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root/group/trunk/OOPSE/libmdtools/SimSetup.cpp
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Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 394 by gezelter, Mon Mar 24 21:55:34 2003 UTC vs.
Revision 572 by mmeineke, Wed Jul 2 21:26:55 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 <  if( simnfo->n_SRI ){
419 <    the_sris = new SRI*[simnfo->n_SRI];
420 <    the_excludes = new int[2 * simnfo->n_SRI];
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 >    
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  
482 <  
482 >  double boxVector[3];
483    if( the_globals->haveBox() ){
484 <    simnfo->box_x = the_globals->getBox();
485 <    simnfo->box_y = the_globals->getBox();
486 <    simnfo->box_z = the_globals->getBox();
484 >    boxVector[0] = the_globals->getBox();
485 >    boxVector[1] = the_globals->getBox();
486 >    boxVector[2] = the_globals->getBox();
487 >    
488 >    simnfo->setBox( boxVector );
489    }
490    else if( the_globals->haveDensity() ){
491  
492      double vol;
493      vol = (double)tot_nmol / the_globals->getDensity();
494 <    simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
495 <    simnfo->box_y = simnfo->box_x;
496 <    simnfo->box_z = simnfo->box_x;
494 >     boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
495 >     boxVector[1] = boxVector[0];
496 >     boxVector[2] = boxVector[0];
497 >
498 >    simnfo->setBox( boxVector );
499    }
500    else{
501      if( !the_globals->haveBoxX() ){
# Line 354 | Line 504 | void SimSetup::createSim( void ){
504        painCave.isFatal = 1;
505        simError();
506      }
507 <    simnfo->box_x = the_globals->getBoxX();
507 >    boxVector[0] = the_globals->getBoxX();
508  
509      if( !the_globals->haveBoxY() ){
510        sprintf( painCave.errMsg,
# Line 362 | Line 512 | void SimSetup::createSim( void ){
512        painCave.isFatal = 1;
513        simError();
514      }
515 <    simnfo->box_y = the_globals->getBoxY();
515 >    boxVector[1] = the_globals->getBoxY();
516  
517      if( !the_globals->haveBoxZ() ){
518        sprintf( painCave.errMsg,
# Line 370 | Line 520 | void SimSetup::createSim( void ){
520        painCave.isFatal = 1;
521        simError();
522      }
523 <    simnfo->box_z = the_globals->getBoxZ();
523 >    boxVector[2] = the_globals->getBoxZ();
524 >
525 >    simnfo->setBox( boxVector );
526    }
527  
528   #ifdef IS_MPI
# Line 383 | Line 535 | void SimSetup::createSim( void ){
535  
536    the_ff->setSimInfo( simnfo );
537  
538 <  makeAtoms();
538 >  makeMolecules();
539    simnfo->identArray = new int[simnfo->n_atoms];
540    for(i=0; i<simnfo->n_atoms; i++){
541      simnfo->identArray[i] = the_atoms[i]->getIdent();
542    }
543    
392 –  if( tot_bonds ){
393 –    makeBonds();
394 –  }
395 –
396 –  if( tot_bends ){
397 –    makeBends();
398 –  }
399 –
400 –  if( tot_torsions ){
401 –    makeTorsions();
402 –  }
403 –
404 –
544    if (the_globals->getUseRF() ) {
545      simnfo->useReactionField = 1;
546    
# Line 413 | Line 552 | void SimSetup::createSim( void ){
552        painCave.isFatal = 0;
553        simError();
554        double smallest;
555 <      smallest = simnfo->box_x;
556 <      if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
557 <      if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
555 >      smallest = simnfo->boxLx;
556 >      if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy;
557 >      if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz;
558        simnfo->ecr = 0.5 * smallest;
559      } else {
560        simnfo->ecr        = the_globals->getECR();
# Line 443 | Line 582 | void SimSetup::createSim( void ){
582      }
583      simnfo->dielectric = the_globals->getDielectric();  
584    } else {
585 <    if (simnfo->n_dipoles) {
585 >    if (usesDipoles) {
586        
587        if( !the_globals->haveECR() ){
588          sprintf( painCave.errMsg,
589 <                 "SimSetup Warning: using default value of 1/2 the smallest"
589 >                 "SimSetup Warning: using default value of 1/2 the smallest "
590                   "box length for the electrostaticCutoffRadius.\n"
591                   "I hope you have a very fast processor!\n");
592          painCave.isFatal = 0;
593          simError();
594          double smallest;
595 <        smallest = simnfo->box_x;
596 <        if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
597 <        if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
595 >        smallest = simnfo->boxLx;
596 >        if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy;
597 >        if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz;
598          simnfo->ecr = 0.5 * smallest;
599        } else {
600          simnfo->ecr        = the_globals->getECR();
# Line 463 | Line 602 | void SimSetup::createSim( void ){
602        
603        if( !the_globals->haveEST() ){
604          sprintf( painCave.errMsg,
605 <                 "SimSetup Warning: using default value of 5% of the"
605 >                 "SimSetup Warning: using default value of 5%% of the "
606                   "electrostaticCutoffRadius for the "
607                   "electrostaticSkinThickness\n"
608                   );
# Line 634 | Line 773 | void SimSetup::createSim( void ){
773    if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
774  
775  
776 < //   // make the longe range forces and the integrator
776 >  // make the integrator
777 >  
778 >  
779 >  NVT* myNVT = NULL;
780 >  switch( ensembleCase ){
781  
782 < //   new AllLong( simnfo );
782 >  case NVE_ENS:
783 >    new NVE( simnfo, the_ff );
784 >    break;
785  
786 <  if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff );
787 <  if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff );
788 <  if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff );
789 <  if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff );
786 >  case NVT_ENS:
787 >    myNVT = new NVT( simnfo, the_ff );
788 >    myNVT->setTargetTemp(the_globals->getTargetTemp());
789 >
790 >    if (the_globals->haveTauThermostat())
791 >      myNVT->setTauThermostat(the_globals->getTauThermostat());
792 > //     else if (the_globals->haveQmass())
793 > //       myNVT->setQmass(the_globals->getQmass());
794 >    else {
795 >      sprintf( painCave.errMsg,
796 >               "SimSetup error: If you use the NVT\n"
797 >               "    ensemble, you must set either tauThermostat or qMass.\n"
798 >               "    Neither of these was found in the BASS file.\n");
799 >      painCave.isFatal = 1;
800 >      simError();
801 >    }
802 >    break;
803  
804 +  default:
805 +    sprintf( painCave.errMsg,
806 +             "SimSetup Error. Unrecognized ensemble in case statement.\n");
807 +    painCave.isFatal = 1;
808 +    simError();
809 +  }
810  
811  
812 + #ifdef IS_MPI
813 +  mpiSim->mpiRefresh();
814 + #endif
815 +
816    // initialize the Fortran
817 <  
817 >
818 >
819    simnfo->refreshSim();
820    
821    if( !strcmp( simnfo->mixingRule, "standard") ){
# Line 671 | Line 840 | void SimSetup::makeAtoms( void ){
840   #endif // is_mpi
841   }
842  
674 – void SimSetup::makeAtoms( void ){
843  
844 <  int i, j, k, index;
677 <  double ux, uy, uz, uSqr, u;
678 <  AtomStamp* current_atom;
844 > void SimSetup::makeMolecules( void ){
845  
846 +  int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
847 +  molInit info;
848    DirectionalAtom* dAtom;
849 <  int molIndex, molStart, molEnd, nMemb, lMolIndex;
849 >  LinkedAssign* extras;
850 >  LinkedAssign* current_extra;
851 >  AtomStamp* currentAtom;
852 >  BondStamp* currentBond;
853 >  BendStamp* currentBend;
854 >  TorsionStamp* currentTorsion;
855  
856 <  lMolIndex = 0;
857 <  molIndex = 0;
858 <  index = 0;
686 <  for( i=0; i<n_components; i++ ){
856 >  bond_pair* theBonds;
857 >  bend_set* theBends;
858 >  torsion_set* theTorsions;
859  
860 <    for( j=0; j<components_nmol[i]; j++ ){
860 >  
861 >  //init the forceField paramters
862  
863 < #ifdef IS_MPI
691 <      if( mpiSim->getMyMolStart() <= molIndex &&
692 <          molIndex <= mpiSim->getMyMolEnd() ){
693 < #endif // is_mpi        
863 >  the_ff->readParams();
864  
865 <        molStart = index;
866 <        nMemb = comp_stamps[i]->getNAtoms();
697 <        for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){
698 <          
699 <          current_atom = comp_stamps[i]->getAtom( k );
700 <          if( current_atom->haveOrientation() ){
701 <            
702 <            dAtom = new DirectionalAtom(index);
703 <            simnfo->n_oriented++;
704 <            the_atoms[index] = dAtom;
705 <            
706 <            ux = current_atom->getOrntX();
707 <            uy = current_atom->getOrntY();
708 <            uz = current_atom->getOrntZ();
709 <            
710 <            uSqr = (ux * ux) + (uy * uy) + (uz * uz);
711 <            
712 <            u = sqrt( uSqr );
713 <            ux = ux / u;
714 <            uy = uy / u;
715 <            uz = uz / u;
716 <            
717 <            dAtom->setSUx( ux );
718 <            dAtom->setSUy( uy );
719 <            dAtom->setSUz( uz );
720 <          }
721 <          else{
722 <            the_atoms[index] = new GeneralAtom(index);
723 <          }
724 <          the_atoms[index]->setType( current_atom->getType() );
725 <          the_atoms[index]->setIndex( index );
726 <          
727 <          // increment the index and repeat;
728 <          index++;
729 <        }
730 <        
731 <        molEnd = index -1;
732 <        the_molecules[lMolIndex].setNMembers( nMemb );
733 <        the_molecules[lMolIndex].setStartAtom( molStart );
734 <        the_molecules[lMolIndex].setEndAtom( molEnd );
735 <        the_molecules[lMolIndex].setStampID( i );
736 <        lMolIndex++;
865 >  
866 >  // init the atoms
867  
868 < #ifdef IS_MPI
869 <      }
870 < #endif //is_mpi
871 <      
872 <      molIndex++;
743 <    }
744 <  }
745 <
746 < #ifdef IS_MPI
747 <    for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] );
868 >  double ux, uy, uz, u, uSqr;
869 >  
870 >  atomOffset = 0;
871 >  excludeOffset = 0;
872 >  for(i=0; i<simnfo->n_mol; i++){
873      
874 <    delete[] globalIndex;
874 >    stampID = the_molecules[i].getStampID();
875  
876 <    mpiSim->mpiRefresh();
877 < #endif //IS_MPI
878 <          
879 <  the_ff->initializeAtoms();
880 < }
876 >    info.nAtoms    = comp_stamps[stampID]->getNAtoms();
877 >    info.nBonds    = comp_stamps[stampID]->getNBonds();
878 >    info.nBends    = comp_stamps[stampID]->getNBends();
879 >    info.nTorsions = comp_stamps[stampID]->getNTorsions();
880 >    info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
881  
882 < void SimSetup::makeBonds( void ){
883 <
884 <  int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
885 <  bond_pair* the_bonds;
886 <  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++ ){
769 <
770 <    for( j=0; j<components_nmol[i]; j++ ){
771 <
772 < #ifdef IS_MPI
773 <      if( mpiSim->getMyMolStart() <= molIndex &&
774 <          molIndex <= mpiSim->getMyMolEnd() ){
775 < #endif // is_mpi        
776 <        
777 <        for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){
778 <          
779 <          current_bond = comp_stamps[i]->getBond( k );
780 <          the_bonds[index].a = current_bond->getA() + offset;
781 <          the_bonds[index].b = current_bond->getB() + offset;
782 <
783 <          exI = the_bonds[index].a;
784 <          exJ = the_bonds[index].b;
882 >    info.myAtoms = &the_atoms[atomOffset];
883 >    info.myExcludes = &the_excludes[excludeOffset];
884 >    info.myBonds = new Bond*[info.nBonds];
885 >    info.myBends = new Bend*[info.nBends];
886 >    info.myTorsions = new Torsion*[info.nTorsions];
887  
888 <          // exclude_I must always be the smaller of the pair
889 <          if( exI > exJ ){
890 <            tempEx = exI;
891 <            exI = exJ;
892 <            exJ = tempEx;
893 <          }
894 <
895 <          
896 < #ifdef IS_MPI
897 <
796 <          the_excludes[index*2] =    
797 <            the_atoms[exI]->getGlobalIndex() + 1;
798 <          the_excludes[index*2 + 1] =
799 <            the_atoms[exJ]->getGlobalIndex() + 1;
800 <
801 < #else  // isn't MPI
802 <          
803 <          the_excludes[index*2] =     exI + 1;
804 <          the_excludes[index*2 + 1] = exJ + 1;
805 <          // fortran index from 1 (hence the +1 in the indexing)
806 < #endif  //is_mpi
807 <          
808 <          // increment the index and repeat;
809 <          index++;
810 <        }
811 <        offset += comp_stamps[i]->getNAtoms();
888 >    theBonds = new bond_pair[info.nBonds];
889 >    theBends = new bend_set[info.nBends];
890 >    theTorsions = new torsion_set[info.nTorsions];
891 >    
892 >    // make the Atoms
893 >    
894 >    for(j=0; j<info.nAtoms; j++){
895 >      
896 >      currentAtom = comp_stamps[stampID]->getAtom( j );
897 >      if( currentAtom->haveOrientation() ){
898          
899 < #ifdef IS_MPI
899 >        dAtom = new DirectionalAtom(j + atomOffset);
900 >        simnfo->n_oriented++;
901 >        info.myAtoms[j] = dAtom;
902 >        
903 >        ux = currentAtom->getOrntX();
904 >        uy = currentAtom->getOrntY();
905 >        uz = currentAtom->getOrntZ();
906 >        
907 >        uSqr = (ux * ux) + (uy * uy) + (uz * uz);
908 >        
909 >        u = sqrt( uSqr );
910 >        ux = ux / u;
911 >        uy = uy / u;
912 >        uz = uz / u;
913 >        
914 >        dAtom->setSUx( ux );
915 >        dAtom->setSUy( uy );
916 >        dAtom->setSUz( uz );
917        }
918 < #endif //is_mpi
918 >      else{
919 >        info.myAtoms[j] = new GeneralAtom(j + atomOffset);
920 >      }
921 >      info.myAtoms[j]->setType( currentAtom->getType() );
922 >    
923 > #ifdef IS_MPI
924        
925 <      molIndex++;
926 <    }      
927 <  }
925 >      info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
926 >      
927 > #endif // is_mpi
928 >    }
929 >    
930 >    // make the bonds
931 >    for(j=0; j<info.nBonds; j++){
932 >      
933 >      currentBond = comp_stamps[stampID]->getBond( j );
934 >      theBonds[j].a = currentBond->getA() + atomOffset;
935 >      theBonds[j].b = currentBond->getB() + atomOffset;
936  
937 <  the_ff->initializeBonds( the_bonds );
938 < }
937 >      exI = theBonds[j].a;
938 >      exJ = theBonds[j].b;
939  
940 < void SimSetup::makeBends( void ){
941 <
942 <  int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
943 <  bend_set* the_bends;
944 <  BendStamp* current_bend;
945 <  LinkedAssign* extras;
830 <  LinkedAssign* current_extra;
831 <  
832 <
833 <  the_bends = new bend_set[tot_bends];
834 <  index = 0;
835 <  offset = 0;
836 <  molIndex = 0;
837 <  for( i=0; i<n_components; i++ ){
838 <
839 <    for( j=0; j<components_nmol[i]; j++ ){
840 <
940 >      // exclude_I must always be the smaller of the pair
941 >      if( exI > exJ ){
942 >        tempEx = exI;
943 >        exI = exJ;
944 >        exJ = tempEx;
945 >      }
946   #ifdef IS_MPI
947 <      if( mpiSim->getMyMolStart() <= molIndex &&
948 <          molIndex <= mpiSim->getMyMolEnd() ){
949 < #endif // is_mpi        
947 >      tempEx = exI;
948 >      exI = the_atoms[tempEx]->getGlobalIndex() + 1;
949 >      tempEx = exJ;
950 >      exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
951 >      
952 >      the_excludes[j+excludeOffset]->setPair( exI, exJ );
953 > #else  // isn't MPI
954  
955 <        for( k=0; k<comp_stamps[i]->getNBends(); k++ ){
955 >      the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
956 > #endif  //is_mpi
957 >    }
958 >    excludeOffset += info.nBonds;
959 >
960 >    //make the bends
961 >    for(j=0; j<info.nBends; j++){
962 >      
963 >      currentBend = comp_stamps[stampID]->getBend( j );
964 >      theBends[j].a = currentBend->getA() + atomOffset;
965 >      theBends[j].b = currentBend->getB() + atomOffset;
966 >      theBends[j].c = currentBend->getC() + atomOffset;
967            
968 <          current_bend = comp_stamps[i]->getBend( k );
849 <          the_bends[index].a = current_bend->getA() + offset;
850 <          the_bends[index].b = current_bend->getB() + offset;
851 <          the_bends[index].c = current_bend->getC() + offset;
852 <          
853 <          if( current_bend->haveExtras() ){
968 >      if( currentBend->haveExtras() ){
969              
970 <            extras = current_bend->getExtras();
971 <            current_extra = extras;
970 >        extras = currentBend->getExtras();
971 >        current_extra = extras;
972              
973 <            while( current_extra != NULL ){
974 <              if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
973 >        while( current_extra != NULL ){
974 >          if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
975                  
976 <                switch( current_extra->getType() ){
976 >            switch( current_extra->getType() ){
977 >              
978 >            case 0:
979 >              theBends[j].ghost =
980 >                current_extra->getInt() + atomOffset;
981 >              theBends[j].isGhost = 1;
982 >              break;
983                    
984 <                case 0:
985 <                  the_bends[index].ghost =
986 <                    current_extra->getInt() + offset;
987 <                  the_bends[index].isGhost = 1;
988 <                  break;
868 <                  
869 <                case 1:
870 <                  the_bends[index].ghost =
871 <                    (int)current_extra->getDouble() + offset;
872 <                  the_bends[index].isGhost = 1;
873 <                  break;
874 <                  
875 <                default:
876 <                  sprintf( painCave.errMsg,
877 <                           "SimSetup Error: ghostVectorSource was neiter a "
878 <                           "double nor an int.\n"
879 <                           "-->Bend[%d] in %s\n",
880 <                           k, comp_stamps[i]->getID() );
881 <                  painCave.isFatal = 1;
882 <                  simError();
883 <                }
884 <              }
984 >            case 1:
985 >              theBends[j].ghost =
986 >                (int)current_extra->getDouble() + atomOffset;
987 >              theBends[j].isGhost = 1;
988 >              break;
989                
990 <              else{
991 <                
992 <                sprintf( painCave.errMsg,
993 <                         "SimSetup Error: unhandled bend assignment:\n"
994 <                         "    -->%s in Bend[%d] in %s\n",
995 <                         current_extra->getlhs(),
996 <                         k, comp_stamps[i]->getID() );
997 <                painCave.isFatal = 1;
894 <                simError();
895 <              }
896 <              
897 <              current_extra = current_extra->getNext();
990 >            default:
991 >              sprintf( painCave.errMsg,
992 >                       "SimSetup Error: ghostVectorSource was neither a "
993 >                       "double nor an int.\n"
994 >                       "-->Bend[%d] in %s\n",
995 >                       j, comp_stamps[stampID]->getID() );
996 >              painCave.isFatal = 1;
997 >              simError();
998              }
999            }
1000            
901 –          if( !the_bends[index].isGhost ){
902 –            
903 –            exI = the_bends[index].a;
904 –            exJ = the_bends[index].c;
905 –          }
1001            else{
1002              
1003 <            exI = the_bends[index].a;
1004 <            exJ = the_bends[index].b;
1003 >            sprintf( painCave.errMsg,
1004 >                     "SimSetup Error: unhandled bend assignment:\n"
1005 >                     "    -->%s in Bend[%d] in %s\n",
1006 >                     current_extra->getlhs(),
1007 >                     j, comp_stamps[stampID]->getID() );
1008 >            painCave.isFatal = 1;
1009 >            simError();
1010            }
1011            
1012 <          // exclude_I must always be the smaller of the pair
1013 <          if( exI > exJ ){
1014 <            tempEx = exI;
1015 <            exI = exJ;
1016 <            exJ = tempEx;
1017 <          }
1012 >          current_extra = current_extra->getNext();
1013 >        }
1014 >      }
1015 >          
1016 >      if( !theBends[j].isGhost ){
1017 >            
1018 >        exI = theBends[j].a;
1019 >        exJ = theBends[j].c;
1020 >      }
1021 >      else{
1022 >        
1023 >        exI = theBends[j].a;
1024 >        exJ = theBends[j].b;
1025 >      }
1026 >      
1027 >      // exclude_I must always be the smaller of the pair
1028 >      if( exI > exJ ){
1029 >        tempEx = exI;
1030 >        exI = exJ;
1031 >        exJ = tempEx;
1032 >      }
1033 > #ifdef IS_MPI
1034 >      tempEx = exI;
1035 >      exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1036 >      tempEx = exJ;
1037 >      exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1038 >      
1039 >      the_excludes[j+excludeOffset]->setPair( exI, exJ );
1040 > #else  // isn't MPI
1041 >      the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1042 > #endif  //is_mpi
1043 >    }
1044 >    excludeOffset += info.nBends;
1045  
1046 +    for(j=0; j<info.nTorsions; j++){
1047 +      
1048 +      currentTorsion = comp_stamps[stampID]->getTorsion( j );
1049 +      theTorsions[j].a = currentTorsion->getA() + atomOffset;
1050 +      theTorsions[j].b = currentTorsion->getB() + atomOffset;
1051 +      theTorsions[j].c = currentTorsion->getC() + atomOffset;
1052 +      theTorsions[j].d = currentTorsion->getD() + atomOffset;
1053 +      
1054 +      exI = theTorsions[j].a;
1055 +      exJ = theTorsions[j].d;
1056  
1057 +      // exclude_I must always be the smaller of the pair
1058 +      if( exI > exJ ){
1059 +        tempEx = exI;
1060 +        exI = exJ;
1061 +        exJ = tempEx;
1062 +      }
1063   #ifdef IS_MPI
1064 <
1065 <          the_excludes[(index + tot_bonds)*2] =    
1066 <            the_atoms[exI]->getGlobalIndex() + 1;
1067 <          the_excludes[(index + tot_bonds)*2 + 1] =
1068 <            the_atoms[exJ]->getGlobalIndex() + 1;
1069 <          
1064 >      tempEx = exI;
1065 >      exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1066 >      tempEx = exJ;
1067 >      exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1068 >      
1069 >      the_excludes[j+excludeOffset]->setPair( exI, exJ );
1070   #else  // isn't MPI
1071 <          
929 <          the_excludes[(index + tot_bonds)*2] =     exI + 1;
930 <          the_excludes[(index + tot_bonds)*2 + 1] = exJ + 1;
931 <          // fortran index from 1 (hence the +1 in the indexing)
1071 >      the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1072   #endif  //is_mpi
933 –          
934 –          
935 –          // increment the index and repeat;
936 –          index++;
937 –        }
938 –        offset += comp_stamps[i]->getNAtoms();
939 –        
940 – #ifdef IS_MPI
941 –      }
942 – #endif //is_mpi
943 –
944 –      molIndex++;
1073      }
1074 +    excludeOffset += info.nTorsions;
1075 +
1076 +    
1077 +    // send the arrays off to the forceField for init.
1078 +
1079 +    the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
1080 +    the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
1081 +    the_ff->initializeBends( info.nBends, info.myBends, theBends );
1082 +    the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
1083 +
1084 +
1085 +    the_molecules[i].initialize( info );
1086 +
1087 +
1088 +    atomOffset += info.nAtoms;
1089 +    delete[] theBonds;
1090 +    delete[] theBends;
1091 +    delete[] theTorsions;
1092    }
1093  
1094   #ifdef IS_MPI
1095 <  sprintf( checkPointMsg,
950 <           "Successfully created the bends list.\n" );
1095 >  sprintf( checkPointMsg, "all molecules initialized succesfully" );
1096    MPIcheckPoint();
1097   #endif // is_mpi
953 –  
1098  
1099 <  the_ff->initializeBends( the_bends );
1100 < }
1099 >  // clean up the forcefield
1100 >  the_ff->calcRcut();
1101 >  the_ff->cleanMe();
1102  
958 – void SimSetup::makeTorsions( void ){
959 –
960 –  int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
961 –  torsion_set* the_torsions;
962 –  TorsionStamp* current_torsion;
963 –
964 –  the_torsions = new torsion_set[tot_torsions];
965 –  index = 0;
966 –  offset = 0;
967 –  molIndex = 0;
968 –  for( i=0; i<n_components; i++ ){
969 –
970 –    for( j=0; j<components_nmol[i]; j++ ){
971 –
972 – #ifdef IS_MPI
973 –      if( mpiSim->getMyMolStart() <= molIndex &&
974 –          molIndex <= mpiSim->getMyMolEnd() ){
975 – #endif // is_mpi        
976 –
977 –      for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){
978 –
979 –        current_torsion = comp_stamps[i]->getTorsion( k );
980 –        the_torsions[index].a = current_torsion->getA() + offset;
981 –        the_torsions[index].b = current_torsion->getB() + offset;
982 –        the_torsions[index].c = current_torsion->getC() + offset;
983 –        the_torsions[index].d = current_torsion->getD() + offset;
984 –
985 –        exI = the_torsions[index].a;
986 –        exJ = the_torsions[index].d;
987 –
988 –        
989 –        // exclude_I must always be the smaller of the pair
990 –        if( exI > exJ ){
991 –          tempEx = exI;
992 –          exI = exJ;
993 –          exJ = tempEx;
994 –        }
995 –
996 –
997 – #ifdef IS_MPI
998 –        
999 –        the_excludes[(index + tot_bonds + tot_bends)*2] =    
1000 –          the_atoms[exI]->getGlobalIndex() + 1;
1001 –        the_excludes[(index + tot_bonds + tot_bends)*2 + 1] =
1002 –          the_atoms[exJ]->getGlobalIndex() + 1;
1003 –        
1004 – #else  // isn't MPI
1005 –        
1006 –        the_excludes[(index + tot_bonds + tot_bends)*2] =     exI + 1;
1007 –        the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = exJ + 1;
1008 –        // fortran indexes from 1 (hence the +1 in the indexing)
1009 – #endif  //is_mpi
1010 –        
1011 –
1012 –        // increment the index and repeat;
1013 –        index++;
1014 –      }
1015 –      offset += comp_stamps[i]->getNAtoms();
1016 –
1017 – #ifdef IS_MPI
1018 –      }
1019 – #endif //is_mpi      
1020 –
1021 –      molIndex++;
1022 –    }
1023 –  }
1024 –
1025 –  the_ff->initializeTorsions( the_torsions );
1103   }
1104  
1105   void SimSetup::initFromBass( void ){
# Line 1044 | Line 1121 | void SimSetup::initFromBass( void ){
1121      have_extra =1;
1122  
1123      n_cells = (int)temp3 - 1;
1124 <    cellx = simnfo->box_x / temp3;
1125 <    celly = simnfo->box_y / temp3;
1126 <    cellz = simnfo->box_z / temp3;
1124 >    cellx = simnfo->boxLx / temp3;
1125 >    celly = simnfo->boxLy / temp3;
1126 >    cellz = simnfo->boxLz / temp3;
1127      n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
1128      temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1129      n_per_extra = (int)ceil( temp1 );
# Line 1061 | Line 1138 | void SimSetup::initFromBass( void ){
1138    }
1139    else{
1140      n_cells = (int)temp3;
1141 <    cellx = simnfo->box_x / temp3;
1142 <    celly = simnfo->box_y / temp3;
1143 <    cellz = simnfo->box_z / temp3;
1141 >    cellx = simnfo->boxLx / temp3;
1142 >    celly = simnfo->boxLy / temp3;
1143 >    cellz = simnfo->boxLz / temp3;
1144    }
1145  
1146    current_mol = 0;

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