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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 561 by mmeineke, Fri Jun 20 20:29:36 2003 UTC

# Line 12 | Line 12 | SimSetup::SimSetup(){
12   #include "mpiSimulation.hpp"
13   #endif
14  
15 + // some defines for ensemble and Forcefield  cases
16 +
17 + #define NVE_ENS 0
18 + #define NVT_ENS 1
19 + #define NPT_ENS 2
20 +
21 + #define FF_DUFF 0
22 + #define FF_LJ   1
23 +
24 +
25   SimSetup::SimSetup(){
26    stamps = new MakeStamps();
27    globals = new Globals();
# Line 66 | Line 76 | void SimSetup::createSim( void ){
76  
77    MakeStamps *the_stamps;
78    Globals* the_globals;
79 <  int i, j;
79 >  int i, j, k, globalAtomIndex;
80 >  
81 >  int ensembleCase;
82 >  int ffCase;
83 >  
84 >  ensembleCase = -1;
85 >  ffCase = -1;
86  
87    // get the stamps and globals;
88    the_stamps = stamps;
# Line 80 | Line 96 | void SimSetup::createSim( void ){
96    // get the ones we know are there, yet still may need some work.
97    n_components = the_globals->getNComponents();
98    strcpy( force_field, the_globals->getForceField() );
99 +
100 +  if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
101 +  else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
102 +  else{
103 +    sprintf( painCave.errMsg,
104 +             "SimSetup Error. Unrecognized force field -> %s\n",
105 +             force_field );
106 +    painCave.isFatal = 1;
107 +    simError();
108 +  }
109 +
110 +  // get the ensemble:
111    strcpy( ensemble, the_globals->getEnsemble() );
112 +
113 +  if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
114 +  else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
115 +  else if( !strcasecmp( ensemble, "NPT" )) ensembleCase = NPT_ENS;
116 +  else{
117 +    sprintf( painCave.errMsg,
118 +             "SimSetup Warning. Unrecognized Ensemble -> %s, "
119 +             "reverting to NVE for this simulation.\n",
120 +             ensemble );
121 +    painCave.isFatal = 0;
122 +    simError();
123 +    strcpy( ensemble, "NVE" );
124 +    ensembleCase = NVE_ENS;
125 +  }  
126    strcpy( simnfo->ensemble, ensemble );
127 +
128 +
129 + //   if( !strcasecmp( ensemble, "NPT" ) ) {
130 + //     the_extendedsystem = new ExtendedSystem( simnfo );
131 + //     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
132 + //     if (the_globals->haveTargetPressure())
133 + //       the_extendedsystem->setTargetPressure(the_globals->getTargetPressure());
134 + //     else {
135 + //       sprintf( painCave.errMsg,
136 + //                "SimSetup error: If you use the constant pressure\n"
137 + //                "    ensemble, you must set targetPressure.\n"
138 + //                "    This was found in the BASS file.\n");
139 + //       painCave.isFatal = 1;
140 + //       simError();
141 + //     }
142 +
143 + //     if (the_globals->haveTauThermostat())
144 + //       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
145 + //     else if (the_globals->haveQmass())
146 + //       the_extendedsystem->setQmass(the_globals->getQmass());
147 + //     else {
148 + //       sprintf( painCave.errMsg,
149 + //                "SimSetup error: If you use one of the constant temperature\n"
150 + //                "    ensembles, you must set either tauThermostat or qMass.\n"
151 + //                "    Neither of these was found in the BASS file.\n");
152 + //       painCave.isFatal = 1;
153 + //       simError();
154 + //     }
155  
156 + //     if (the_globals->haveTauBarostat())
157 + //       the_extendedsystem->setTauBarostat(the_globals->getTauBarostat());
158 + //     else {
159 + //       sprintf( painCave.errMsg,
160 + //                "SimSetup error: If you use the constant pressure\n"
161 + //                "    ensemble, you must set tauBarostat.\n"
162 + //                "    This was found in the BASS file.\n");
163 + //       painCave.isFatal = 1;
164 + //       simError();
165 + //     }
166 +
167 + //   } else if ( !strcasecmp( ensemble, "NVT") ) {
168 + //     the_extendedsystem = new ExtendedSystem( simnfo );
169 + //     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
170 +
171 + //     if (the_globals->haveTauThermostat())
172 + //       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
173 + //     else if (the_globals->haveQmass())
174 + //       the_extendedsystem->setQmass(the_globals->getQmass());
175 + //     else {
176 + //       sprintf( painCave.errMsg,
177 + //                "SimSetup error: If you use one of the constant temperature\n"
178 + //                "    ensembles, you must set either tauThermostat or qMass.\n"
179 + //                "    Neither of these was found in the BASS file.\n");
180 + //       painCave.isFatal = 1;
181 + //       simError();
182 + //     }
183 +
184    strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
185    simnfo->usePBC = the_globals->getPBC();
186            
187 +  int usesDipoles = 0;
188 +  switch( ffCase ){
189  
190 +  case FF_DUFF:
191 +    the_ff = new DUFF();
192 +    usesDipoles = 1;
193 +    break;
194  
195 <  if( !strcmp( force_field, "TraPPE" ) ) the_ff = new TraPPEFF();
196 <  else if( !strcmp( force_field, "DipoleTest" ) ) the_ff = new DipoleTestFF();
197 <  else if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF();
198 <  else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
199 <  else{
195 >  case FF_LJ:
196 >    the_ff = new LJFF();
197 >    break;
198 >
199 >  default:
200      sprintf( painCave.errMsg,
201 <             "SimSetup Error. Unrecognized force field -> %s\n",
98 <             force_field );
201 >             "SimSetup Error. Unrecognized force field in case statement.\n");
202      painCave.isFatal = 1;
203      simError();
204    }
# Line 105 | Line 208 | void SimSetup::createSim( void ){
208    MPIcheckPoint();
209   #endif // is_mpi
210  
108 –  
109 –
211    // get the components and calculate the tot_nMol and indvidual n_mol
212    the_components = the_globals->getComponents();
213    components_nmol = new int[n_components];
# Line 230 | Line 331 | void SimSetup::createSim( void ){
331    simnfo->n_torsions = tot_torsions;
332    simnfo->n_SRI = tot_SRI;
333    simnfo->n_mol = tot_nmol;
233 –
334    
335 +  simnfo->molMembershipArray = new int[tot_atoms];
336 +
337   #ifdef IS_MPI
338  
339    // divide the molecules among processors here.
340    
341    mpiSim = new mpiSimulation( simnfo );
342    
241 –  
242 –
343    globalIndex = mpiSim->divideLabor();
344  
245 –
246 –
345    // set up the local variables
346    
347    int localMol, allMol;
348    int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
349 +
350 +  int* mol2proc = mpiSim->getMolToProcMap();
351 +  int* molCompType = mpiSim->getMolComponentType();
352    
353    allMol = 0;
354    localMol = 0;
# Line 255 | Line 356 | void SimSetup::createSim( void ){
356    local_bonds = 0;
357    local_bends = 0;
358    local_torsions = 0;
359 +  globalAtomIndex = 0;
360 +
361 +
362    for( i=0; i<n_components; i++ ){
363  
364      for( j=0; j<components_nmol[i]; j++ ){
365        
366 <      if( mpiSim->getMyMolStart() <= allMol &&
263 <          allMol <= mpiSim->getMyMolEnd() ){
366 >      if( mol2proc[allMol] == worldRank ){
367          
368          local_atoms +=    comp_stamps[i]->getNAtoms();
369          local_bonds +=    comp_stamps[i]->getNBonds();
# Line 268 | Line 371 | void SimSetup::createSim( void ){
371          local_torsions += comp_stamps[i]->getNTorsions();
372          localMol++;
373        }      
374 <      allMol++;
374 >      for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
375 >        simnfo->molMembershipArray[globalAtomIndex] = allMol;
376 >        globalAtomIndex++;
377 >      }
378 >
379 >      allMol++;      
380      }
381    }
382    local_SRI = local_bonds + local_bends + local_torsions;
383    
276 –
384    simnfo->n_atoms = mpiSim->getMyNlocal();  
385    
386    if( local_atoms != simnfo->n_atoms ){
387      sprintf( painCave.errMsg,
388               "SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
389 <             " localAtom (%d) are note equal.\n",
389 >             " localAtom (%d) are not equal.\n",
390               simnfo->n_atoms,
391               local_atoms );
392      painCave.isFatal = 1;
# Line 304 | Line 411 | void SimSetup::createSim( void ){
411    Atom::createArrays(simnfo->n_atoms);
412    the_atoms = new Atom*[simnfo->n_atoms];
413    the_molecules = new Molecule[simnfo->n_mol];
414 +  int molIndex;
415  
416 +  // initialize the molecule's stampID's
417  
418 + #ifdef IS_MPI
419 +  
420 +
421 +  molIndex = 0;
422 +  for(i=0; i<mpiSim->getTotNmol(); i++){
423 +    
424 +    if(mol2proc[i] == worldRank ){
425 +      the_molecules[molIndex].setStampID( molCompType[i] );
426 +      the_molecules[molIndex].setMyIndex( molIndex );
427 +      the_molecules[molIndex].setGlobalIndex( i );
428 +      molIndex++;
429 +    }
430 +  }
431 +
432 + #else // is_mpi
433 +  
434 +  molIndex = 0;
435 +  globalAtomIndex = 0;
436 +  for(i=0; i<n_components; i++){
437 +    for(j=0; j<components_nmol[i]; j++ ){
438 +      the_molecules[molIndex].setStampID( i );
439 +      the_molecules[molIndex].setMyIndex( molIndex );
440 +      the_molecules[molIndex].setGlobalIndex( molIndex );
441 +      for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
442 +        simnfo->molMembershipArray[globalAtomIndex] = molIndex;
443 +        globalAtomIndex++;
444 +      }
445 +      molIndex++;
446 +    }
447 +  }
448 +    
449 +
450 + #endif // is_mpi
451 +
452 +
453    if( simnfo->n_SRI ){
454 <    the_sris = new SRI*[simnfo->n_SRI];
455 <    the_excludes = new int[2 * simnfo->n_SRI];
454 >    
455 >    Exclude::createArray(simnfo->n_SRI);
456 >    the_excludes = new Exclude*[simnfo->n_SRI];
457 >    for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
458      simnfo->globalExcludes = new int;
459 <    simnfo->n_exclude = tot_SRI;
459 >    simnfo->n_exclude = simnfo->n_SRI;
460    }
461    else{
462      
463 <    the_excludes = new int[2];
464 <    the_excludes[0] = 0;
465 <    the_excludes[1] = 0;
463 >    Exclude::createArray( 1 );
464 >    the_excludes = new Exclude*;
465 >    the_excludes[0] = new Exclude(0);
466 >    the_excludes[0]->setPair( 0,0 );
467      simnfo->globalExcludes = new int;
468      simnfo->globalExcludes[0] = 0;
469 <
323 <    simnfo->n_exclude = 1;
469 >    simnfo->n_exclude = 0;
470    }
471  
472    // set the arrays into the SimInfo object
473  
474    simnfo->atoms = the_atoms;
475 <  simnfo->sr_interactions = the_sris;
475 >  simnfo->molecules = the_molecules;
476    simnfo->nGlobalExcludes = 0;
477    simnfo->excludes = the_excludes;
478  
479  
480    // get some of the tricky things that may still be in the globals
481  
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
482    
483    if( the_globals->haveBox() ){
484      simnfo->box_x = the_globals->getBox();
# Line 407 | Line 529 | void SimSetup::createSim( void ){
529  
530    the_ff->setSimInfo( simnfo );
531  
532 <  makeAtoms();
532 >  makeMolecules();
533    simnfo->identArray = new int[simnfo->n_atoms];
534    for(i=0; i<simnfo->n_atoms; i++){
535      simnfo->identArray[i] = the_atoms[i]->getIdent();
536    }
537    
538 <  if( tot_bonds ){
539 <    makeBonds();
540 <  }
541 <
542 <  if( tot_bends ){
543 <    makeBends();
544 <  }
545 <
546 <  if( tot_torsions ){
547 <    makeTorsions();
548 <  }
549 <
550 <
551 <
538 >  if (the_globals->getUseRF() ) {
539 >    simnfo->useReactionField = 1;
540 >  
541 >    if( !the_globals->haveECR() ){
542 >      sprintf( painCave.errMsg,
543 >               "SimSetup Warning: using default value of 1/2 the smallest "
544 >               "box length for the electrostaticCutoffRadius.\n"
545 >               "I hope you have a very fast processor!\n");
546 >      painCave.isFatal = 0;
547 >      simError();
548 >      double smallest;
549 >      smallest = simnfo->box_x;
550 >      if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
551 >      if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
552 >      simnfo->ecr = 0.5 * smallest;
553 >    } else {
554 >      simnfo->ecr        = the_globals->getECR();
555 >    }
556  
557 +    if( !the_globals->haveEST() ){
558 +      sprintf( painCave.errMsg,
559 +               "SimSetup Warning: using default value of 0.05 * the "
560 +               "electrostaticCutoffRadius for the electrostaticSkinThickness\n"
561 +               );
562 +      painCave.isFatal = 0;
563 +      simError();
564 +      simnfo->est = 0.05 * simnfo->ecr;
565 +    } else {
566 +      simnfo->est        = the_globals->getEST();
567 +    }
568 +    
569 +    if(!the_globals->haveDielectric() ){
570 +      sprintf( painCave.errMsg,
571 +               "SimSetup Error: You are trying to use Reaction Field without"
572 +               "setting a dielectric constant!\n"
573 +               );
574 +      painCave.isFatal = 1;
575 +      simError();
576 +    }
577 +    simnfo->dielectric = the_globals->getDielectric();  
578 +  } else {
579 +    if (usesDipoles) {
580 +      
581 +      if( !the_globals->haveECR() ){
582 +        sprintf( painCave.errMsg,
583 +                 "SimSetup Warning: using default value of 1/2 the smallest "
584 +                 "box length for the electrostaticCutoffRadius.\n"
585 +                 "I hope you have a very fast processor!\n");
586 +        painCave.isFatal = 0;
587 +        simError();
588 +        double smallest;
589 +        smallest = simnfo->box_x;
590 +        if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
591 +        if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
592 +        simnfo->ecr = 0.5 * smallest;
593 +      } else {
594 +        simnfo->ecr        = the_globals->getECR();
595 +      }
596 +      
597 +      if( !the_globals->haveEST() ){
598 +        sprintf( painCave.errMsg,
599 +                 "SimSetup Warning: using default value of 5%% of the "
600 +                 "electrostaticCutoffRadius for the "
601 +                 "electrostaticSkinThickness\n"
602 +                 );
603 +        painCave.isFatal = 0;
604 +        simError();
605 +        simnfo->est = 0.05 * simnfo->ecr;
606 +      } else {
607 +        simnfo->est        = the_globals->getEST();
608 +      }
609 +    }
610 +  }  
611  
612 + #ifdef IS_MPI
613 +  strcpy( checkPointMsg, "electrostatic parameters check out" );
614 +  MPIcheckPoint();
615 + #endif // is_mpi
616  
617   if( the_globals->haveInitialConfig() ){
618  
# Line 583 | Line 767 | void SimSetup::createSim( void ){
767    if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
768  
769  
770 < //   // make the longe range forces and the integrator
770 >  // make the integrator
771 >  
772 >  
773 >  NVT* myNVT = NULL;
774 >  switch( ensembleCase ){
775  
776 < //   new AllLong( simnfo );
776 >  case NVE_ENS:
777 >    new NVE( simnfo, the_ff );
778 >    break;
779  
780 <  if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff );
781 <  if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff );
782 <  if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff );
593 <  if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff );
780 >  case NVT_ENS:
781 >    myNVT = new NVT( simnfo, the_ff );
782 >    myNVT->setTargetTemp(the_globals->getTargetTemp());
783  
784 +    if (the_globals->haveTauThermostat())
785 +      myNVT->setTauThermostat(the_globals->getTauThermostat());
786 +    else if (the_globals->haveQmass())
787 +      myNVT->setQmass(the_globals->getQmass());
788 +    else {
789 +      sprintf( painCave.errMsg,
790 +               "SimSetup error: If you use the NVT\n"
791 +               "    ensemble, you must set either tauThermostat or qMass.\n"
792 +               "    Neither of these was found in the BASS file.\n");
793 +      painCave.isFatal = 1;
794 +      simError();
795 +    }
796 +    break;
797  
798 +  default:
799 +    sprintf( painCave.errMsg,
800 +             "SimSetup Error. Unrecognized ensemble in case statement.\n");
801 +    painCave.isFatal = 1;
802 +    simError();
803 +  }
804  
805 +
806 + #ifdef IS_MPI
807 +  mpiSim->mpiRefresh();
808 + #endif
809 +
810    // initialize the Fortran
811 <  
811 >
812 >
813    simnfo->refreshSim();
814    
815    if( !strcmp( simnfo->mixingRule, "standard") ){
# Line 620 | Line 834 | void SimSetup::makeAtoms( void ){
834   #endif // is_mpi
835   }
836  
623 – void SimSetup::makeAtoms( void ){
837  
838 <  int i, j, k, index;
626 <  double ux, uy, uz, uSqr, u;
627 <  AtomStamp* current_atom;
838 > void SimSetup::makeMolecules( void ){
839  
840 +  int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
841 +  molInit info;
842    DirectionalAtom* dAtom;
843 <  int molIndex, molStart, molEnd, nMemb, lMolIndex;
843 >  LinkedAssign* extras;
844 >  LinkedAssign* current_extra;
845 >  AtomStamp* currentAtom;
846 >  BondStamp* currentBond;
847 >  BendStamp* currentBend;
848 >  TorsionStamp* currentTorsion;
849  
850 <  lMolIndex = 0;
851 <  molIndex = 0;
852 <  index = 0;
635 <  for( i=0; i<n_components; i++ ){
850 >  bond_pair* theBonds;
851 >  bend_set* theBends;
852 >  torsion_set* theTorsions;
853  
854 <    for( j=0; j<components_nmol[i]; j++ ){
854 >  
855 >  //init the forceField paramters
856  
857 < #ifdef IS_MPI
640 <      if( mpiSim->getMyMolStart() <= molIndex &&
641 <          molIndex <= mpiSim->getMyMolEnd() ){
642 < #endif // is_mpi        
857 >  the_ff->readParams();
858  
859 <        molStart = index;
860 <        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++;
859 >  
860 >  // init the atoms
861  
862 < #ifdef IS_MPI
863 <      }
864 < #endif //is_mpi
865 <      
866 <      molIndex++;
692 <    }
693 <  }
694 <
695 < #ifdef IS_MPI
696 <    for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] );
862 >  double ux, uy, uz, u, uSqr;
863 >  
864 >  atomOffset = 0;
865 >  excludeOffset = 0;
866 >  for(i=0; i<simnfo->n_mol; i++){
867      
868 <    delete[] globalIndex;
868 >    stampID = the_molecules[i].getStampID();
869  
870 <    mpiSim->mpiRefresh();
871 < #endif //IS_MPI
872 <          
873 <  the_ff->initializeAtoms();
874 < }
705 <
706 < void SimSetup::makeBonds( void ){
870 >    info.nAtoms    = comp_stamps[stampID]->getNAtoms();
871 >    info.nBonds    = comp_stamps[stampID]->getNBonds();
872 >    info.nBends    = comp_stamps[stampID]->getNBends();
873 >    info.nTorsions = comp_stamps[stampID]->getNTorsions();
874 >    info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
875  
876 <  int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
877 <  bond_pair* the_bonds;
878 <  BondStamp* current_bond;
876 >    info.myAtoms = &the_atoms[atomOffset];
877 >    info.myExcludes = &the_excludes[excludeOffset];
878 >    info.myBonds = new Bond*[info.nBonds];
879 >    info.myBends = new Bend*[info.nBends];
880 >    info.myTorsions = new Torsion*[info.nTorsions];
881  
882 <  the_bonds = new bond_pair[tot_bonds];
883 <  index = 0;
884 <  offset = 0;
885 <  molIndex = 0;
886 <
887 <  for( i=0; i<n_components; i++ ){
888 <
889 <    for( j=0; j<components_nmol[i]; j++ ){
890 <
891 < #ifdef IS_MPI
722 <      if( mpiSim->getMyMolStart() <= molIndex &&
723 <          molIndex <= mpiSim->getMyMolEnd() ){
724 < #endif // is_mpi        
882 >    theBonds = new bond_pair[info.nBonds];
883 >    theBends = new bend_set[info.nBends];
884 >    theTorsions = new torsion_set[info.nTorsions];
885 >    
886 >    // make the Atoms
887 >    
888 >    for(j=0; j<info.nAtoms; j++){
889 >      
890 >      currentAtom = comp_stamps[stampID]->getAtom( j );
891 >      if( currentAtom->haveOrientation() ){
892          
893 <        for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){
894 <          
895 <          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
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();
893 >        dAtom = new DirectionalAtom(j + atomOffset);
894 >        simnfo->n_oriented++;
895 >        info.myAtoms[j] = dAtom;
896          
897 < #ifdef IS_MPI
897 >        ux = currentAtom->getOrntX();
898 >        uy = currentAtom->getOrntY();
899 >        uz = currentAtom->getOrntZ();
900 >        
901 >        uSqr = (ux * ux) + (uy * uy) + (uz * uz);
902 >        
903 >        u = sqrt( uSqr );
904 >        ux = ux / u;
905 >        uy = uy / u;
906 >        uz = uz / u;
907 >        
908 >        dAtom->setSUx( ux );
909 >        dAtom->setSUy( uy );
910 >        dAtom->setSUz( uz );
911        }
912 < #endif //is_mpi
912 >      else{
913 >        info.myAtoms[j] = new GeneralAtom(j + atomOffset);
914 >      }
915 >      info.myAtoms[j]->setType( currentAtom->getType() );
916 >    
917 > #ifdef IS_MPI
918        
919 <      molIndex++;
920 <    }      
921 <  }
919 >      info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
920 >      
921 > #endif // is_mpi
922 >    }
923 >    
924 >    // make the bonds
925 >    for(j=0; j<info.nBonds; j++){
926 >      
927 >      currentBond = comp_stamps[stampID]->getBond( j );
928 >      theBonds[j].a = currentBond->getA() + atomOffset;
929 >      theBonds[j].b = currentBond->getB() + atomOffset;
930  
931 <  the_ff->initializeBonds( the_bonds );
932 < }
931 >      exI = theBonds[j].a;
932 >      exJ = theBonds[j].b;
933  
934 < void SimSetup::makeBends( void ){
935 <
936 <  int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
937 <  bend_set* the_bends;
938 <  BendStamp* current_bend;
939 <  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 <
934 >      // exclude_I must always be the smaller of the pair
935 >      if( exI > exJ ){
936 >        tempEx = exI;
937 >        exI = exJ;
938 >        exJ = tempEx;
939 >      }
940   #ifdef IS_MPI
941 <      if( mpiSim->getMyMolStart() <= molIndex &&
942 <          molIndex <= mpiSim->getMyMolEnd() ){
943 < #endif // is_mpi        
941 >      tempEx = exI;
942 >      exI = the_atoms[tempEx]->getGlobalIndex() + 1;
943 >      tempEx = exJ;
944 >      exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
945 >      
946 >      the_excludes[j+excludeOffset]->setPair( exI, exJ );
947 > #else  // isn't MPI
948  
949 <        for( k=0; k<comp_stamps[i]->getNBends(); k++ ){
949 >      the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
950 > #endif  //is_mpi
951 >    }
952 >    excludeOffset += info.nBonds;
953 >
954 >    //make the bends
955 >    for(j=0; j<info.nBends; j++){
956 >      
957 >      currentBend = comp_stamps[stampID]->getBend( j );
958 >      theBends[j].a = currentBend->getA() + atomOffset;
959 >      theBends[j].b = currentBend->getB() + atomOffset;
960 >      theBends[j].c = currentBend->getC() + atomOffset;
961            
962 <          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() ){
962 >      if( currentBend->haveExtras() ){
963              
964 <            extras = current_bend->getExtras();
965 <            current_extra = extras;
964 >        extras = currentBend->getExtras();
965 >        current_extra = extras;
966              
967 <            while( current_extra != NULL ){
968 <              if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
967 >        while( current_extra != NULL ){
968 >          if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
969                  
970 <                switch( current_extra->getType() ){
811 <                  
812 <                case 0:
813 <                  the_bends[index].ghost =
814 <                    current_extra->getInt() + offset;
815 <                  the_bends[index].isGhost = 1;
816 <                  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 <              }
970 >            switch( current_extra->getType() ){
971                
972 <              else{
973 <                
974 <                sprintf( painCave.errMsg,
975 <                         "SimSetup Error: unhandled bend assignment:\n"
976 <                         "    -->%s in Bend[%d] in %s\n",
977 <                         current_extra->getlhs(),
978 <                         k, comp_stamps[i]->getID() );
979 <                painCave.isFatal = 1;
980 <                simError();
981 <              }
972 >            case 0:
973 >              theBends[j].ghost =
974 >                current_extra->getInt() + atomOffset;
975 >              theBends[j].isGhost = 1;
976 >              break;
977 >                  
978 >            case 1:
979 >              theBends[j].ghost =
980 >                (int)current_extra->getDouble() + atomOffset;
981 >              theBends[j].isGhost = 1;
982 >              break;
983                
984 <              current_extra = current_extra->getNext();
984 >            default:
985 >              sprintf( painCave.errMsg,
986 >                       "SimSetup Error: ghostVectorSource was neither a "
987 >                       "double nor an int.\n"
988 >                       "-->Bend[%d] in %s\n",
989 >                       j, comp_stamps[stampID]->getID() );
990 >              painCave.isFatal = 1;
991 >              simError();
992              }
993            }
994            
850 –          if( !the_bends[index].isGhost ){
851 –            
852 –            exI = the_bends[index].a;
853 –            exJ = the_bends[index].c;
854 –          }
995            else{
996              
997 <            exI = the_bends[index].a;
998 <            exJ = the_bends[index].b;
997 >            sprintf( painCave.errMsg,
998 >                     "SimSetup Error: unhandled bend assignment:\n"
999 >                     "    -->%s in Bend[%d] in %s\n",
1000 >                     current_extra->getlhs(),
1001 >                     j, comp_stamps[stampID]->getID() );
1002 >            painCave.isFatal = 1;
1003 >            simError();
1004            }
1005            
1006 <          // exclude_I must always be the smaller of the pair
862 <          if( exI > exJ ){
863 <            tempEx = exI;
864 <            exI = exJ;
865 <            exJ = tempEx;
866 <          }
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;
875 <          
876 < #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++;
1006 >          current_extra = current_extra->getNext();
1007          }
1008 <        offset += comp_stamps[i]->getNAtoms();
1008 >      }
1009 >          
1010 >      if( !theBends[j].isGhost ){
1011 >            
1012 >        exI = theBends[j].a;
1013 >        exJ = theBends[j].c;
1014 >      }
1015 >      else{
1016          
1017 < #ifdef IS_MPI
1017 >        exI = theBends[j].a;
1018 >        exJ = theBends[j].b;
1019        }
1020 < #endif //is_mpi
1020 >      
1021 >      // exclude_I must always be the smaller of the pair
1022 >      if( exI > exJ ){
1023 >        tempEx = exI;
1024 >        exI = exJ;
1025 >        exJ = tempEx;
1026 >      }
1027 > #ifdef IS_MPI
1028 >      tempEx = exI;
1029 >      exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1030 >      tempEx = exJ;
1031 >      exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1032 >      
1033 >      the_excludes[j+excludeOffset]->setPair( exI, exJ );
1034 > #else  // isn't MPI
1035 >      the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1036 > #endif  //is_mpi
1037 >    }
1038 >    excludeOffset += info.nBends;
1039  
1040 <      molIndex++;
1040 >    for(j=0; j<info.nTorsions; j++){
1041 >      
1042 >      currentTorsion = comp_stamps[stampID]->getTorsion( j );
1043 >      theTorsions[j].a = currentTorsion->getA() + atomOffset;
1044 >      theTorsions[j].b = currentTorsion->getB() + atomOffset;
1045 >      theTorsions[j].c = currentTorsion->getC() + atomOffset;
1046 >      theTorsions[j].d = currentTorsion->getD() + atomOffset;
1047 >      
1048 >      exI = theTorsions[j].a;
1049 >      exJ = theTorsions[j].d;
1050 >
1051 >      // exclude_I must always be the smaller of the pair
1052 >      if( exI > exJ ){
1053 >        tempEx = exI;
1054 >        exI = exJ;
1055 >        exJ = tempEx;
1056 >      }
1057 > #ifdef IS_MPI
1058 >      tempEx = exI;
1059 >      exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1060 >      tempEx = exJ;
1061 >      exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1062 >      
1063 >      the_excludes[j+excludeOffset]->setPair( exI, exJ );
1064 > #else  // isn't MPI
1065 >      the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1066 > #endif  //is_mpi
1067      }
1068 <  }
1068 >    excludeOffset += info.nTorsions;
1069  
1070 < #ifdef IS_MPI
1071 <  sprintf( checkPointMsg,
899 <           "Successfully created the bends list.\n" );
900 <  MPIcheckPoint();
901 < #endif // is_mpi
902 <  
1070 >    
1071 >    // send the arrays off to the forceField for init.
1072  
1073 <  the_ff->initializeBends( the_bends );
1074 < }
1073 >    the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
1074 >    the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
1075 >    the_ff->initializeBends( info.nBends, info.myBends, theBends );
1076 >    the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
1077  
907 – void SimSetup::makeTorsions( void ){
1078  
1079 <  int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
910 <  torsion_set* the_torsions;
911 <  TorsionStamp* current_torsion;
1079 >    the_molecules[i].initialize( info );
1080  
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++ ){
1081  
1082 <    for( j=0; j<components_nmol[i]; j++ ){
1082 >    atomOffset += info.nAtoms;
1083 >    delete[] theBonds;
1084 >    delete[] theBends;
1085 >    delete[] theTorsions;
1086 >  }
1087  
1088   #ifdef IS_MPI
1089 <      if( mpiSim->getMyMolStart() <= molIndex &&
1090 <          molIndex <= mpiSim->getMyMolEnd() ){
1091 < #endif // is_mpi        
1089 >  sprintf( checkPointMsg, "all molecules initialized succesfully" );
1090 >  MPIcheckPoint();
1091 > #endif // is_mpi
1092  
1093 <      for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){
1093 >  // clean up the forcefield
1094 >  the_ff->calcRcut();
1095 >  the_ff->cleanMe();
1096  
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 );
1097   }
1098  
1099   void SimSetup::initFromBass( void ){

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