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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 474 by gezelter, Mon Apr 7 21:42:19 2003 UTC

# Line 66 | Line 66 | void SimSetup::createSim( void ){
66  
67    MakeStamps *the_stamps;
68    Globals* the_globals;
69 +  ExtendedSystem* the_extendedsystem;
70    int i, j;
71  
72    // get the stamps and globals;
# Line 80 | Line 81 | void SimSetup::createSim( void ){
81    // get the ones we know are there, yet still may need some work.
82    n_components = the_globals->getNComponents();
83    strcpy( force_field, the_globals->getForceField() );
84 +
85 +  // get the ensemble and set up an extended system if we need it:
86    strcpy( ensemble, the_globals->getEnsemble() );
87 +  if( !strcasecmp( ensemble, "NPT" ) ) {
88 +    the_extendedsystem = new ExtendedSystem( simnfo );
89 +    the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
90 +    the_extendedsystem->setTargetPressure(the_globals->getTargetPressure());
91 +    the_extendedsystem->setQmass(the_globals->getQmass());
92 +    the_extendedsystem->setTauRelax(the_globals->getTauRelax());
93 +  } else if ( !strcasecmp( ensemble, "NVT") ) {
94 +    the_extendedsystem = new ExtendedSystem( simnfo );
95 +    the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
96 +    the_extendedsystem->setQmass(the_globals->getQmass());    
97 +  } else if ( !strcasecmp( ensemble, "NVE") ) {
98 +  } else {
99 +    sprintf( painCave.errMsg,
100 +             "SimSetup Warning. Unrecognized Ensemble -> %s, "
101 +             "reverting to NVE for this simulation.\n",
102 +             ensemble );
103 +    painCave.isFatal = 0;
104 +    simError();
105 +    strcpy( ensemble, "NVE" );
106 +  }  
107    strcpy( simnfo->ensemble, ensemble );
108  
109    strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
110    simnfo->usePBC = the_globals->getPBC();
111            
112 <
113 <
114 <  if( !strcmp( force_field, "TraPPE" ) ) the_ff = new TraPPEFF();
115 <  else if( !strcmp( force_field, "DipoleTest" ) ) the_ff = new DipoleTestFF();
116 <  else if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF();
117 <  else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
112 >  int usesDipoles = 0;
113 >  if( !strcmp( force_field, "TraPPE_Ex" ) ){
114 >    the_ff = new TraPPE_ExFF();
115 >    usesDipoles = 1;
116 >  }
117 >  else if( !strcasecmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
118    else{
119      sprintf( painCave.errMsg,
120               "SimSetup Error. Unrecognized force field -> %s\n",
# Line 242 | Line 265 | void SimSetup::createSim( void ){
265  
266    globalIndex = mpiSim->divideLabor();
267  
245 –
246 –
268    // set up the local variables
269    
270    int localMol, allMol;
271    int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
272 +
273 +  int* mol2proc = mpiSim->getMolToProcMap();
274 +  int* molCompType = mpiSim->getMolComponentType();
275    
276    allMol = 0;
277    localMol = 0;
# Line 259 | Line 283 | void SimSetup::createSim( void ){
283  
284      for( j=0; j<components_nmol[i]; j++ ){
285        
286 <      if( mpiSim->getMyMolStart() <= allMol &&
263 <          allMol <= mpiSim->getMyMolEnd() ){
286 >      if( mol2proc[j] == worldRank ){
287          
288          local_atoms +=    comp_stamps[i]->getNAtoms();
289          local_bonds +=    comp_stamps[i]->getNBonds();
# Line 279 | Line 302 | void SimSetup::createSim( void ){
302    if( local_atoms != simnfo->n_atoms ){
303      sprintf( painCave.errMsg,
304               "SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
305 <             " localAtom (%d) are note equal.\n",
305 >             " localAtom (%d) are not equal.\n",
306               simnfo->n_atoms,
307               local_atoms );
308      painCave.isFatal = 1;
# Line 304 | Line 327 | void SimSetup::createSim( void ){
327    Atom::createArrays(simnfo->n_atoms);
328    the_atoms = new Atom*[simnfo->n_atoms];
329    the_molecules = new Molecule[simnfo->n_mol];
330 +  int molIndex;
331  
332 +  // initialize the molecule's stampID's
333  
334 <  if( simnfo->n_SRI ){
335 <    the_sris = new SRI*[simnfo->n_SRI];
336 <    the_excludes = new int[2 * simnfo->n_SRI];
334 > #ifdef IS_MPI
335 >  
336 >
337 >  molIndex = 0;
338 >  for(i=0; i<mpiSim->getTotNmol(); i++){
339 >    
340 >    if(mol2proc[i] == worldRank ){
341 >      the_molecules[molIndex].setStampID( molCompType[i] );
342 >      the_molecules[molIndex].setMyIndex( molIndex );
343 >      molIndex++;
344 >    }
345 >  }
346 >
347 > #else // is_mpi
348 >  
349 >  molIndex = 0;
350 >  for(i=0; i<n_components; i++){
351 >    for(j=0; j<components_nmol[i]; j++ ){
352 >      the_molecules[molIndex].setStampID( i );
353 >      the_molecules[molIndex].setMyIndex( molIndex );
354 >      molIndex++;
355 >    }
356 >  }
357 >    
358 >
359 > #endif // is_mpi
360 >
361 >
362 >  if( simnfo->n_SRI ){
363 >    
364 >    Exclude::createArray(simnfo->n_SRI);
365 >    the_excludes = new Exclude*[simnfo->n_SRI];
366 >    for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
367      simnfo->globalExcludes = new int;
368 <    simnfo->n_exclude = tot_SRI;
368 >    simnfo->n_exclude = simnfo->n_SRI;
369    }
370    else{
371      
372 <    the_excludes = new int[2];
373 <    the_excludes[0] = 0;
374 <    the_excludes[1] = 0;
372 >    Exclude::createArray( 1 );
373 >    the_excludes = new Exclude*;
374 >    the_excludes[0] = new Exclude(0);
375 >    the_excludes[0]->setPair( 0,0 );
376      simnfo->globalExcludes = new int;
377      simnfo->globalExcludes[0] = 0;
378 <
323 <    simnfo->n_exclude = 1;
378 >    simnfo->n_exclude = 0;
379    }
380  
381    // set the arrays into the SimInfo object
382  
383    simnfo->atoms = the_atoms;
384 <  simnfo->sr_interactions = the_sris;
384 >  simnfo->molecules = the_molecules;
385    simnfo->nGlobalExcludes = 0;
386    simnfo->excludes = the_excludes;
387  
388  
389    // get some of the tricky things that may still be in the globals
335 –
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 –    }
390  
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
391    
392    if( the_globals->haveBox() ){
393      simnfo->box_x = the_globals->getBox();
# Line 407 | Line 438 | void SimSetup::createSim( void ){
438  
439    the_ff->setSimInfo( simnfo );
440  
441 <  makeAtoms();
441 >  makeMolecules();
442    simnfo->identArray = new int[simnfo->n_atoms];
443    for(i=0; i<simnfo->n_atoms; i++){
444      simnfo->identArray[i] = the_atoms[i]->getIdent();
445    }
446    
447 <  if( tot_bonds ){
448 <    makeBonds();
449 <  }
447 >  if (the_globals->getUseRF() ) {
448 >    simnfo->useReactionField = 1;
449 >  
450 >    if( !the_globals->haveECR() ){
451 >      sprintf( painCave.errMsg,
452 >               "SimSetup Warning: using default value of 1/2 the smallest "
453 >               "box length for the electrostaticCutoffRadius.\n"
454 >               "I hope you have a very fast processor!\n");
455 >      painCave.isFatal = 0;
456 >      simError();
457 >      double smallest;
458 >      smallest = simnfo->box_x;
459 >      if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
460 >      if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
461 >      simnfo->ecr = 0.5 * smallest;
462 >    } else {
463 >      simnfo->ecr        = the_globals->getECR();
464 >    }
465  
466 <  if( tot_bends ){
467 <    makeBends();
468 <  }
466 >    if( !the_globals->haveEST() ){
467 >      sprintf( painCave.errMsg,
468 >               "SimSetup Warning: using default value of 0.05 * the "
469 >               "electrostaticCutoffRadius for the electrostaticSkinThickness\n"
470 >               );
471 >      painCave.isFatal = 0;
472 >      simError();
473 >      simnfo->est = 0.05 * simnfo->ecr;
474 >    } else {
475 >      simnfo->est        = the_globals->getEST();
476 >    }
477 >    
478 >    if(!the_globals->haveDielectric() ){
479 >      sprintf( painCave.errMsg,
480 >               "SimSetup Error: You are trying to use Reaction Field without"
481 >               "setting a dielectric constant!\n"
482 >               );
483 >      painCave.isFatal = 1;
484 >      simError();
485 >    }
486 >    simnfo->dielectric = the_globals->getDielectric();  
487 >  } else {
488 >    if (usesDipoles) {
489 >      
490 >      if( !the_globals->haveECR() ){
491 >        sprintf( painCave.errMsg,
492 >                 "SimSetup Warning: using default value of 1/2 the smallest "
493 >                 "box length for the electrostaticCutoffRadius.\n"
494 >                 "I hope you have a very fast processor!\n");
495 >        painCave.isFatal = 0;
496 >        simError();
497 >        double smallest;
498 >        smallest = simnfo->box_x;
499 >        if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
500 >        if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
501 >        simnfo->ecr = 0.5 * smallest;
502 >      } else {
503 >        simnfo->ecr        = the_globals->getECR();
504 >      }
505 >      
506 >      if( !the_globals->haveEST() ){
507 >        sprintf( painCave.errMsg,
508 >                 "SimSetup Warning: using default value of 5%% of the "
509 >                 "electrostaticCutoffRadius for the "
510 >                 "electrostaticSkinThickness\n"
511 >                 );
512 >        painCave.isFatal = 0;
513 >        simError();
514 >        simnfo->est = 0.05 * simnfo->ecr;
515 >      } else {
516 >        simnfo->est        = the_globals->getEST();
517 >      }
518 >    }
519 >  }  
520  
521 <  if( tot_torsions ){
522 <    makeTorsions();
523 <  }
524 <
428 <
429 <
430 <
431 <
521 > #ifdef IS_MPI
522 >  strcpy( checkPointMsg, "electrostatic parameters check out" );
523 >  MPIcheckPoint();
524 > #endif // is_mpi
525  
526   if( the_globals->haveInitialConfig() ){
527  
# Line 587 | Line 680 | void SimSetup::createSim( void ){
680  
681   //   new AllLong( simnfo );
682  
590 –  if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff );
591 –  if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff );
592 –  if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff );
593 –  if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff );
683  
684 +  if( !strcmp( force_field, "TraPPE_Ex" ) ){
685 +    new Symplectic(simnfo, the_ff, the_extendedsystem);
686 +    std::cerr << "called new Symplecic\n";
687 +    fprintf( stderr, "called new Symplectic. stderr\n" );
688 +  }
689 +  else if( !strcmp( force_field, "LJ" ) ){
690 +    new Verlet( *simnfo, the_ff, the_extendedsystem );
691 +    std::cerr << "called new Verlet\n";
692 +    fprintf( stderr, "called new Verlet. stderr\n" );
693 +  }
694 +  else {
695 +    std::cerr << "I'm a bug.\n";
696 +    fprintf( stderr, "Ima bug. stderr %s\n", force_field);
697 +  }
698 + #ifdef IS_MPI
699 +  mpiSim->mpiRefresh();
700 + #endif
701  
596 –
702    // initialize the Fortran
703 <  
703 >
704 >
705    simnfo->refreshSim();
706    
707    if( !strcmp( simnfo->mixingRule, "standard") ){
# Line 620 | Line 726 | void SimSetup::createSim( void ){
726   #endif // is_mpi
727   }
728  
623 – void SimSetup::makeAtoms( void ){
729  
730 <  int i, j, k, index;
626 <  double ux, uy, uz, uSqr, u;
627 <  AtomStamp* current_atom;
730 > void SimSetup::makeMolecules( void ){
731  
732 +  int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
733 +  molInit info;
734    DirectionalAtom* dAtom;
735 <  int molIndex, molStart, molEnd, nMemb, lMolIndex;
735 >  LinkedAssign* extras;
736 >  LinkedAssign* current_extra;
737 >  AtomStamp* currentAtom;
738 >  BondStamp* currentBond;
739 >  BendStamp* currentBend;
740 >  TorsionStamp* currentTorsion;
741  
742 <  lMolIndex = 0;
743 <  molIndex = 0;
744 <  index = 0;
635 <  for( i=0; i<n_components; i++ ){
742 >  bond_pair* theBonds;
743 >  bend_set* theBends;
744 >  torsion_set* theTorsions;
745  
746 <    for( j=0; j<components_nmol[i]; j++ ){
746 >  
747 >  //init the forceField paramters
748  
749 < #ifdef IS_MPI
640 <      if( mpiSim->getMyMolStart() <= molIndex &&
641 <          molIndex <= mpiSim->getMyMolEnd() ){
642 < #endif // is_mpi        
749 >  the_ff->readParams();
750  
751 <        molStart = index;
752 <        nMemb = comp_stamps[i]->getNAtoms();
753 <        for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){
754 <          
755 <          current_atom = comp_stamps[i]->getAtom( k );
756 <          if( current_atom->haveOrientation() ){
757 <            
758 <            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] );
751 >  
752 >  // init the atoms
753 >
754 >  double ux, uy, uz, u, uSqr;
755 >  
756 >  atomOffset = 0;
757 >  excludeOffset = 0;
758 >  for(i=0; i<simnfo->n_mol; i++){
759      
760 <    delete[] globalIndex;
760 >    stampID = the_molecules[i].getStampID();
761  
762 <    mpiSim->mpiRefresh();
763 < #endif //IS_MPI
764 <          
765 <  the_ff->initializeAtoms();
766 < }
762 >    info.nAtoms    = comp_stamps[stampID]->getNAtoms();
763 >    info.nBonds    = comp_stamps[stampID]->getNBonds();
764 >    info.nBends    = comp_stamps[stampID]->getNBends();
765 >    info.nTorsions = comp_stamps[stampID]->getNTorsions();
766 >    info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
767  
768 < void SimSetup::makeBonds( void ){
768 >    info.myAtoms = &the_atoms[atomOffset];
769 >    info.myExcludes = &the_excludes[excludeOffset];
770 >    info.myBonds = new Bond*[info.nBonds];
771 >    info.myBends = new Bend*[info.nBends];
772 >    info.myTorsions = new Torsion*[info.nTorsions];
773  
774 <  int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
775 <  bond_pair* the_bonds;
776 <  BondStamp* current_bond;
777 <
778 <  the_bonds = new bond_pair[tot_bonds];
779 <  index = 0;
780 <  offset = 0;
781 <  molIndex = 0;
782 <
783 <  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        
774 >    theBonds = new bond_pair[info.nBonds];
775 >    theBends = new bend_set[info.nBends];
776 >    theTorsions = new torsion_set[info.nTorsions];
777 >    
778 >    // make the Atoms
779 >    
780 >    for(j=0; j<info.nAtoms; j++){
781 >      
782 >      currentAtom = comp_stamps[stampID]->getAtom( j );
783 >      if( currentAtom->haveOrientation() ){
784          
785 <        for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){
786 <          
787 <          current_bond = comp_stamps[i]->getBond( k );
788 <          the_bonds[index].a = current_bond->getA() + offset;
789 <          the_bonds[index].b = current_bond->getB() + offset;
790 <
791 <          exI = the_bonds[index].a;
733 <          exJ = the_bonds[index].b;
734 <
735 <          // exclude_I must always be the smaller of the pair
736 <          if( exI > exJ ){
737 <            tempEx = exI;
738 <            exI = exJ;
739 <            exJ = tempEx;
740 <          }
741 <
742 <          
743 < #ifdef IS_MPI
744 <
745 <          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();
785 >        dAtom = new DirectionalAtom(j + atomOffset);
786 >        simnfo->n_oriented++;
787 >        info.myAtoms[j] = dAtom;
788 >        
789 >        ux = currentAtom->getOrntX();
790 >        uy = currentAtom->getOrntY();
791 >        uz = currentAtom->getOrntZ();
792          
793 < #ifdef IS_MPI
793 >        uSqr = (ux * ux) + (uy * uy) + (uz * uz);
794 >        
795 >        u = sqrt( uSqr );
796 >        ux = ux / u;
797 >        uy = uy / u;
798 >        uz = uz / u;
799 >        
800 >        dAtom->setSUx( ux );
801 >        dAtom->setSUy( uy );
802 >        dAtom->setSUz( uz );
803        }
804 < #endif //is_mpi
804 >      else{
805 >        info.myAtoms[j] = new GeneralAtom(j + atomOffset);
806 >      }
807 >      info.myAtoms[j]->setType( currentAtom->getType() );
808 >    
809 > #ifdef IS_MPI
810        
811 <      molIndex++;
812 <    }      
813 <  }
811 >      info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
812 >      
813 > #endif // is_mpi
814 >    }
815 >    
816 >    // make the bonds
817 >    for(j=0; j<info.nBonds; j++){
818 >      
819 >      currentBond = comp_stamps[stampID]->getBond( j );
820 >      theBonds[j].a = currentBond->getA() + atomOffset;
821 >      theBonds[j].b = currentBond->getB() + atomOffset;
822  
823 <  the_ff->initializeBonds( the_bonds );
824 < }
823 >      exI = theBonds[j].a;
824 >      exJ = theBonds[j].b;
825  
826 < void SimSetup::makeBends( void ){
827 <
828 <  int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
829 <  bend_set* the_bends;
830 <  BendStamp* current_bend;
831 <  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 <
826 >      // exclude_I must always be the smaller of the pair
827 >      if( exI > exJ ){
828 >        tempEx = exI;
829 >        exI = exJ;
830 >        exJ = tempEx;
831 >      }
832   #ifdef IS_MPI
833 <      if( mpiSim->getMyMolStart() <= molIndex &&
834 <          molIndex <= mpiSim->getMyMolEnd() ){
835 < #endif // is_mpi        
833 >      tempEx = exI;
834 >      exI = the_atoms[tempEx]->getGlobalIndex() + 1;
835 >      tempEx = exJ;
836 >      exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
837 >      
838 >      the_excludes[j+excludeOffset]->setPair( exI, exJ );
839 > #else  // isn't MPI
840  
841 <        for( k=0; k<comp_stamps[i]->getNBends(); k++ ){
841 >      the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
842 > #endif  //is_mpi
843 >    }
844 >    excludeOffset += info.nBonds;
845 >
846 >    //make the bends
847 >    for(j=0; j<info.nBends; j++){
848 >      
849 >      currentBend = comp_stamps[stampID]->getBend( j );
850 >      theBends[j].a = currentBend->getA() + atomOffset;
851 >      theBends[j].b = currentBend->getB() + atomOffset;
852 >      theBends[j].c = currentBend->getC() + atomOffset;
853            
854 <          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() ){
854 >      if( currentBend->haveExtras() ){
855              
856 <            extras = current_bend->getExtras();
857 <            current_extra = extras;
856 >        extras = currentBend->getExtras();
857 >        current_extra = extras;
858              
859 <            while( current_extra != NULL ){
860 <              if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
859 >        while( current_extra != NULL ){
860 >          if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
861                  
862 <                switch( current_extra->getType() ){
862 >            switch( current_extra->getType() ){
863 >              
864 >            case 0:
865 >              theBends[j].ghost =
866 >                current_extra->getInt() + atomOffset;
867 >              theBends[j].isGhost = 1;
868 >              break;
869                    
870 <                case 0:
871 <                  the_bends[index].ghost =
872 <                    current_extra->getInt() + offset;
873 <                  the_bends[index].isGhost = 1;
874 <                  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 <              }
870 >            case 1:
871 >              theBends[j].ghost =
872 >                (int)current_extra->getDouble() + atomOffset;
873 >              theBends[j].isGhost = 1;
874 >              break;
875                
876 <              else{
877 <                
878 <                sprintf( painCave.errMsg,
879 <                         "SimSetup Error: unhandled bend assignment:\n"
880 <                         "    -->%s in Bend[%d] in %s\n",
881 <                         current_extra->getlhs(),
882 <                         k, comp_stamps[i]->getID() );
883 <                painCave.isFatal = 1;
843 <                simError();
844 <              }
845 <              
846 <              current_extra = current_extra->getNext();
876 >            default:
877 >              sprintf( painCave.errMsg,
878 >                       "SimSetup Error: ghostVectorSource was neither a "
879 >                       "double nor an int.\n"
880 >                       "-->Bend[%d] in %s\n",
881 >                       j, comp_stamps[stampID]->getID() );
882 >              painCave.isFatal = 1;
883 >              simError();
884              }
885            }
886            
850 –          if( !the_bends[index].isGhost ){
851 –            
852 –            exI = the_bends[index].a;
853 –            exJ = the_bends[index].c;
854 –          }
887            else{
888              
889 <            exI = the_bends[index].a;
890 <            exJ = the_bends[index].b;
891 <          }
892 <          
893 <          // exclude_I must always be the smaller of the pair
894 <          if( exI > exJ ){
895 <            tempEx = exI;
864 <            exI = exJ;
865 <            exJ = tempEx;
889 >            sprintf( painCave.errMsg,
890 >                     "SimSetup Error: unhandled bend assignment:\n"
891 >                     "    -->%s in Bend[%d] in %s\n",
892 >                     current_extra->getlhs(),
893 >                     j, comp_stamps[stampID]->getID() );
894 >            painCave.isFatal = 1;
895 >            simError();
896            }
867 –
868 –
869 – #ifdef IS_MPI
870 –
871 –          the_excludes[(index + tot_bonds)*2] =    
872 –            the_atoms[exI]->getGlobalIndex() + 1;
873 –          the_excludes[(index + tot_bonds)*2 + 1] =
874 –            the_atoms[exJ]->getGlobalIndex() + 1;
897            
898 < #else  // isn't MPI
877 <          
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)
881 < #endif  //is_mpi
882 <          
883 <          
884 <          // increment the index and repeat;
885 <          index++;
898 >          current_extra = current_extra->getNext();
899          }
900 <        offset += comp_stamps[i]->getNAtoms();
900 >      }
901 >          
902 >      if( !theBends[j].isGhost ){
903 >            
904 >        exI = theBends[j].a;
905 >        exJ = theBends[j].c;
906 >      }
907 >      else{
908          
909 < #ifdef IS_MPI
909 >        exI = theBends[j].a;
910 >        exJ = theBends[j].b;
911        }
912 < #endif //is_mpi
912 >      
913 >      // exclude_I must always be the smaller of the pair
914 >      if( exI > exJ ){
915 >        tempEx = exI;
916 >        exI = exJ;
917 >        exJ = tempEx;
918 >      }
919 > #ifdef IS_MPI
920 >      tempEx = exI;
921 >      exI = the_atoms[tempEx]->getGlobalIndex() + 1;
922 >      tempEx = exJ;
923 >      exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
924 >      
925 >      the_excludes[j+excludeOffset]->setPair( exI, exJ );
926 > #else  // isn't MPI
927 >      the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
928 > #endif  //is_mpi
929 >    }
930 >    excludeOffset += info.nBends;
931  
932 <      molIndex++;
932 >    for(j=0; j<info.nTorsions; j++){
933 >      
934 >      currentTorsion = comp_stamps[stampID]->getTorsion( j );
935 >      theTorsions[j].a = currentTorsion->getA() + atomOffset;
936 >      theTorsions[j].b = currentTorsion->getB() + atomOffset;
937 >      theTorsions[j].c = currentTorsion->getC() + atomOffset;
938 >      theTorsions[j].d = currentTorsion->getD() + atomOffset;
939 >      
940 >      exI = theTorsions[j].a;
941 >      exJ = theTorsions[j].d;
942 >
943 >      // exclude_I must always be the smaller of the pair
944 >      if( exI > exJ ){
945 >        tempEx = exI;
946 >        exI = exJ;
947 >        exJ = tempEx;
948 >      }
949 > #ifdef IS_MPI
950 >      tempEx = exI;
951 >      exI = the_atoms[tempEx]->getGlobalIndex() + 1;
952 >      tempEx = exJ;
953 >      exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
954 >      
955 >      the_excludes[j+excludeOffset]->setPair( exI, exJ );
956 > #else  // isn't MPI
957 >      the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
958 > #endif  //is_mpi
959      }
960 <  }
960 >    excludeOffset += info.nTorsions;
961 >
962 >    
963 >    // send the arrays off to the forceField for init.
964 >
965 >    the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
966 >    the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
967 >    the_ff->initializeBends( info.nBends, info.myBends, theBends );
968 >    the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
969  
897 – #ifdef IS_MPI
898 –  sprintf( checkPointMsg,
899 –           "Successfully created the bends list.\n" );
900 –  MPIcheckPoint();
901 – #endif // is_mpi
902 –  
970  
971 <  the_ff->initializeBends( the_bends );
905 < }
971 >    the_molecules[i].initialize( info );
972  
907 – void SimSetup::makeTorsions( void ){
973  
974 <  int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
975 <  torsion_set* the_torsions;
976 <  TorsionStamp* current_torsion;
974 >    atomOffset += info.nAtoms;
975 >    delete[] theBonds;
976 >    delete[] theBends;
977 >    delete[] theTorsions;
978 >  }
979  
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 –
980   #ifdef IS_MPI
981 <      if( mpiSim->getMyMolStart() <= molIndex &&
982 <          molIndex <= mpiSim->getMyMolEnd() ){
983 < #endif // is_mpi        
981 >  sprintf( checkPointMsg, "all molecules initialized succesfully" );
982 >  MPIcheckPoint();
983 > #endif // is_mpi
984  
985 <      for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){
985 >  // clean up the forcefield
986 >  the_ff->calcRcut();
987 >  the_ff->cleanMe();
988  
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 );
989   }
990  
991   void SimSetup::initFromBass( void ){

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