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root/group/branches/no-template-branch/OOPSE/libmdtools/SimSetup.cpp
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Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 414 by mmeineke, Wed Mar 26 22:02:36 2003 UTC vs.
Revision 572 by mmeineke, Wed Jul 2 21:26:55 2003 UTC

# Line 12 | Line 12
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 +    
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      
# Line 326 | Line 472 | void SimSetup::createSim( void ){
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 );
644 <  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 683 | Line 852 | void SimSetup::makeMolecules( void ){
852    BondStamp* currentBond;
853    BendStamp* currentBend;
854    TorsionStamp* currentTorsion;
855 +
856 +  bond_pair* theBonds;
857 +  bend_set* theBends;
858 +  torsion_set* theTorsions;
859 +
860    
861    //init the forceField paramters
862  
863    the_ff->readParams();
864  
865    
866 <  // init the molecules
866 >  // init the atoms
867  
868 +  double ux, uy, uz, u, uSqr;
869 +  
870    atomOffset = 0;
871    excludeOffset = 0;
872    for(i=0; i<simnfo->n_mol; i++){
# Line 707 | Line 883 | void SimSetup::makeMolecules( void ){
883      info.myExcludes = &the_excludes[excludeOffset];
884      info.myBonds = new Bond*[info.nBonds];
885      info.myBends = new Bend*[info.nBends];
886 <    info.myTorsions = new Torsions*[info.nTorsions];
886 >    info.myTorsions = new Torsion*[info.nTorsions];
887  
888      theBonds = new bond_pair[info.nBonds];
889      theBends = new bend_set[info.nBends];
# Line 717 | Line 893 | void SimSetup::makeMolecules( void ){
893      
894      for(j=0; j<info.nAtoms; j++){
895        
896 <      currentAtom = theComponents[stampID]->getAtom( j );
896 >      currentAtom = comp_stamps[stampID]->getAtom( j );
897        if( currentAtom->haveOrientation() ){
898          
899          dAtom = new DirectionalAtom(j + atomOffset);
# Line 758 | Line 934 | void SimSetup::makeMolecules( void ){
934        theBonds[j].a = currentBond->getA() + atomOffset;
935        theBonds[j].b = currentBond->getB() + atomOffset;
936  
937 <      exI = theBonds[i].a;
938 <      exJ = theBonds[i].b;
937 >      exI = theBonds[j].a;
938 >      exJ = theBonds[j].b;
939  
940        // exclude_I must always be the smaller of the pair
941        if( exI > exJ ){
# Line 775 | Line 951 | void SimSetup::makeMolecules( void ){
951        
952        the_excludes[j+excludeOffset]->setPair( exI, exJ );
953   #else  // isn't MPI
954 +
955        the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
956   #endif  //is_mpi
957      }
# Line 790 | Line 967 | void SimSetup::makeMolecules( void ){
967            
968        if( currentBend->haveExtras() ){
969              
970 <        extras = current_bend->getExtras();
970 >        extras = currentBend->getExtras();
971          current_extra = extras;
972              
973          while( current_extra != NULL ){
# Line 812 | Line 989 | void SimSetup::makeMolecules( void ){
989                
990              default:
991                sprintf( painCave.errMsg,
992 <                       "SimSetup Error: ghostVectorSource was neiter a "
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() );
# Line 906 | Line 1083 | void SimSetup::makeMolecules( void ){
1083  
1084  
1085      the_molecules[i].initialize( info );
909 –    atomOffset += info.nAtoms;
910 –  }
911 –
912 –  // clean up the forcefield
913 –
914 –  the_ff->cleanMe();
915 – }
916 –
917 –
918 –
919 – void SimSetup::makeAtoms( void ){
920 –
921 –  int i, j, k, index;
922 –  double ux, uy, uz, uSqr, u;
923 –  AtomStamp* current_atom;
924 –
925 –  DirectionalAtom* dAtom;
926 –  int molIndex, molStart, molEnd, nMemb, lMolIndex;
927 –
928 –  lMolIndex = 0;
929 –  molIndex = 0;
930 –  index = 0;
931 –  for( i=0; i<n_components; i++ ){
932 –
933 –    for( j=0; j<components_nmol[i]; j++ ){
934 –
935 – #ifdef IS_MPI
936 –      if( mpiSim->getMyMolStart() <= molIndex &&
937 –          molIndex <= mpiSim->getMyMolEnd() ){
938 – #endif // is_mpi        
939 –
940 –        molStart = index;
941 –        nMemb = comp_stamps[i]->getNAtoms();
942 –        for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){
943 –          
944 –          current_atom = comp_stamps[i]->getAtom( k );
945 –          if( current_atom->haveOrientation() ){
946 –            
947 –            dAtom = new DirectionalAtom(index);
948 –            simnfo->n_oriented++;
949 –            the_atoms[index] = dAtom;
950 –            
951 –            ux = current_atom->getOrntX();
952 –            uy = current_atom->getOrntY();
953 –            uz = current_atom->getOrntZ();
954 –            
955 –            uSqr = (ux * ux) + (uy * uy) + (uz * uz);
956 –            
957 –            u = sqrt( uSqr );
958 –            ux = ux / u;
959 –            uy = uy / u;
960 –            uz = uz / u;
961 –            
962 –            dAtom->setSUx( ux );
963 –            dAtom->setSUy( uy );
964 –            dAtom->setSUz( uz );
965 –          }
966 –          else{
967 –            the_atoms[index] = new GeneralAtom(index);
968 –          }
969 –          the_atoms[index]->setType( current_atom->getType() );
970 –          the_atoms[index]->setIndex( index );
971 –          
972 –          // increment the index and repeat;
973 –          index++;
974 –        }
975 –        
976 –        molEnd = index -1;
977 –        the_molecules[lMolIndex].setNMembers( nMemb );
978 –        the_molecules[lMolIndex].setStartAtom( molStart );
979 –        the_molecules[lMolIndex].setEndAtom( molEnd );
980 –        the_molecules[lMolIndex].setStampID( i );
981 –        lMolIndex++;
982 –
983 – #ifdef IS_MPI
984 –      }
985 – #endif //is_mpi
986 –      
987 –      molIndex++;
988 –    }
989 –  }
990 –
991 – #ifdef IS_MPI
992 –    for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] );
993 –    
994 –    delete[] globalIndex;
995 –
996 –    mpiSim->mpiRefresh();
997 – #endif //IS_MPI
998 –          
999 –  the_ff->initializeAtoms();
1000 – }
1001 –
1002 – void SimSetup::makeBonds( void ){
1003 –
1004 –  int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
1005 –  bond_pair* the_bonds;
1006 –  BondStamp* current_bond;
1007 –
1008 –  the_bonds = new bond_pair[tot_bonds];
1009 –  index = 0;
1010 –  offset = 0;
1011 –  molIndex = 0;
1012 –
1013 –  for( i=0; i<n_components; i++ ){
1014 –
1015 –    for( j=0; j<components_nmol[i]; j++ ){
1016 –
1017 – #ifdef IS_MPI
1018 –      if( mpiSim->getMyMolStart() <= molIndex &&
1019 –          molIndex <= mpiSim->getMyMolEnd() ){
1020 – #endif // is_mpi        
1021 –        
1022 –        for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){
1023 –          
1024 –          current_bond = comp_stamps[i]->getBond( k );
1025 –          the_bonds[index].a = current_bond->getA() + offset;
1026 –          the_bonds[index].b = current_bond->getB() + offset;
1027 –
1028 –          exI = the_bonds[index].a;
1029 –          exJ = the_bonds[index].b;
1030 –
1031 –          // exclude_I must always be the smaller of the pair
1032 –          if( exI > exJ ){
1033 –            tempEx = exI;
1034 –            exI = exJ;
1035 –            exJ = tempEx;
1036 –          }
1037 –
1038 –          
1039 – #ifdef IS_MPI
1040 –
1041 –          the_excludes[index*2] =    
1042 –            the_atoms[exI]->getGlobalIndex() + 1;
1043 –          the_excludes[index*2 + 1] =
1044 –            the_atoms[exJ]->getGlobalIndex() + 1;
1045 –
1046 – #else  // isn't MPI
1047 –          
1048 –          the_excludes[index*2] =     exI + 1;
1049 –          the_excludes[index*2 + 1] = exJ + 1;
1050 –          // fortran index from 1 (hence the +1 in the indexing)
1051 – #endif  //is_mpi
1052 –          
1053 –          // increment the index and repeat;
1054 –          index++;
1055 –        }
1056 –        offset += comp_stamps[i]->getNAtoms();
1057 –        
1058 – #ifdef IS_MPI
1059 –      }
1060 – #endif //is_mpi
1061 –      
1062 –      molIndex++;
1063 –    }      
1064 –  }
1065 –
1066 –  the_ff->initializeBonds( the_bonds );
1067 – }
1068 –
1069 – void SimSetup::makeBends( void ){
1070 –
1071 –  int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
1072 –  bend_set* the_bends;
1073 –  BendStamp* current_bend;
1074 –  LinkedAssign* extras;
1075 –  LinkedAssign* current_extra;
1076 –  
1077 –
1078 –  the_bends = new bend_set[tot_bends];
1079 –  index = 0;
1080 –  offset = 0;
1081 –  molIndex = 0;
1082 –  for( i=0; i<n_components; i++ ){
1083 –
1084 –    for( j=0; j<components_nmol[i]; j++ ){
1085 –
1086 – #ifdef IS_MPI
1087 –      if( mpiSim->getMyMolStart() <= molIndex &&
1088 –          molIndex <= mpiSim->getMyMolEnd() ){
1089 – #endif // is_mpi        
1090 –
1091 –        for( k=0; k<comp_stamps[i]->getNBends(); k++ ){
1092 –          
1093 –          current_bend = comp_stamps[i]->getBend( k );
1094 –          the_bends[index].a = current_bend->getA() + offset;
1095 –          the_bends[index].b = current_bend->getB() + offset;
1096 –          the_bends[index].c = current_bend->getC() + offset;
1097 –          
1098 –          if( current_bend->haveExtras() ){
1099 –            
1100 –            extras = current_bend->getExtras();
1101 –            current_extra = extras;
1102 –            
1103 –            while( current_extra != NULL ){
1104 –              if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
1105 –                
1106 –                switch( current_extra->getType() ){
1107 –                  
1108 –                case 0:
1109 –                  the_bends[index].ghost =
1110 –                    current_extra->getInt() + offset;
1111 –                  the_bends[index].isGhost = 1;
1112 –                  break;
1113 –                  
1114 –                case 1:
1115 –                  the_bends[index].ghost =
1116 –                    (int)current_extra->getDouble() + offset;
1117 –                  the_bends[index].isGhost = 1;
1118 –                  break;
1119 –                  
1120 –                default:
1121 –                  sprintf( painCave.errMsg,
1122 –                           "SimSetup Error: ghostVectorSource was neiter a "
1123 –                           "double nor an int.\n"
1124 –                           "-->Bend[%d] in %s\n",
1125 –                           k, comp_stamps[i]->getID() );
1126 –                  painCave.isFatal = 1;
1127 –                  simError();
1128 –                }
1129 –              }
1130 –              
1131 –              else{
1132 –                
1133 –                sprintf( painCave.errMsg,
1134 –                         "SimSetup Error: unhandled bend assignment:\n"
1135 –                         "    -->%s in Bend[%d] in %s\n",
1136 –                         current_extra->getlhs(),
1137 –                         k, comp_stamps[i]->getID() );
1138 –                painCave.isFatal = 1;
1139 –                simError();
1140 –              }
1141 –              
1142 –              current_extra = current_extra->getNext();
1143 –            }
1144 –          }
1145 –          
1146 –          if( !the_bends[index].isGhost ){
1147 –            
1148 –            exI = the_bends[index].a;
1149 –            exJ = the_bends[index].c;
1150 –          }
1151 –          else{
1152 –            
1153 –            exI = the_bends[index].a;
1154 –            exJ = the_bends[index].b;
1155 –          }
1156 –          
1157 –          // exclude_I must always be the smaller of the pair
1158 –          if( exI > exJ ){
1159 –            tempEx = exI;
1160 –            exI = exJ;
1161 –            exJ = tempEx;
1162 –          }
1086  
1087  
1088 < #ifdef IS_MPI
1089 <
1090 <          the_excludes[(index + tot_bonds)*2] =    
1091 <            the_atoms[exI]->getGlobalIndex() + 1;
1169 <          the_excludes[(index + tot_bonds)*2 + 1] =
1170 <            the_atoms[exJ]->getGlobalIndex() + 1;
1171 <          
1172 < #else  // isn't MPI
1173 <          
1174 <          the_excludes[(index + tot_bonds)*2] =     exI + 1;
1175 <          the_excludes[(index + tot_bonds)*2 + 1] = exJ + 1;
1176 <          // fortran index from 1 (hence the +1 in the indexing)
1177 < #endif  //is_mpi
1178 <          
1179 <          
1180 <          // increment the index and repeat;
1181 <          index++;
1182 <        }
1183 <        offset += comp_stamps[i]->getNAtoms();
1184 <        
1185 < #ifdef IS_MPI
1186 <      }
1187 < #endif //is_mpi
1188 <
1189 <      molIndex++;
1190 <    }
1088 >    atomOffset += info.nAtoms;
1089 >    delete[] theBonds;
1090 >    delete[] theBends;
1091 >    delete[] theTorsions;
1092    }
1093  
1094   #ifdef IS_MPI
1095 <  sprintf( checkPointMsg,
1195 <           "Successfully created the bends list.\n" );
1095 >  sprintf( checkPointMsg, "all molecules initialized succesfully" );
1096    MPIcheckPoint();
1097   #endif // is_mpi
1198 –  
1098  
1099 <  the_ff->initializeBends( the_bends );
1100 < }
1099 >  // clean up the forcefield
1100 >  the_ff->calcRcut();
1101 >  the_ff->cleanMe();
1102  
1203 – void SimSetup::makeTorsions( void ){
1204 –
1205 –  int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
1206 –  torsion_set* the_torsions;
1207 –  TorsionStamp* current_torsion;
1208 –
1209 –  the_torsions = new torsion_set[tot_torsions];
1210 –  index = 0;
1211 –  offset = 0;
1212 –  molIndex = 0;
1213 –  for( i=0; i<n_components; i++ ){
1214 –
1215 –    for( j=0; j<components_nmol[i]; j++ ){
1216 –
1217 – #ifdef IS_MPI
1218 –      if( mpiSim->getMyMolStart() <= molIndex &&
1219 –          molIndex <= mpiSim->getMyMolEnd() ){
1220 – #endif // is_mpi        
1221 –
1222 –      for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){
1223 –
1224 –        current_torsion = comp_stamps[i]->getTorsion( k );
1225 –        the_torsions[index].a = current_torsion->getA() + offset;
1226 –        the_torsions[index].b = current_torsion->getB() + offset;
1227 –        the_torsions[index].c = current_torsion->getC() + offset;
1228 –        the_torsions[index].d = current_torsion->getD() + offset;
1229 –
1230 –        exI = the_torsions[index].a;
1231 –        exJ = the_torsions[index].d;
1232 –
1233 –        
1234 –        // exclude_I must always be the smaller of the pair
1235 –        if( exI > exJ ){
1236 –          tempEx = exI;
1237 –          exI = exJ;
1238 –          exJ = tempEx;
1239 –        }
1240 –
1241 –
1242 – #ifdef IS_MPI
1243 –        
1244 –        the_excludes[(index + tot_bonds + tot_bends)*2] =    
1245 –          the_atoms[exI]->getGlobalIndex() + 1;
1246 –        the_excludes[(index + tot_bonds + tot_bends)*2 + 1] =
1247 –          the_atoms[exJ]->getGlobalIndex() + 1;
1248 –        
1249 – #else  // isn't MPI
1250 –        
1251 –        the_excludes[(index + tot_bonds + tot_bends)*2] =     exI + 1;
1252 –        the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = exJ + 1;
1253 –        // fortran indexes from 1 (hence the +1 in the indexing)
1254 – #endif  //is_mpi
1255 –        
1256 –
1257 –        // increment the index and repeat;
1258 –        index++;
1259 –      }
1260 –      offset += comp_stamps[i]->getNAtoms();
1261 –
1262 – #ifdef IS_MPI
1263 –      }
1264 – #endif //is_mpi      
1265 –
1266 –      molIndex++;
1267 –    }
1268 –  }
1269 –
1270 –  the_ff->initializeTorsions( the_torsions );
1103   }
1104  
1105   void SimSetup::initFromBass( void ){
# Line 1289 | 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 1306 | 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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