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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 466 by gezelter, Mon Apr 7 14:30:36 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 +  } else if ( !strcasecmp( ensemble, "NVT") ) {
92 +    the_extendedsystem = new ExtendedSystem( simnfo );
93 +    the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
94 +  } else if ( !strcasecmp( ensemble, "NVE") ) {
95 +  } else {
96 +    sprintf( painCave.errMsg,
97 +             "SimSetup Warning. Unrecognized Ensemble -> %s, "
98 +             "reverting to NVE for this simulation.\n",
99 +             ensemble );
100 +    painCave.isFatal = 0;
101 +    simError();
102 +    strcpy( ensemble, "NVE" );
103 +  }  
104    strcpy( simnfo->ensemble, ensemble );
105  
106    strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
107    simnfo->usePBC = the_globals->getPBC();
108            
109 <
110 <
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();
94 <  else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
109 >  if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF();
110 >  else if( !strcasecmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
111    else{
112      sprintf( painCave.errMsg,
113               "SimSetup Error. Unrecognized force field -> %s\n",
# Line 242 | Line 258 | void SimSetup::createSim( void ){
258  
259    globalIndex = mpiSim->divideLabor();
260  
245 –
246 –
261    // set up the local variables
262    
263    int localMol, allMol;
264    int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
265 +
266 +  int* mol2proc = mpiSim->getMolToProcMap();
267 +  int* molCompType = mpiSim->getMolComponentType();
268    
269    allMol = 0;
270    localMol = 0;
# Line 259 | Line 276 | void SimSetup::createSim( void ){
276  
277      for( j=0; j<components_nmol[i]; j++ ){
278        
279 <      if( mpiSim->getMyMolStart() <= allMol &&
263 <          allMol <= mpiSim->getMyMolEnd() ){
279 >      if( mol2proc[j] == worldRank ){
280          
281          local_atoms +=    comp_stamps[i]->getNAtoms();
282          local_bonds +=    comp_stamps[i]->getNBonds();
# Line 279 | Line 295 | void SimSetup::createSim( void ){
295    if( local_atoms != simnfo->n_atoms ){
296      sprintf( painCave.errMsg,
297               "SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
298 <             " localAtom (%d) are note equal.\n",
298 >             " localAtom (%d) are not equal.\n",
299               simnfo->n_atoms,
300               local_atoms );
301      painCave.isFatal = 1;
# Line 304 | Line 320 | void SimSetup::createSim( void ){
320    Atom::createArrays(simnfo->n_atoms);
321    the_atoms = new Atom*[simnfo->n_atoms];
322    the_molecules = new Molecule[simnfo->n_mol];
323 +  int molIndex;
324  
325 +  // initialize the molecule's stampID's
326  
327 <  if( simnfo->n_SRI ){
328 <    the_sris = new SRI*[simnfo->n_SRI];
329 <    the_excludes = new int[2 * simnfo->n_SRI];
327 > #ifdef IS_MPI
328 >  
329 >
330 >  molIndex = 0;
331 >  for(i=0; i<mpiSim->getTotNmol(); i++){
332 >    
333 >    if(mol2proc[i] == worldRank ){
334 >      the_molecules[molIndex].setStampID( molCompType[i] );
335 >      the_molecules[molIndex].setMyIndex( molIndex );
336 >      molIndex++;
337 >    }
338 >  }
339 >
340 > #else // is_mpi
341 >  
342 >  molIndex = 0;
343 >  for(i=0; i<n_components; i++){
344 >    for(j=0; j<components_nmol[i]; j++ ){
345 >      the_molecules[molIndex].setStampID( i );
346 >      the_molecules[molIndex].setMyIndex( molIndex );
347 >      molIndex++;
348 >    }
349 >  }
350 >    
351 >
352 > #endif // is_mpi
353 >
354 >
355 >  if( simnfo->n_SRI ){
356 >    
357 >    Exclude::createArray(simnfo->n_SRI);
358 >    the_excludes = new Exclude*[simnfo->n_SRI];
359 >    for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
360      simnfo->globalExcludes = new int;
361 <    simnfo->n_exclude = tot_SRI;
361 >    simnfo->n_exclude = simnfo->n_SRI;
362    }
363    else{
364      
365 <    the_excludes = new int[2];
366 <    the_excludes[0] = 0;
367 <    the_excludes[1] = 0;
365 >    Exclude::createArray( 1 );
366 >    the_excludes = new Exclude*;
367 >    the_excludes[0] = new Exclude(0);
368 >    the_excludes[0]->setPair( 0,0 );
369      simnfo->globalExcludes = new int;
370      simnfo->globalExcludes[0] = 0;
371 <
323 <    simnfo->n_exclude = 1;
371 >    simnfo->n_exclude = 0;
372    }
373  
374    // set the arrays into the SimInfo object
375  
376    simnfo->atoms = the_atoms;
377 <  simnfo->sr_interactions = the_sris;
377 >  simnfo->molecules = the_molecules;
378    simnfo->nGlobalExcludes = 0;
379    simnfo->excludes = the_excludes;
380  
381  
382    // get some of the tricky things that may still be in the globals
383  
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
384    
385    if( the_globals->haveBox() ){
386      simnfo->box_x = the_globals->getBox();
# Line 407 | Line 431 | void SimSetup::createSim( void ){
431  
432    the_ff->setSimInfo( simnfo );
433  
434 <  makeAtoms();
434 >  makeMolecules();
435    simnfo->identArray = new int[simnfo->n_atoms];
436    for(i=0; i<simnfo->n_atoms; i++){
437      simnfo->identArray[i] = the_atoms[i]->getIdent();
438    }
439    
440 <  if( tot_bonds ){
441 <    makeBonds();
442 <  }
440 >  if (the_globals->getUseRF() ) {
441 >    simnfo->useReactionField = 1;
442 >  
443 >    if( !the_globals->haveECR() ){
444 >      sprintf( painCave.errMsg,
445 >               "SimSetup Warning: using default value of 1/2 the smallest "
446 >               "box length for the electrostaticCutoffRadius.\n"
447 >               "I hope you have a very fast processor!\n");
448 >      painCave.isFatal = 0;
449 >      simError();
450 >      double smallest;
451 >      smallest = simnfo->box_x;
452 >      if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
453 >      if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
454 >      simnfo->ecr = 0.5 * smallest;
455 >    } else {
456 >      simnfo->ecr        = the_globals->getECR();
457 >    }
458  
459 <  if( tot_bends ){
460 <    makeBends();
461 <  }
462 <
463 <  if( tot_torsions ){
464 <    makeTorsions();
465 <  }
466 <
467 <
468 <
469 <
459 >    if( !the_globals->haveEST() ){
460 >      sprintf( painCave.errMsg,
461 >               "SimSetup Warning: using default value of 0.05 * the "
462 >               "electrostaticCutoffRadius for the electrostaticSkinThickness\n"
463 >               );
464 >      painCave.isFatal = 0;
465 >      simError();
466 >      simnfo->est = 0.05 * simnfo->ecr;
467 >    } else {
468 >      simnfo->est        = the_globals->getEST();
469 >    }
470 >    
471 >    if(!the_globals->haveDielectric() ){
472 >      sprintf( painCave.errMsg,
473 >               "SimSetup Error: You are trying to use Reaction Field without"
474 >               "setting a dielectric constant!\n"
475 >               );
476 >      painCave.isFatal = 1;
477 >      simError();
478 >    }
479 >    simnfo->dielectric = the_globals->getDielectric();  
480 >  } else {
481 >    if (simnfo->n_dipoles) {
482 >      
483 >      if( !the_globals->haveECR() ){
484 >        sprintf( painCave.errMsg,
485 >                 "SimSetup Warning: using default value of 1/2 the smallest"
486 >                 "box length for the electrostaticCutoffRadius.\n"
487 >                 "I hope you have a very fast processor!\n");
488 >        painCave.isFatal = 0;
489 >        simError();
490 >        double smallest;
491 >        smallest = simnfo->box_x;
492 >        if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
493 >        if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
494 >        simnfo->ecr = 0.5 * smallest;
495 >      } else {
496 >        simnfo->ecr        = the_globals->getECR();
497 >      }
498 >      
499 >      if( !the_globals->haveEST() ){
500 >        sprintf( painCave.errMsg,
501 >                 "SimSetup Warning: using default value of 5% of the"
502 >                 "electrostaticCutoffRadius for the "
503 >                 "electrostaticSkinThickness\n"
504 >                 );
505 >        painCave.isFatal = 0;
506 >        simError();
507 >        simnfo->est = 0.05 * simnfo->ecr;
508 >      } else {
509 >        simnfo->est        = the_globals->getEST();
510 >      }
511 >    }
512 >  }  
513  
514 + #ifdef IS_MPI
515 +  strcpy( checkPointMsg, "electrostatic parameters check out" );
516 +  MPIcheckPoint();
517 + #endif // is_mpi
518  
519   if( the_globals->haveInitialConfig() ){
520  
# Line 587 | Line 673 | void SimSetup::createSim( void ){
673  
674   //   new AllLong( simnfo );
675  
676 <  if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff );
677 <  if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff );
678 <  if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff );
679 <  if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff );
676 >  if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic(simnfo,
677 >                                                           the_ff,
678 >                                                           the_extendedsystem);
679 >  if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo,
680 >                                                 the_ff,
681 >                                                 the_extendedsystem );
682  
683 + #ifdef IS_MPI
684 +  mpiSim->mpiRefresh();
685 + #endif
686  
596 –
687    // initialize the Fortran
688 <  
688 >
689 >
690    simnfo->refreshSim();
691    
692    if( !strcmp( simnfo->mixingRule, "standard") ){
# Line 620 | Line 711 | void SimSetup::createSim( void ){
711   #endif // is_mpi
712   }
713  
623 – void SimSetup::makeAtoms( void ){
714  
715 <  int i, j, k, index;
626 <  double ux, uy, uz, uSqr, u;
627 <  AtomStamp* current_atom;
715 > void SimSetup::makeMolecules( void ){
716  
717 +  int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
718 +  molInit info;
719    DirectionalAtom* dAtom;
720 <  int molIndex, molStart, molEnd, nMemb, lMolIndex;
720 >  LinkedAssign* extras;
721 >  LinkedAssign* current_extra;
722 >  AtomStamp* currentAtom;
723 >  BondStamp* currentBond;
724 >  BendStamp* currentBend;
725 >  TorsionStamp* currentTorsion;
726  
727 <  lMolIndex = 0;
728 <  molIndex = 0;
729 <  index = 0;
635 <  for( i=0; i<n_components; i++ ){
727 >  bond_pair* theBonds;
728 >  bend_set* theBends;
729 >  torsion_set* theTorsions;
730  
731 <    for( j=0; j<components_nmol[i]; j++ ){
731 >  
732 >  //init the forceField paramters
733  
734 < #ifdef IS_MPI
640 <      if( mpiSim->getMyMolStart() <= molIndex &&
641 <          molIndex <= mpiSim->getMyMolEnd() ){
642 < #endif // is_mpi        
734 >  the_ff->readParams();
735  
736 <        molStart = index;
737 <        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++;
736 >  
737 >  // init the atoms
738  
739 < #ifdef IS_MPI
740 <      }
741 < #endif //is_mpi
742 <      
743 <      molIndex++;
692 <    }
693 <  }
694 <
695 < #ifdef IS_MPI
696 <    for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] );
739 >  double ux, uy, uz, u, uSqr;
740 >  
741 >  atomOffset = 0;
742 >  excludeOffset = 0;
743 >  for(i=0; i<simnfo->n_mol; i++){
744      
745 <    delete[] globalIndex;
745 >    stampID = the_molecules[i].getStampID();
746  
747 <    mpiSim->mpiRefresh();
748 < #endif //IS_MPI
749 <          
750 <  the_ff->initializeAtoms();
751 < }
747 >    info.nAtoms    = comp_stamps[stampID]->getNAtoms();
748 >    info.nBonds    = comp_stamps[stampID]->getNBonds();
749 >    info.nBends    = comp_stamps[stampID]->getNBends();
750 >    info.nTorsions = comp_stamps[stampID]->getNTorsions();
751 >    info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
752  
753 < void SimSetup::makeBonds( void ){
753 >    info.myAtoms = &the_atoms[atomOffset];
754 >    info.myExcludes = &the_excludes[excludeOffset];
755 >    info.myBonds = new Bond*[info.nBonds];
756 >    info.myBends = new Bend*[info.nBends];
757 >    info.myTorsions = new Torsion*[info.nTorsions];
758  
759 <  int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
760 <  bond_pair* the_bonds;
761 <  BondStamp* current_bond;
762 <
763 <  the_bonds = new bond_pair[tot_bonds];
764 <  index = 0;
765 <  offset = 0;
766 <  molIndex = 0;
767 <
768 <  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        
759 >    theBonds = new bond_pair[info.nBonds];
760 >    theBends = new bend_set[info.nBends];
761 >    theTorsions = new torsion_set[info.nTorsions];
762 >    
763 >    // make the Atoms
764 >    
765 >    for(j=0; j<info.nAtoms; j++){
766 >      
767 >      currentAtom = comp_stamps[stampID]->getAtom( j );
768 >      if( currentAtom->haveOrientation() ){
769          
770 <        for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){
771 <          
772 <          current_bond = comp_stamps[i]->getBond( k );
773 <          the_bonds[index].a = current_bond->getA() + offset;
774 <          the_bonds[index].b = current_bond->getB() + offset;
775 <
776 <          exI = the_bonds[index].a;
777 <          exJ = the_bonds[index].b;
778 <
779 <          // exclude_I must always be the smaller of the pair
780 <          if( exI > exJ ){
781 <            tempEx = exI;
782 <            exI = exJ;
783 <            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();
770 >        dAtom = new DirectionalAtom(j + atomOffset);
771 >        simnfo->n_oriented++;
772 >        info.myAtoms[j] = dAtom;
773 >        
774 >        ux = currentAtom->getOrntX();
775 >        uy = currentAtom->getOrntY();
776 >        uz = currentAtom->getOrntZ();
777 >        
778 >        uSqr = (ux * ux) + (uy * uy) + (uz * uz);
779 >        
780 >        u = sqrt( uSqr );
781 >        ux = ux / u;
782 >        uy = uy / u;
783 >        uz = uz / u;
784          
785 < #ifdef IS_MPI
785 >        dAtom->setSUx( ux );
786 >        dAtom->setSUy( uy );
787 >        dAtom->setSUz( uz );
788        }
789 < #endif //is_mpi
789 >      else{
790 >        info.myAtoms[j] = new GeneralAtom(j + atomOffset);
791 >      }
792 >      info.myAtoms[j]->setType( currentAtom->getType() );
793 >    
794 > #ifdef IS_MPI
795        
796 <      molIndex++;
797 <    }      
798 <  }
796 >      info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
797 >      
798 > #endif // is_mpi
799 >    }
800 >    
801 >    // make the bonds
802 >    for(j=0; j<info.nBonds; j++){
803 >      
804 >      currentBond = comp_stamps[stampID]->getBond( j );
805 >      theBonds[j].a = currentBond->getA() + atomOffset;
806 >      theBonds[j].b = currentBond->getB() + atomOffset;
807  
808 <  the_ff->initializeBonds( the_bonds );
809 < }
808 >      exI = theBonds[j].a;
809 >      exJ = theBonds[j].b;
810  
811 < void SimSetup::makeBends( void ){
812 <
813 <  int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
814 <  bend_set* the_bends;
815 <  BendStamp* current_bend;
816 <  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 <
811 >      // exclude_I must always be the smaller of the pair
812 >      if( exI > exJ ){
813 >        tempEx = exI;
814 >        exI = exJ;
815 >        exJ = tempEx;
816 >      }
817   #ifdef IS_MPI
818 <      if( mpiSim->getMyMolStart() <= molIndex &&
819 <          molIndex <= mpiSim->getMyMolEnd() ){
820 < #endif // is_mpi        
818 >      tempEx = exI;
819 >      exI = the_atoms[tempEx]->getGlobalIndex() + 1;
820 >      tempEx = exJ;
821 >      exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
822 >      
823 >      the_excludes[j+excludeOffset]->setPair( exI, exJ );
824 > #else  // isn't MPI
825  
826 <        for( k=0; k<comp_stamps[i]->getNBends(); k++ ){
826 >      the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
827 > #endif  //is_mpi
828 >    }
829 >    excludeOffset += info.nBonds;
830 >
831 >    //make the bends
832 >    for(j=0; j<info.nBends; j++){
833 >      
834 >      currentBend = comp_stamps[stampID]->getBend( j );
835 >      theBends[j].a = currentBend->getA() + atomOffset;
836 >      theBends[j].b = currentBend->getB() + atomOffset;
837 >      theBends[j].c = currentBend->getC() + atomOffset;
838            
839 <          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() ){
839 >      if( currentBend->haveExtras() ){
840              
841 <            extras = current_bend->getExtras();
842 <            current_extra = extras;
841 >        extras = currentBend->getExtras();
842 >        current_extra = extras;
843              
844 <            while( current_extra != NULL ){
845 <              if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
844 >        while( current_extra != NULL ){
845 >          if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
846                  
847 <                switch( current_extra->getType() ){
847 >            switch( current_extra->getType() ){
848 >              
849 >            case 0:
850 >              theBends[j].ghost =
851 >                current_extra->getInt() + atomOffset;
852 >              theBends[j].isGhost = 1;
853 >              break;
854                    
855 <                case 0:
856 <                  the_bends[index].ghost =
857 <                    current_extra->getInt() + offset;
858 <                  the_bends[index].isGhost = 1;
859 <                  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 <              }
855 >            case 1:
856 >              theBends[j].ghost =
857 >                (int)current_extra->getDouble() + atomOffset;
858 >              theBends[j].isGhost = 1;
859 >              break;
860                
861 <              else{
862 <                
863 <                sprintf( painCave.errMsg,
864 <                         "SimSetup Error: unhandled bend assignment:\n"
865 <                         "    -->%s in Bend[%d] in %s\n",
866 <                         current_extra->getlhs(),
867 <                         k, comp_stamps[i]->getID() );
868 <                painCave.isFatal = 1;
843 <                simError();
844 <              }
845 <              
846 <              current_extra = current_extra->getNext();
861 >            default:
862 >              sprintf( painCave.errMsg,
863 >                       "SimSetup Error: ghostVectorSource was neither a "
864 >                       "double nor an int.\n"
865 >                       "-->Bend[%d] in %s\n",
866 >                       j, comp_stamps[stampID]->getID() );
867 >              painCave.isFatal = 1;
868 >              simError();
869              }
870            }
871            
850 –          if( !the_bends[index].isGhost ){
851 –            
852 –            exI = the_bends[index].a;
853 –            exJ = the_bends[index].c;
854 –          }
872            else{
873              
874 <            exI = the_bends[index].a;
875 <            exJ = the_bends[index].b;
876 <          }
877 <          
878 <          // exclude_I must always be the smaller of the pair
879 <          if( exI > exJ ){
880 <            tempEx = exI;
864 <            exI = exJ;
865 <            exJ = tempEx;
874 >            sprintf( painCave.errMsg,
875 >                     "SimSetup Error: unhandled bend assignment:\n"
876 >                     "    -->%s in Bend[%d] in %s\n",
877 >                     current_extra->getlhs(),
878 >                     j, comp_stamps[stampID]->getID() );
879 >            painCave.isFatal = 1;
880 >            simError();
881            }
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;
882            
883 < #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++;
883 >          current_extra = current_extra->getNext();
884          }
885 <        offset += comp_stamps[i]->getNAtoms();
885 >      }
886 >          
887 >      if( !theBends[j].isGhost ){
888 >            
889 >        exI = theBends[j].a;
890 >        exJ = theBends[j].c;
891 >      }
892 >      else{
893          
894 < #ifdef IS_MPI
894 >        exI = theBends[j].a;
895 >        exJ = theBends[j].b;
896        }
897 < #endif //is_mpi
897 >      
898 >      // exclude_I must always be the smaller of the pair
899 >      if( exI > exJ ){
900 >        tempEx = exI;
901 >        exI = exJ;
902 >        exJ = tempEx;
903 >      }
904 > #ifdef IS_MPI
905 >      tempEx = exI;
906 >      exI = the_atoms[tempEx]->getGlobalIndex() + 1;
907 >      tempEx = exJ;
908 >      exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
909 >      
910 >      the_excludes[j+excludeOffset]->setPair( exI, exJ );
911 > #else  // isn't MPI
912 >      the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
913 > #endif  //is_mpi
914 >    }
915 >    excludeOffset += info.nBends;
916  
917 <      molIndex++;
917 >    for(j=0; j<info.nTorsions; j++){
918 >      
919 >      currentTorsion = comp_stamps[stampID]->getTorsion( j );
920 >      theTorsions[j].a = currentTorsion->getA() + atomOffset;
921 >      theTorsions[j].b = currentTorsion->getB() + atomOffset;
922 >      theTorsions[j].c = currentTorsion->getC() + atomOffset;
923 >      theTorsions[j].d = currentTorsion->getD() + atomOffset;
924 >      
925 >      exI = theTorsions[j].a;
926 >      exJ = theTorsions[j].d;
927 >
928 >      // exclude_I must always be the smaller of the pair
929 >      if( exI > exJ ){
930 >        tempEx = exI;
931 >        exI = exJ;
932 >        exJ = tempEx;
933 >      }
934 > #ifdef IS_MPI
935 >      tempEx = exI;
936 >      exI = the_atoms[tempEx]->getGlobalIndex() + 1;
937 >      tempEx = exJ;
938 >      exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
939 >      
940 >      the_excludes[j+excludeOffset]->setPair( exI, exJ );
941 > #else  // isn't MPI
942 >      the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
943 > #endif  //is_mpi
944      }
945 <  }
945 >    excludeOffset += info.nTorsions;
946 >
947 >    
948 >    // send the arrays off to the forceField for init.
949 >
950 >    the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
951 >    the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
952 >    the_ff->initializeBends( info.nBends, info.myBends, theBends );
953 >    the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
954  
897 – #ifdef IS_MPI
898 –  sprintf( checkPointMsg,
899 –           "Successfully created the bends list.\n" );
900 –  MPIcheckPoint();
901 – #endif // is_mpi
902 –  
955  
956 <  the_ff->initializeBends( the_bends );
905 < }
956 >    the_molecules[i].initialize( info );
957  
907 – void SimSetup::makeTorsions( void ){
958  
959 <  int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
960 <  torsion_set* the_torsions;
961 <  TorsionStamp* current_torsion;
959 >    atomOffset += info.nAtoms;
960 >    delete[] theBonds;
961 >    delete[] theBends;
962 >    delete[] theTorsions;
963 >  }
964  
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 –
965   #ifdef IS_MPI
966 <      if( mpiSim->getMyMolStart() <= molIndex &&
967 <          molIndex <= mpiSim->getMyMolEnd() ){
968 < #endif // is_mpi        
966 >  sprintf( checkPointMsg, "all molecules initialized succesfully" );
967 >  MPIcheckPoint();
968 > #endif // is_mpi
969  
970 <      for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){
970 >  // clean up the forcefield
971 >  the_ff->calcRcut();
972 >  the_ff->cleanMe();
973  
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 );
974   }
975  
976   void SimSetup::initFromBass( void ){

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