJ]->getGlobalIndex() + 1;
874 <          
869 >      tempEx = exI;
870 >      exI = the_atoms[tempEx]->getGlobalIndex() + 1;
871 >      tempEx = exJ;
872 >      exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
873 >      
874 >      the_excludes[j+excludeOffset]->setPair( exI, exJ );
875   #else  // isn't MPI
876 <          
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)
876 >      the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
877   #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++;
878      }
879 <  }
879 >    excludeOffset += info.nBends;
880  
881 < #ifdef IS_MPI
882 <  sprintf( checkPointMsg,
883 <           "Successfully created the bends list.\n" );
884 <  MPIcheckPoint();
885 < #endif // is_mpi
886 <  
887 <
888 <  the_ff->initializeBends( the_bends );
889 < }
890 <
907 < void SimSetup::makeTorsions( void ){
908 <
909 <  int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
910 <  torsion_set* the_torsions;
911 <  TorsionStamp* current_torsion;
912 <
913 <  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++ ){
881 >    for(j=0; j<info.nTorsions; j++){
882 >      
883 >      currentTorsion = comp_stamps[stampID]->getTorsion( j );
884 >      theTorsions[j].a = currentTorsion->getA() + atomOffset;
885 >      theTorsions[j].b = currentTorsion->getB() + atomOffset;
886 >      theTorsions[j].c = currentTorsion->getC() + atomOffset;
887 >      theTorsions[j].d = currentTorsion->getD() + atomOffset;
888 >      
889 >      exI = theTorsions[j].a;
890 >      exJ = theTorsions[j].d;
891  
892 +      // exclude_I must always be the smaller of the pair
893 +      if( exI > exJ ){
894 +        tempEx = exI;
895 +        exI = exJ;
896 +        exJ = tempEx;
897 +      }
898   #ifdef IS_MPI
899 <      if( mpiSim->getMyMolStart() <= molIndex &&
900 <          molIndex <= mpiSim->getMyMolEnd() ){
901 < #endif // is_mpi        
902 <
903 <      for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){
904 <
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 <        
899 >      tempEx = exI;
900 >      exI = the_atoms[tempEx]->getGlobalIndex() + 1;
901 >      tempEx = exJ;
902 >      exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
903 >      
904 >      the_excludes[j+excludeOffset]->setPair( exI, exJ );
905   #else  // isn't MPI
906 <        
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)
906 >      the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
907   #endif  //is_mpi
908 <        
908 >    }
909 >    excludeOffset += info.nTorsions;
910  
911 <        // increment the index and repeat;
912 <        index++;
963 <      }
964 <      offset += comp_stamps[i]->getNAtoms();
911 >    
912 >    // send the arrays off to the forceField for init.
913  
914 < #ifdef IS_MPI
915 <      }
916 < #endif //is_mpi      
914 >    the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
915 >    the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
916 >    the_ff->initializeBends( info.nBends, info.myBends, theBends );
917 >    the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
918  
919 <      molIndex++;
920 <    }
919 >
920 >    the_molecules[i].initialize( info );
921 >    atomOffset += info.nAtoms;
922    }
923  
924 <  the_ff->initializeTorsions( the_torsions );
924 >  // clean up the forcefield
925 >  the_ff->calcRcut();
926 >  the_ff->cleanMe();
927   }
928  
929   void SimSetup::initFromBass( void ){

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