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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 483 by gezelter, Wed Apr 9 04:06:43 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 +    if (the_globals->haveTargetPressure())
91 +      the_extendedsystem->setTargetPressure(the_globals->getTargetPressure());
92 +    else {
93 +      sprintf( painCave.errMsg,
94 +               "SimSetup error: If you use the constant pressure\n"
95 +               "    ensemble, you must set targetPressure.\n"
96 +               "    This was found in the BASS file.\n");
97 +      painCave.isFatal = 1;
98 +      simError();
99 +    }
100 +
101 +    if (the_globals->haveTauThermostat())
102 +      the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
103 +    else if (the_globals->haveQmass())
104 +      the_extendedsystem->setQmass(the_globals->getQmass());
105 +    else {
106 +      sprintf( painCave.errMsg,
107 +               "SimSetup error: If you use one of the constant temperature\n"
108 +               "    ensembles, you must set either tauThermostat or qMass.\n"
109 +               "    Neither of these was found in the BASS file.\n");
110 +      painCave.isFatal = 1;
111 +      simError();
112 +    }
113 +
114 +    if (the_globals->haveTauBarostat())
115 +      the_extendedsystem->setTauBarostat(the_globals->getTauBarostat());
116 +    else {
117 +      sprintf( painCave.errMsg,
118 +               "SimSetup error: If you use the constant pressure\n"
119 +               "    ensemble, you must set tauBarostat.\n"
120 +               "    This was found in the BASS file.\n");
121 +      painCave.isFatal = 1;
122 +      simError();
123 +    }
124 +
125 +  } else if ( !strcasecmp( ensemble, "NVT") ) {
126 +    the_extendedsystem = new ExtendedSystem( simnfo );
127 +    the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
128 +
129 +    if (the_globals->haveTauThermostat())
130 +      the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
131 +    else if (the_globals->haveQmass())
132 +      the_extendedsystem->setQmass(the_globals->getQmass());
133 +    else {
134 +      sprintf( painCave.errMsg,
135 +               "SimSetup error: If you use one of the constant temperature\n"
136 +               "    ensembles, you must set either tauThermostat or qMass.\n"
137 +               "    Neither of these was found in the BASS file.\n");
138 +      painCave.isFatal = 1;
139 +      simError();
140 +    }
141 +
142 +  } else if ( !strcasecmp( ensemble, "NVE") ) {
143 +  } else {
144 +    sprintf( painCave.errMsg,
145 +             "SimSetup Warning. Unrecognized Ensemble -> %s, "
146 +             "reverting to NVE for this simulation.\n",
147 +             ensemble );
148 +    painCave.isFatal = 0;
149 +    simError();
150 +    strcpy( ensemble, "NVE" );
151 +  }  
152    strcpy( simnfo->ensemble, ensemble );
153  
154    strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
155    simnfo->usePBC = the_globals->getPBC();
156            
157 <
158 <
159 <  if( !strcmp( force_field, "TraPPE" ) ) the_ff = new TraPPEFF();
160 <  else if( !strcmp( force_field, "DipoleTest" ) ) the_ff = new DipoleTestFF();
161 <  else if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF();
162 <  else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
157 >  int usesDipoles = 0;
158 >  if( !strcmp( force_field, "TraPPE_Ex" ) ){
159 >    the_ff = new TraPPE_ExFF();
160 >    usesDipoles = 1;
161 >  }
162 >  else if( !strcasecmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
163    else{
164      sprintf( painCave.errMsg,
165               "SimSetup Error. Unrecognized force field -> %s\n",
# Line 242 | Line 310 | void SimSetup::createSim( void ){
310  
311    globalIndex = mpiSim->divideLabor();
312  
245 –
246 –
313    // set up the local variables
314    
315    int localMol, allMol;
316    int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
317 +
318 +  int* mol2proc = mpiSim->getMolToProcMap();
319 +  int* molCompType = mpiSim->getMolComponentType();
320    
321    allMol = 0;
322    localMol = 0;
# Line 259 | Line 328 | void SimSetup::createSim( void ){
328  
329      for( j=0; j<components_nmol[i]; j++ ){
330        
331 <      if( mpiSim->getMyMolStart() <= allMol &&
263 <          allMol <= mpiSim->getMyMolEnd() ){
331 >      if( mol2proc[j] == worldRank ){
332          
333          local_atoms +=    comp_stamps[i]->getNAtoms();
334          local_bonds +=    comp_stamps[i]->getNBonds();
# Line 279 | Line 347 | void SimSetup::createSim( void ){
347    if( local_atoms != simnfo->n_atoms ){
348      sprintf( painCave.errMsg,
349               "SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
350 <             " localAtom (%d) are note equal.\n",
350 >             " localAtom (%d) are not equal.\n",
351               simnfo->n_atoms,
352               local_atoms );
353      painCave.isFatal = 1;
# Line 304 | Line 372 | void SimSetup::createSim( void ){
372    Atom::createArrays(simnfo->n_atoms);
373    the_atoms = new Atom*[simnfo->n_atoms];
374    the_molecules = new Molecule[simnfo->n_mol];
375 +  int molIndex;
376  
377 +  // initialize the molecule's stampID's
378  
379 <  if( simnfo->n_SRI ){
380 <    the_sris = new SRI*[simnfo->n_SRI];
381 <    the_excludes = new int[2 * simnfo->n_SRI];
379 > #ifdef IS_MPI
380 >  
381 >
382 >  molIndex = 0;
383 >  for(i=0; i<mpiSim->getTotNmol(); i++){
384 >    
385 >    if(mol2proc[i] == worldRank ){
386 >      the_molecules[molIndex].setStampID( molCompType[i] );
387 >      the_molecules[molIndex].setMyIndex( molIndex );
388 >      molIndex++;
389 >    }
390 >  }
391 >
392 > #else // is_mpi
393 >  
394 >  molIndex = 0;
395 >  for(i=0; i<n_components; i++){
396 >    for(j=0; j<components_nmol[i]; j++ ){
397 >      the_molecules[molIndex].setStampID( i );
398 >      the_molecules[molIndex].setMyIndex( molIndex );
399 >      molIndex++;
400 >    }
401 >  }
402 >    
403 >
404 > #endif // is_mpi
405 >
406 >
407 >  if( simnfo->n_SRI ){
408 >    
409 >    Exclude::createArray(simnfo->n_SRI);
410 >    the_excludes = new Exclude*[simnfo->n_SRI];
411 >    for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
412      simnfo->globalExcludes = new int;
413 <    simnfo->n_exclude = tot_SRI;
413 >    simnfo->n_exclude = simnfo->n_SRI;
414    }
415    else{
416      
417 <    the_excludes = new int[2];
418 <    the_excludes[0] = 0;
419 <    the_excludes[1] = 0;
417 >    Exclude::createArray( 1 );
418 >    the_excludes = new Exclude*;
419 >    the_excludes[0] = new Exclude(0);
420 >    the_excludes[0]->setPair( 0,0 );
421      simnfo->globalExcludes = new int;
422      simnfo->globalExcludes[0] = 0;
423 <
323 <    simnfo->n_exclude = 1;
423 >    simnfo->n_exclude = 0;
424    }
425  
426    // set the arrays into the SimInfo object
427  
428    simnfo->atoms = the_atoms;
429 <  simnfo->sr_interactions = the_sris;
429 >  simnfo->molecules = the_molecules;
430    simnfo->nGlobalExcludes = 0;
431    simnfo->excludes = the_excludes;
432  
433  
434    // get some of the tricky things that may still be in the globals
435  
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
436    
437    if( the_globals->haveBox() ){
438      simnfo->box_x = the_globals->getBox();
# Line 407 | Line 483 | void SimSetup::createSim( void ){
483  
484    the_ff->setSimInfo( simnfo );
485  
486 <  makeAtoms();
486 >  makeMolecules();
487    simnfo->identArray = new int[simnfo->n_atoms];
488 +  simnfo->molMembershipArray = new int[simnfo->n_atoms];
489    for(i=0; i<simnfo->n_atoms; i++){
490      simnfo->identArray[i] = the_atoms[i]->getIdent();
491    }
492 <  
493 <  if( tot_bonds ){
417 <    makeBonds();
492 >  for(i=0; i< simnfo->n_mol; i++) {
493 >    the_molecules[i].atomicRollCall(simnfo->molMembershipArray);
494    }
495 +  
496 +  if (the_globals->getUseRF() ) {
497 +    simnfo->useReactionField = 1;
498 +  
499 +    if( !the_globals->haveECR() ){
500 +      sprintf( painCave.errMsg,
501 +               "SimSetup Warning: using default value of 1/2 the smallest "
502 +               "box length for the electrostaticCutoffRadius.\n"
503 +               "I hope you have a very fast processor!\n");
504 +      painCave.isFatal = 0;
505 +      simError();
506 +      double smallest;
507 +      smallest = simnfo->box_x;
508 +      if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
509 +      if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
510 +      simnfo->ecr = 0.5 * smallest;
511 +    } else {
512 +      simnfo->ecr        = the_globals->getECR();
513 +    }
514  
515 <  if( tot_bends ){
516 <    makeBends();
517 <  }
518 <
519 <  if( tot_torsions ){
520 <    makeTorsions();
521 <  }
522 <
523 <
524 <
525 <
515 >    if( !the_globals->haveEST() ){
516 >      sprintf( painCave.errMsg,
517 >               "SimSetup Warning: using default value of 0.05 * the "
518 >               "electrostaticCutoffRadius for the electrostaticSkinThickness\n"
519 >               );
520 >      painCave.isFatal = 0;
521 >      simError();
522 >      simnfo->est = 0.05 * simnfo->ecr;
523 >    } else {
524 >      simnfo->est        = the_globals->getEST();
525 >    }
526 >    
527 >    if(!the_globals->haveDielectric() ){
528 >      sprintf( painCave.errMsg,
529 >               "SimSetup Error: You are trying to use Reaction Field without"
530 >               "setting a dielectric constant!\n"
531 >               );
532 >      painCave.isFatal = 1;
533 >      simError();
534 >    }
535 >    simnfo->dielectric = the_globals->getDielectric();  
536 >  } else {
537 >    if (usesDipoles) {
538 >      
539 >      if( !the_globals->haveECR() ){
540 >        sprintf( painCave.errMsg,
541 >                 "SimSetup Warning: using default value of 1/2 the smallest "
542 >                 "box length for the electrostaticCutoffRadius.\n"
543 >                 "I hope you have a very fast processor!\n");
544 >        painCave.isFatal = 0;
545 >        simError();
546 >        double smallest;
547 >        smallest = simnfo->box_x;
548 >        if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
549 >        if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
550 >        simnfo->ecr = 0.5 * smallest;
551 >      } else {
552 >        simnfo->ecr        = the_globals->getECR();
553 >      }
554 >      
555 >      if( !the_globals->haveEST() ){
556 >        sprintf( painCave.errMsg,
557 >                 "SimSetup Warning: using default value of 5%% of the "
558 >                 "electrostaticCutoffRadius for the "
559 >                 "electrostaticSkinThickness\n"
560 >                 );
561 >        painCave.isFatal = 0;
562 >        simError();
563 >        simnfo->est = 0.05 * simnfo->ecr;
564 >      } else {
565 >        simnfo->est        = the_globals->getEST();
566 >      }
567 >    }
568 >  }  
569  
570 + #ifdef IS_MPI
571 +  strcpy( checkPointMsg, "electrostatic parameters check out" );
572 +  MPIcheckPoint();
573 + #endif // is_mpi
574  
575   if( the_globals->haveInitialConfig() ){
576  
# Line 587 | Line 729 | void SimSetup::createSim( void ){
729  
730   //   new AllLong( simnfo );
731  
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 );
732  
733 +  if( !strcmp( force_field, "TraPPE_Ex" ) ){
734 +    new Symplectic(simnfo, the_ff, the_extendedsystem);
735 +  }
736 +  else if( !strcmp( force_field, "LJ" ) ){
737 +    new Verlet( *simnfo, the_ff, the_extendedsystem );
738 +  }
739 +  else {
740 +    std::cerr << "I'm a bug.\n";
741 +    fprintf( stderr, "Ima bug. stderr %s\n", force_field);
742 +  }
743 + #ifdef IS_MPI
744 +  mpiSim->mpiRefresh();
745 + #endif
746  
596 –
747    // initialize the Fortran
748 <  
748 >
749 >
750    simnfo->refreshSim();
751    
752    if( !strcmp( simnfo->mixingRule, "standard") ){
# Line 620 | Line 771 | void SimSetup::makeAtoms( void ){
771   #endif // is_mpi
772   }
773  
623 – void SimSetup::makeAtoms( void ){
774  
775 <  int i, j, k, index;
626 <  double ux, uy, uz, uSqr, u;
627 <  AtomStamp* current_atom;
775 > void SimSetup::makeMolecules( void ){
776  
777 +  int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
778 +  molInit info;
779    DirectionalAtom* dAtom;
780 <  int molIndex, molStart, molEnd, nMemb, lMolIndex;
780 >  LinkedAssign* extras;
781 >  LinkedAssign* current_extra;
782 >  AtomStamp* currentAtom;
783 >  BondStamp* currentBond;
784 >  BendStamp* currentBend;
785 >  TorsionStamp* currentTorsion;
786  
787 <  lMolIndex = 0;
788 <  molIndex = 0;
789 <  index = 0;
635 <  for( i=0; i<n_components; i++ ){
787 >  bond_pair* theBonds;
788 >  bend_set* theBends;
789 >  torsion_set* theTorsions;
790  
791 <    for( j=0; j<components_nmol[i]; j++ ){
791 >  
792 >  //init the forceField paramters
793  
794 < #ifdef IS_MPI
640 <      if( mpiSim->getMyMolStart() <= molIndex &&
641 <          molIndex <= mpiSim->getMyMolEnd() ){
642 < #endif // is_mpi        
794 >  the_ff->readParams();
795  
796 <        molStart = index;
797 <        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++;
796 >  
797 >  // init the atoms
798  
799 < #ifdef IS_MPI
800 <      }
801 < #endif //is_mpi
802 <      
803 <      molIndex++;
692 <    }
693 <  }
694 <
695 < #ifdef IS_MPI
696 <    for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] );
799 >  double ux, uy, uz, u, uSqr;
800 >  
801 >  atomOffset = 0;
802 >  excludeOffset = 0;
803 >  for(i=0; i<simnfo->n_mol; i++){
804      
805 <    delete[] globalIndex;
805 >    stampID = the_molecules[i].getStampID();
806  
807 <    mpiSim->mpiRefresh();
808 < #endif //IS_MPI
809 <          
810 <  the_ff->initializeAtoms();
811 < }
705 <
706 < void SimSetup::makeBonds( void ){
707 <
708 <  int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
709 <  bond_pair* the_bonds;
710 <  BondStamp* current_bond;
711 <
712 <  the_bonds = new bond_pair[tot_bonds];
713 <  index = 0;
714 <  offset = 0;
715 <  molIndex = 0;
716 <
717 <  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        
725 <        
726 <        for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){
727 <          
728 <          current_bond = comp_stamps[i]->getBond( k );
729 <          the_bonds[index].a = current_bond->getA() + offset;
730 <          the_bonds[index].b = current_bond->getB() + offset;
731 <
732 <          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
807 >    info.nAtoms    = comp_stamps[stampID]->getNAtoms();
808 >    info.nBonds    = comp_stamps[stampID]->getNBonds();
809 >    info.nBends    = comp_stamps[stampID]->getNBends();
810 >    info.nTorsions = comp_stamps[stampID]->getNTorsions();
811 >    info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
812  
813 <          the_excludes[index*2] =    
814 <            the_atoms[exI]->getGlobalIndex() + 1;
815 <          the_excludes[index*2 + 1] =
816 <            the_atoms[exJ]->getGlobalIndex() + 1;
813 >    info.myAtoms = &the_atoms[atomOffset];
814 >    info.myExcludes = &the_excludes[excludeOffset];
815 >    info.myBonds = new Bond*[info.nBonds];
816 >    info.myBends = new Bend*[info.nBends];
817 >    info.myTorsions = new Torsion*[info.nTorsions];
818  
819 < #else  // isn't MPI
820 <          
821 <          the_excludes[index*2] =     exI + 1;
822 <          the_excludes[index*2 + 1] = exJ + 1;
823 <          // fortran index from 1 (hence the +1 in the indexing)
824 < #endif  //is_mpi
825 <          
826 <          // increment the index and repeat;
827 <          index++;
828 <        }
760 <        offset += comp_stamps[i]->getNAtoms();
819 >    theBonds = new bond_pair[info.nBonds];
820 >    theBends = new bend_set[info.nBends];
821 >    theTorsions = new torsion_set[info.nTorsions];
822 >    
823 >    // make the Atoms
824 >    
825 >    for(j=0; j<info.nAtoms; j++){
826 >      
827 >      currentAtom = comp_stamps[stampID]->getAtom( j );
828 >      if( currentAtom->haveOrientation() ){
829          
830 < #ifdef IS_MPI
830 >        dAtom = new DirectionalAtom(j + atomOffset);
831 >        simnfo->n_oriented++;
832 >        info.myAtoms[j] = dAtom;
833 >        
834 >        ux = currentAtom->getOrntX();
835 >        uy = currentAtom->getOrntY();
836 >        uz = currentAtom->getOrntZ();
837 >        
838 >        uSqr = (ux * ux) + (uy * uy) + (uz * uz);
839 >        
840 >        u = sqrt( uSqr );
841 >        ux = ux / u;
842 >        uy = uy / u;
843 >        uz = uz / u;
844 >        
845 >        dAtom->setSUx( ux );
846 >        dAtom->setSUy( uy );
847 >        dAtom->setSUz( uz );
848        }
849 < #endif //is_mpi
849 >      else{
850 >        info.myAtoms[j] = new GeneralAtom(j + atomOffset);
851 >      }
852 >      info.myAtoms[j]->setType( currentAtom->getType() );
853 >    
854 > #ifdef IS_MPI
855        
856 <      molIndex++;
857 <    }      
858 <  }
856 >      info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
857 >      
858 > #endif // is_mpi
859 >    }
860 >    
861 >    // make the bonds
862 >    for(j=0; j<info.nBonds; j++){
863 >      
864 >      currentBond = comp_stamps[stampID]->getBond( j );
865 >      theBonds[j].a = currentBond->getA() + atomOffset;
866 >      theBonds[j].b = currentBond->getB() + atomOffset;
867  
868 <  the_ff->initializeBonds( the_bonds );
869 < }
868 >      exI = theBonds[j].a;
869 >      exJ = theBonds[j].b;
870  
871 < void SimSetup::makeBends( void ){
872 <
873 <  int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
874 <  bend_set* the_bends;
875 <  BendStamp* current_bend;
876 <  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 <
871 >      // exclude_I must always be the smaller of the pair
872 >      if( exI > exJ ){
873 >        tempEx = exI;
874 >        exI = exJ;
875 >        exJ = tempEx;
876 >      }
877   #ifdef IS_MPI
878 <      if( mpiSim->getMyMolStart() <= molIndex &&
879 <          molIndex <= mpiSim->getMyMolEnd() ){
880 < #endif // is_mpi        
878 >      tempEx = exI;
879 >      exI = the_atoms[tempEx]->getGlobalIndex() + 1;
880 >      tempEx = exJ;
881 >      exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
882 >      
883 >      the_excludes[j+excludeOffset]->setPair( exI, exJ );
884 > #else  // isn't MPI
885  
886 <        for( k=0; k<comp_stamps[i]->getNBends(); k++ ){
886 >      the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
887 > #endif  //is_mpi
888 >    }
889 >    excludeOffset += info.nBonds;
890 >
891 >    //make the bends
892 >    for(j=0; j<info.nBends; j++){
893 >      
894 >      currentBend = comp_stamps[stampID]->getBend( j );
895 >      theBends[j].a = currentBend->getA() + atomOffset;
896 >      theBends[j].b = currentBend->getB() + atomOffset;
897 >      theBends[j].c = currentBend->getC() + atomOffset;
898            
899 <          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() ){
899 >      if( currentBend->haveExtras() ){
900              
901 <            extras = current_bend->getExtras();
902 <            current_extra = extras;
901 >        extras = currentBend->getExtras();
902 >        current_extra = extras;
903              
904 <            while( current_extra != NULL ){
905 <              if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
904 >        while( current_extra != NULL ){
905 >          if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
906                  
907 <                switch( current_extra->getType() ){
907 >            switch( current_extra->getType() ){
908 >              
909 >            case 0:
910 >              theBends[j].ghost =
911 >                current_extra->getInt() + atomOffset;
912 >              theBends[j].isGhost = 1;
913 >              break;
914                    
915 <                case 0:
916 <                  the_bends[index].ghost =
917 <                    current_extra->getInt() + offset;
918 <                  the_bends[index].isGhost = 1;
919 <                  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 <              }
915 >            case 1:
916 >              theBends[j].ghost =
917 >                (int)current_extra->getDouble() + atomOffset;
918 >              theBends[j].isGhost = 1;
919 >              break;
920                
921 <              else{
922 <                
923 <                sprintf( painCave.errMsg,
924 <                         "SimSetup Error: unhandled bend assignment:\n"
925 <                         "    -->%s in Bend[%d] in %s\n",
926 <                         current_extra->getlhs(),
927 <                         k, comp_stamps[i]->getID() );
928 <                painCave.isFatal = 1;
843 <                simError();
844 <              }
845 <              
846 <              current_extra = current_extra->getNext();
921 >            default:
922 >              sprintf( painCave.errMsg,
923 >                       "SimSetup Error: ghostVectorSource was neither a "
924 >                       "double nor an int.\n"
925 >                       "-->Bend[%d] in %s\n",
926 >                       j, comp_stamps[stampID]->getID() );
927 >              painCave.isFatal = 1;
928 >              simError();
929              }
930            }
931            
850 –          if( !the_bends[index].isGhost ){
851 –            
852 –            exI = the_bends[index].a;
853 –            exJ = the_bends[index].c;
854 –          }
932            else{
933              
934 <            exI = the_bends[index].a;
935 <            exJ = the_bends[index].b;
934 >            sprintf( painCave.errMsg,
935 >                     "SimSetup Error: unhandled bend assignment:\n"
936 >                     "    -->%s in Bend[%d] in %s\n",
937 >                     current_extra->getlhs(),
938 >                     j, comp_stamps[stampID]->getID() );
939 >            painCave.isFatal = 1;
940 >            simError();
941            }
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 <          }
943 >          current_extra = current_extra->getNext();
944 >        }
945 >      }
946 >          
947 >      if( !theBends[j].isGhost ){
948 >            
949 >        exI = theBends[j].a;
950 >        exJ = theBends[j].c;
951 >      }
952 >      else{
953 >        
954 >        exI = theBends[j].a;
955 >        exJ = theBends[j].b;
956 >      }
957 >      
958 >      // exclude_I must always be the smaller of the pair
959 >      if( exI > exJ ){
960 >        tempEx = exI;
961 >        exI = exJ;
962 >        exJ = tempEx;
963 >      }
964 > #ifdef IS_MPI
965 >      tempEx = exI;
966 >      exI = the_atoms[tempEx]->getGlobalIndex() + 1;
967 >      tempEx = exJ;
968 >      exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
969 >      
970 >      the_excludes[j+excludeOffset]->setPair( exI, exJ );
971 > #else  // isn't MPI
972 >      the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
973 > #endif  //is_mpi
974 >    }
975 >    excludeOffset += info.nBends;
976  
977 +    for(j=0; j<info.nTorsions; j++){
978 +      
979 +      currentTorsion = comp_stamps[stampID]->getTorsion( j );
980 +      theTorsions[j].a = currentTorsion->getA() + atomOffset;
981 +      theTorsions[j].b = currentTorsion->getB() + atomOffset;
982 +      theTorsions[j].c = currentTorsion->getC() + atomOffset;
983 +      theTorsions[j].d = currentTorsion->getD() + atomOffset;
984 +      
985 +      exI = theTorsions[j].a;
986 +      exJ = theTorsions[j].d;
987  
988 +      // exclude_I must always be the smaller of the pair
989 +      if( exI > exJ ){
990 +        tempEx = exI;
991 +        exI = exJ;
992 +        exJ = tempEx;
993 +      }
994   #ifdef IS_MPI
995 <
996 <          the_excludes[(index + tot_bonds)*2] =    
997 <            the_atoms[exI]->getGlobalIndex() + 1;
998 <          the_excludes[(index + tot_bonds)*2 + 1] =
999 <            the_atoms[exJ]->getGlobalIndex() + 1;
1000 <          
995 >      tempEx = exI;
996 >      exI = the_atoms[tempEx]->getGlobalIndex() + 1;
997 >      tempEx = exJ;
998 >      exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
999 >      
1000 >      the_excludes[j+excludeOffset]->setPair( exI, exJ );
1001   #else  // isn't MPI
1002 <          
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)
1002 >      the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1003   #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++;
1004      }
1005 <  }
1005 >    excludeOffset += info.nTorsions;
1006 >
1007 >    
1008 >    // send the arrays off to the forceField for init.
1009  
1010 < #ifdef IS_MPI
1011 <  sprintf( checkPointMsg,
1012 <           "Successfully created the bends list.\n" );
1013 <  MPIcheckPoint();
901 < #endif // is_mpi
902 <  
1010 >    the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
1011 >    the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
1012 >    the_ff->initializeBends( info.nBends, info.myBends, theBends );
1013 >    the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
1014  
904 –  the_ff->initializeBends( the_bends );
905 – }
1015  
1016 < void SimSetup::makeTorsions( void ){
1016 >    the_molecules[i].initialize( info );
1017  
909 –  int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
910 –  torsion_set* the_torsions;
911 –  TorsionStamp* current_torsion;
1018  
1019 <  the_torsions = new torsion_set[tot_torsions];
1020 <  index = 0;
1021 <  offset = 0;
1022 <  molIndex = 0;
1023 <  for( i=0; i<n_components; i++ ){
1019 >    atomOffset += info.nAtoms;
1020 >    delete[] theBonds;
1021 >    delete[] theBends;
1022 >    delete[] theTorsions;
1023 >  }
1024  
919 –    for( j=0; j<components_nmol[i]; j++ ){
920 –
1025   #ifdef IS_MPI
1026 <      if( mpiSim->getMyMolStart() <= molIndex &&
1027 <          molIndex <= mpiSim->getMyMolEnd() ){
1028 < #endif // is_mpi        
1026 >  sprintf( checkPointMsg, "all molecules initialized succesfully" );
1027 >  MPIcheckPoint();
1028 > #endif // is_mpi
1029  
1030 <      for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){
1030 >  // clean up the forcefield
1031 >  the_ff->calcRcut();
1032 >  the_ff->cleanMe();
1033  
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 );
1034   }
1035  
1036   void SimSetup::initFromBass( void ){

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