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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 434 by chuckv, Fri Mar 28 19:30:59 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 241 | Line 239 | void SimSetup::createSim( void ){
239    
240  
241    globalIndex = mpiSim->divideLabor();
244 –
245 –
242  
243    // set up the local variables
244    
245    int localMol, allMol;
246    int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
247 +
248 +  int* mol2proc = mpiSim->getMolToProcMap();
249 +  int* molCompType = mpiSim->getMolComponentType();
250    
251    allMol = 0;
252    localMol = 0;
# Line 259 | Line 258 | void SimSetup::createSim( void ){
258  
259      for( j=0; j<components_nmol[i]; j++ ){
260        
261 <      if( mpiSim->getMyMolStart() <= allMol &&
263 <          allMol <= mpiSim->getMyMolEnd() ){
261 >      if( mol2proc[j] == worldRank ){
262          
263          local_atoms +=    comp_stamps[i]->getNAtoms();
264          local_bonds +=    comp_stamps[i]->getNBonds();
# Line 279 | Line 277 | void SimSetup::createSim( void ){
277    if( local_atoms != simnfo->n_atoms ){
278      sprintf( painCave.errMsg,
279               "SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
280 <             " localAtom (%d) are note equal.\n",
280 >             " localAtom (%d) are not equal.\n",
281               simnfo->n_atoms,
282               local_atoms );
283      painCave.isFatal = 1;
# Line 304 | Line 302 | void SimSetup::createSim( void ){
302    Atom::createArrays(simnfo->n_atoms);
303    the_atoms = new Atom*[simnfo->n_atoms];
304    the_molecules = new Molecule[simnfo->n_mol];
305 +  int molIndex;
306 +
307 +  // initialize the molecule's stampID's
308 +
309 + #ifdef IS_MPI
310 +  
311 +
312 +  molIndex = 0;
313 +  for(i=0; i<mpiSim->getTotNmol(); i++){
314 +    
315 +    if(mol2proc[i] == worldRank ){
316 +      the_molecules[molIndex].setStampID( molCompType[i] );
317 +      molIndex++;
318 +    }
319 +  }
320  
321 + #else // is_mpi
322 +  
323 +  molIndex = 0;
324 +  for(i=0; i<n_components; i++){
325 +    for(j=0; j<components_nmol[i]; j++ ){
326 +      the_molecules[molIndex].setStampID( i );
327 +      molIndex++;
328 +    }
329 +  }
330 +    
331  
332 + #endif // is_mpi
333 +
334 +
335    if( simnfo->n_SRI ){
336 <    the_sris = new SRI*[simnfo->n_SRI];
337 <    the_excludes = new int[2 * 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    }
345    else{
346      
347 <    the_excludes = new int[2];
348 <    the_excludes[0] = 0;
349 <    the_excludes[1] = 0;
347 >    Exclude::createArray( 1 );
348 >    the_excludes = new Exclude*;
349 >    the_excludes[0] = new Exclude(0);
350 >    the_excludes[0]->setPair( 0,0 );
351      simnfo->globalExcludes = new int;
352      simnfo->globalExcludes[0] = 0;
353 <
323 <    simnfo->n_exclude = 1;
353 >    simnfo->n_exclude = 0;
354    }
355  
356    // set the arrays into the SimInfo object
357  
358    simnfo->atoms = the_atoms;
359 <  simnfo->sr_interactions = the_sris;
359 >  simnfo->molecules = the_molecules;
360    simnfo->nGlobalExcludes = 0;
361    simnfo->excludes = the_excludes;
362  
363  
364    // get some of the tricky things that may still be in the globals
365  
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
366    
367    if( the_globals->haveBox() ){
368      simnfo->box_x = the_globals->getBox();
# Line 407 | Line 413 | void SimSetup::createSim( void ){
413  
414    the_ff->setSimInfo( simnfo );
415  
416 <  makeAtoms();
416 >  makeMolecules();
417    simnfo->identArray = new int[simnfo->n_atoms];
418    for(i=0; i<simnfo->n_atoms; i++){
419      simnfo->identArray[i] = the_atoms[i]->getIdent();
420    }
421    
422 <  if( tot_bonds ){
423 <    makeBonds();
424 <  }
425 <
426 <  if( tot_bends ){
427 <    makeBends();
428 <  }
429 <
430 <  if( tot_torsions ){
431 <    makeTorsions();
432 <  }
422 >  if (the_globals->getUseRF() ) {
423 >    simnfo->useReactionField = 1;
424 >  
425 >    if( !the_globals->haveECR() ){
426 >      sprintf( painCave.errMsg,
427 >               "SimSetup Warning: using default value of 1/2 the smallest "
428 >               "box length for the electrostaticCutoffRadius.\n"
429 >               "I hope you have a very fast processor!\n");
430 >      painCave.isFatal = 0;
431 >      simError();
432 >      double smallest;
433 >      smallest = simnfo->box_x;
434 >      if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
435 >      if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
436 >      simnfo->ecr = 0.5 * smallest;
437 >    } else {
438 >      simnfo->ecr        = the_globals->getECR();
439 >    }
440  
441 +    if( !the_globals->haveEST() ){
442 +      sprintf( painCave.errMsg,
443 +               "SimSetup Warning: using default value of 0.05 * the "
444 +               "electrostaticCutoffRadius for the electrostaticSkinThickness\n"
445 +               );
446 +      painCave.isFatal = 0;
447 +      simError();
448 +      simnfo->est = 0.05 * simnfo->ecr;
449 +    } else {
450 +      simnfo->est        = the_globals->getEST();
451 +    }
452 +    
453 +    if(!the_globals->haveDielectric() ){
454 +      sprintf( painCave.errMsg,
455 +               "SimSetup Error: You are trying to use Reaction Field without"
456 +               "setting a dielectric constant!\n"
457 +               );
458 +      painCave.isFatal = 1;
459 +      simError();
460 +    }
461 +    simnfo->dielectric = the_globals->getDielectric();  
462 +  } else {
463 +    if (simnfo->n_dipoles) {
464 +      
465 +      if( !the_globals->haveECR() ){
466 +        sprintf( painCave.errMsg,
467 +                 "SimSetup Warning: using default value of 1/2 the smallest"
468 +                 "box length for the electrostaticCutoffRadius.\n"
469 +                 "I hope you have a very fast processor!\n");
470 +        painCave.isFatal = 0;
471 +        simError();
472 +        double smallest;
473 +        smallest = simnfo->box_x;
474 +        if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
475 +        if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
476 +        simnfo->ecr = 0.5 * smallest;
477 +      } else {
478 +        simnfo->ecr        = the_globals->getECR();
479 +      }
480 +      
481 +      if( !the_globals->haveEST() ){
482 +        sprintf( painCave.errMsg,
483 +                 "SimSetup Warning: using default value of 5% of the"
484 +                 "electrostaticCutoffRadius for the "
485 +                 "electrostaticSkinThickness\n"
486 +                 );
487 +        painCave.isFatal = 0;
488 +        simError();
489 +        simnfo->est = 0.05 * simnfo->ecr;
490 +      } else {
491 +        simnfo->est        = the_globals->getEST();
492 +      }
493 +    }
494 +  }  
495  
496 + #ifdef IS_MPI
497 +  strcpy( checkPointMsg, "electrostatic parameters check out" );
498 +  MPIcheckPoint();
499 + #endif // is_mpi
500  
430 –
431 –
432 –
501   if( the_globals->haveInitialConfig() ){
502  
503       InitializeFromFile* fileInit;
# Line 587 | Line 655 | void SimSetup::createSim( void ){
655  
656   //   new AllLong( simnfo );
657  
590 –  if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff );
591 –  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  
596 –
665    // initialize the Fortran
666 <  
666 >
667 >
668    simnfo->refreshSim();
669    
670    if( !strcmp( simnfo->mixingRule, "standard") ){
# Line 620 | Line 689 | void SimSetup::makeAtoms( void ){
689   #endif // is_mpi
690   }
691  
623 – void SimSetup::makeAtoms( void ){
692  
693 <  int i, j, k, index;
626 <  double ux, uy, uz, uSqr, u;
627 <  AtomStamp* current_atom;
693 > void SimSetup::makeMolecules( void ){
694  
695 +  int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
696 +  molInit info;
697    DirectionalAtom* dAtom;
698 <  int molIndex, molStart, molEnd, nMemb, lMolIndex;
698 >  LinkedAssign* extras;
699 >  LinkedAssign* current_extra;
700 >  AtomStamp* currentAtom;
701 >  BondStamp* currentBond;
702 >  BendStamp* currentBend;
703 >  TorsionStamp* currentTorsion;
704  
705 <  lMolIndex = 0;
706 <  molIndex = 0;
707 <  index = 0;
635 <  for( i=0; i<n_components; i++ ){
705 >  bond_pair* theBonds;
706 >  bend_set* theBends;
707 >  torsion_set* theTorsions;
708  
709 <    for( j=0; j<components_nmol[i]; j++ ){
709 >  
710 >  //init the forceField paramters
711  
712 < #ifdef IS_MPI
640 <      if( mpiSim->getMyMolStart() <= molIndex &&
641 <          molIndex <= mpiSim->getMyMolEnd() ){
642 < #endif // is_mpi        
712 >  the_ff->readParams();
713  
714 <        molStart = index;
715 <        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++;
714 >  
715 >  // init the atoms
716  
717 < #ifdef IS_MPI
718 <      }
719 < #endif //is_mpi
720 <      
721 <      molIndex++;
692 <    }
693 <  }
694 <
695 < #ifdef IS_MPI
696 <    for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] );
717 >  double ux, uy, uz, u, uSqr;
718 >  
719 >  atomOffset = 0;
720 >  excludeOffset = 0;
721 >  for(i=0; i<simnfo->n_mol; i++){
722      
723 <    delete[] globalIndex;
723 >    stampID = the_molecules[i].getStampID();
724  
725 <    mpiSim->mpiRefresh();
726 < #endif //IS_MPI
727 <          
728 <  the_ff->initializeAtoms();
729 < }
725 >    info.nAtoms    = comp_stamps[stampID]->getNAtoms();
726 >    info.nBonds    = comp_stamps[stampID]->getNBonds();
727 >    info.nBends    = comp_stamps[stampID]->getNBends();
728 >    info.nTorsions = comp_stamps[stampID]->getNTorsions();
729 >    info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
730  
731 < void SimSetup::makeBonds( void ){
731 >    info.myAtoms = &the_atoms[atomOffset];
732 >    info.myExcludes = &the_excludes[excludeOffset];
733 >    info.myBonds = new Bond*[info.nBonds];
734 >    info.myBends = new Bend*[info.nBends];
735 >    info.myTorsions = new Torsion*[info.nTorsions];
736  
737 <  int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
738 <  bond_pair* the_bonds;
739 <  BondStamp* current_bond;
740 <
741 <  the_bonds = new bond_pair[tot_bonds];
742 <  index = 0;
743 <  offset = 0;
744 <  molIndex = 0;
745 <
746 <  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        
737 >    theBonds = new bond_pair[info.nBonds];
738 >    theBends = new bend_set[info.nBends];
739 >    theTorsions = new torsion_set[info.nTorsions];
740 >    
741 >    // make the Atoms
742 >    
743 >    for(j=0; j<info.nAtoms; j++){
744 >      
745 >      currentAtom = comp_stamps[stampID]->getAtom( j );
746 >      if( currentAtom->haveOrientation() ){
747          
748 <        for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){
749 <          
750 <          current_bond = comp_stamps[i]->getBond( k );
751 <          the_bonds[index].a = current_bond->getA() + offset;
752 <          the_bonds[index].b = current_bond->getB() + offset;
753 <
754 <          exI = the_bonds[index].a;
755 <          exJ = the_bonds[index].b;
756 <
757 <          // exclude_I must always be the smaller of the pair
758 <          if( exI > exJ ){
759 <            tempEx = exI;
760 <            exI = exJ;
761 <            exJ = tempEx;
762 <          }
763 <
764 <          
748 >        dAtom = new DirectionalAtom(j + atomOffset);
749 >        simnfo->n_oriented++;
750 >        info.myAtoms[j] = dAtom;
751 >        
752 >        ux = currentAtom->getOrntX();
753 >        uy = currentAtom->getOrntY();
754 >        uz = currentAtom->getOrntZ();
755 >        
756 >        uSqr = (ux * ux) + (uy * uy) + (uz * uz);
757 >        
758 >        u = sqrt( uSqr );
759 >        ux = ux / u;
760 >        uy = uy / u;
761 >        uz = uz / u;
762 >        
763 >        dAtom->setSUx( ux );
764 >        dAtom->setSUy( uy );
765 >        dAtom->setSUz( uz );
766 >      }
767 >      else{
768 >        info.myAtoms[j] = new GeneralAtom(j + atomOffset);
769 >      }
770 >      info.myAtoms[j]->setType( currentAtom->getType() );
771 >    
772   #ifdef IS_MPI
773 +      
774 +      info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
775 +      
776 + #endif // is_mpi
777 +    }
778 +    
779 +    // make the bonds
780 +    for(j=0; j<info.nBonds; j++){
781 +      
782 +      currentBond = comp_stamps[stampID]->getBond( j );
783 +      theBonds[j].a = currentBond->getA() + atomOffset;
784 +      theBonds[j].b = currentBond->getB() + atomOffset;
785  
786 <          the_excludes[index*2] =    
787 <            the_atoms[exI]->getGlobalIndex() + 1;
747 <          the_excludes[index*2 + 1] =
748 <            the_atoms[exJ]->getGlobalIndex() + 1;
786 >      exI = theBonds[i].a;
787 >      exJ = theBonds[i].b;
788  
789 < #else  // isn't MPI
790 <          
791 <          the_excludes[index*2] =     exI + 1;
792 <          the_excludes[index*2 + 1] = exJ + 1;
793 <          // 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
789 >      // exclude_I must always be the smaller of the pair
790 >      if( exI > exJ ){
791 >        tempEx = exI;
792 >        exI = exJ;
793 >        exJ = tempEx;
794        }
795 < #endif //is_mpi
795 > #ifdef IS_MPI
796 >      tempEx = exI;
797 >      exI = the_atoms[tempEx]->getGlobalIndex() + 1;
798 >      tempEx = exJ;
799 >      exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
800        
801 <      molIndex++;
802 <    }      
803 <  }
801 >      the_excludes[j+excludeOffset]->setPair( exI, exJ );
802 > #else  // isn't MPI
803 >      the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
804 > #endif  //is_mpi
805 >    }
806 >    excludeOffset += info.nBonds;
807  
808 <  the_ff->initializeBonds( the_bonds );
809 < }
810 <
811 < void SimSetup::makeBends( void ){
812 <
813 <  int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
814 <  bend_set* the_bends;
777 <  BendStamp* current_bend;
778 <  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 <
790 < #ifdef IS_MPI
791 <      if( mpiSim->getMyMolStart() <= molIndex &&
792 <          molIndex <= mpiSim->getMyMolEnd() ){
793 < #endif // is_mpi        
794 <
795 <        for( k=0; k<comp_stamps[i]->getNBends(); k++ ){
808 >    //make the bends
809 >    for(j=0; j<info.nBends; j++){
810 >      
811 >      currentBend = comp_stamps[stampID]->getBend( j );
812 >      theBends[j].a = currentBend->getA() + atomOffset;
813 >      theBends[j].b = currentBend->getB() + atomOffset;
814 >      theBends[j].c = currentBend->getC() + atomOffset;
815            
816 <          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() ){
816 >      if( currentBend->haveExtras() ){
817              
818 <            extras = current_bend->getExtras();
819 <            current_extra = extras;
818 >        extras = currentBend->getExtras();
819 >        current_extra = extras;
820              
821 <            while( current_extra != NULL ){
822 <              if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
821 >        while( current_extra != NULL ){
822 >          if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
823                  
824 <                switch( current_extra->getType() ){
824 >            switch( current_extra->getType() ){
825 >              
826 >            case 0:
827 >              theBends[j].ghost =
828 >                current_extra->getInt() + atomOffset;
829 >              theBends[j].isGhost = 1;
830 >              break;
831                    
832 <                case 0:
833 <                  the_bends[index].ghost =
834 <                    current_extra->getInt() + offset;
835 <                  the_bends[index].isGhost = 1;
836 <                  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 <              }
832 >            case 1:
833 >              theBends[j].ghost =
834 >                (int)current_extra->getDouble() + atomOffset;
835 >              theBends[j].isGhost = 1;
836 >              break;
837                
838 <              else{
839 <                
840 <                sprintf( painCave.errMsg,
841 <                         "SimSetup Error: unhandled bend assignment:\n"
842 <                         "    -->%s in Bend[%d] in %s\n",
843 <                         current_extra->getlhs(),
844 <                         k, comp_stamps[i]->getID() );
845 <                painCave.isFatal = 1;
843 <                simError();
844 <              }
845 <              
846 <              current_extra = current_extra->getNext();
838 >            default:
839 >              sprintf( painCave.errMsg,
840 >                       "SimSetup Error: ghostVectorSource was neither a "
841 >                       "double nor an int.\n"
842 >                       "-->Bend[%d] in %s\n",
843 >                       j, comp_stamps[stampID]->getID() );
844 >              painCave.isFatal = 1;
845 >              simError();
846              }
847            }
848            
850 –          if( !the_bends[index].isGhost ){
851 –            
852 –            exI = the_bends[index].a;
853 –            exJ = the_bends[index].c;
854 –          }
849            else{
850              
851 <            exI = the_bends[index].a;
852 <            exJ = the_bends[index].b;
851 >            sprintf( painCave.errMsg,
852 >                     "SimSetup Error: unhandled bend assignment:\n"
853 >                     "    -->%s in Bend[%d] in %s\n",
854 >                     current_extra->getlhs(),
855 >                     j, comp_stamps[stampID]->getID() );
856 >            painCave.isFatal = 1;
857 >            simError();
858            }
859            
860 <          // exclude_I must always be the smaller of the pair
861 <          if( exI > exJ ){
862 <            tempEx = exI;
863 <            exI = exJ;
864 <            exJ = tempEx;
865 <          }
860 >          current_extra = current_extra->getNext();
861 >        }
862 >      }
863 >          
864 >      if( !theBends[j].isGhost ){
865 >            
866 >        exI = theBends[j].a;
867 >        exJ = theBends[j].c;
868 >      }
869 >      else{
870 >        
871 >        exI = theBends[j].a;
872 >        exJ = theBends[j].b;
873 >      }
874 >      
875 >      // exclude_I must always be the smaller of the pair
876 >      if( exI > exJ ){
877 >        tempEx = exI;
878 >        exI = exJ;
879 >        exJ = tempEx;
880 >      }
881 > #ifdef IS_MPI
882 >      tempEx = exI;
883 >      exI = the_atoms[tempEx]->getGlobalIndex() + 1;
884 >      tempEx = exJ;
885 >      exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
886 >      
887 >      the_excludes[j+excludeOffset]->setPair( exI, exJ );
888 > #else  // isn't MPI
889 >      the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
890 > #endif  //is_mpi
891 >    }
892 >    excludeOffset += info.nBends;
893  
894 +    for(j=0; j<info.nTorsions; j++){
895 +      
896 +      currentTorsion = comp_stamps[stampID]->getTorsion( j );
897 +      theTorsions[j].a = currentTorsion->getA() + atomOffset;
898 +      theTorsions[j].b = currentTorsion->getB() + atomOffset;
899 +      theTorsions[j].c = currentTorsion->getC() + atomOffset;
900 +      theTorsions[j].d = currentTorsion->getD() + atomOffset;
901 +      
902 +      exI = theTorsions[j].a;
903 +      exJ = theTorsions[j].d;
904  
905 +      // exclude_I must always be the smaller of the pair
906 +      if( exI > exJ ){
907 +        tempEx = exI;
908 +        exI = exJ;
909 +        exJ = tempEx;
910 +      }
911   #ifdef IS_MPI
912 <
913 <          the_excludes[(index + tot_bonds)*2] =    
914 <            the_atoms[exI]->getGlobalIndex() + 1;
915 <          the_excludes[(index + tot_bonds)*2 + 1] =
916 <            the_atoms[exJ]->getGlobalIndex() + 1;
917 <          
912 >      tempEx = exI;
913 >      exI = the_atoms[tempEx]->getGlobalIndex() + 1;
914 >      tempEx = exJ;
915 >      exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
916 >      
917 >      the_excludes[j+excludeOffset]->setPair( exI, exJ );
918   #else  // isn't MPI
919 <          
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)
919 >      the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
920   #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++;
921      }
922 +    excludeOffset += info.nTorsions;
923 +
924 +    
925 +    // send the arrays off to the forceField for init.
926 +
927 +    the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
928 +    the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
929 +    the_ff->initializeBends( info.nBends, info.myBends, theBends );
930 +    the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
931 +
932 +
933 +    the_molecules[i].initialize( info );
934 +    atomOffset += info.nAtoms;
935 +    delete[] theBonds;
936 +    delete[] theBends;
937 +    delete[] theTorsions;
938    }
939  
940   #ifdef IS_MPI
941 <  sprintf( checkPointMsg,
899 <           "Successfully created the bends list.\n" );
941 >  sprintf( checkPointMsg, "all molecules initialized succesfully" );
942    MPIcheckPoint();
943   #endif // is_mpi
902 –  
944  
945 <  the_ff->initializeBends( the_bends );
946 < }
945 >  // clean up the forcefield
946 >  the_ff->calcRcut();
947 >  the_ff->cleanMe();
948  
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++ ){
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 –    }
972 –  }
973 –
974 –  the_ff->initializeTorsions( the_torsions );
949   }
950  
951   void SimSetup::initFromBass( void ){

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