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root/group/trunk/OOPSE/libmdtools/SimSetup.cpp
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Comparing:
branches/mmeineke/OOPSE/libmdtools/SimSetup.cpp (file contents), Revision 377 by mmeineke, Fri Mar 21 17:42:12 2003 UTC vs.
trunk/OOPSE/libmdtools/SimSetup.cpp (file contents), Revision 586 by mmeineke, Wed Jul 9 22:14:06 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 NPTi_ENS 2
20 + #define NPTf_ENS 3
21 +
22 +
23 + #define FF_DUFF 0
24 + #define FF_LJ   1
25 +
26 +
27   SimSetup::SimSetup(){
28    stamps = new MakeStamps();
29    globals = new Globals();
# Line 66 | Line 78 | void SimSetup::createSim( void ){
78  
79    MakeStamps *the_stamps;
80    Globals* the_globals;
81 <  int i, j;
81 >  int i, j, k, globalAtomIndex;
82 >  
83 >  int ensembleCase;
84 >  int ffCase;
85 >  
86 >  ensembleCase = -1;
87 >  ffCase = -1;
88  
89    // get the stamps and globals;
90    the_stamps = stamps;
# Line 80 | Line 98 | void SimSetup::createSim( void ){
98    // get the ones we know are there, yet still may need some work.
99    n_components = the_globals->getNComponents();
100    strcpy( force_field, the_globals->getForceField() );
101 +
102 +  if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
103 +  else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
104 +  else{
105 +    sprintf( painCave.errMsg,
106 +             "SimSetup Error. Unrecognized force field -> %s\n",
107 +             force_field );
108 +    painCave.isFatal = 1;
109 +    simError();
110 +  }
111 +
112 +  // get the ensemble:
113    strcpy( ensemble, the_globals->getEnsemble() );
114 +
115 +  if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
116 +  else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
117 +  else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
118 +    ensembleCase = NPTi_ENS;
119 +  else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
120 +  else{
121 +    sprintf( painCave.errMsg,
122 +             "SimSetup Warning. Unrecognized Ensemble -> %s, "
123 +             "reverting to NVE for this simulation.\n",
124 +             ensemble );
125 +    painCave.isFatal = 0;
126 +    simError();
127 +    strcpy( ensemble, "NVE" );
128 +    ensembleCase = NVE_ENS;
129 +  }  
130    strcpy( simnfo->ensemble, ensemble );
131 +
132 +
133 + //   if( !strcasecmp( ensemble, "NPT" ) ) {
134 + //     the_extendedsystem = new ExtendedSystem( simnfo );
135 + //     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
136 + //     if (the_globals->haveTargetPressure())
137 + //       the_extendedsystem->setTargetPressure(the_globals->getTargetPressure());
138 + //     else {
139 + //       sprintf( painCave.errMsg,
140 + //                "SimSetup error: If you use the constant pressure\n"
141 + //                "    ensemble, you must set targetPressure.\n"
142 + //                "    This was found in the BASS file.\n");
143 + //       painCave.isFatal = 1;
144 + //       simError();
145 + //     }
146 +
147 + //     if (the_globals->haveTauThermostat())
148 + //       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
149 + //     else if (the_globals->haveQmass())
150 + //       the_extendedsystem->setQmass(the_globals->getQmass());
151 + //     else {
152 + //       sprintf( painCave.errMsg,
153 + //                "SimSetup error: If you use one of the constant temperature\n"
154 + //                "    ensembles, you must set either tauThermostat or qMass.\n"
155 + //                "    Neither of these was found in the BASS file.\n");
156 + //       painCave.isFatal = 1;
157 + //       simError();
158 + //     }
159  
160 + //     if (the_globals->haveTauBarostat())
161 + //       the_extendedsystem->setTauBarostat(the_globals->getTauBarostat());
162 + //     else {
163 + //       sprintf( painCave.errMsg,
164 + //                "SimSetup error: If you use the constant pressure\n"
165 + //                "    ensemble, you must set tauBarostat.\n"
166 + //                "    This was found in the BASS file.\n");
167 + //       painCave.isFatal = 1;
168 + //       simError();
169 + //     }
170 +
171 + //   } else if ( !strcasecmp( ensemble, "NVT") ) {
172 + //     the_extendedsystem = new ExtendedSystem( simnfo );
173 + //     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
174 +
175 + //     if (the_globals->haveTauThermostat())
176 + //       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
177 + //     else if (the_globals->haveQmass())
178 + //       the_extendedsystem->setQmass(the_globals->getQmass());
179 + //     else {
180 + //       sprintf( painCave.errMsg,
181 + //                "SimSetup error: If you use one of the constant temperature\n"
182 + //                "    ensembles, you must set either tauThermostat or qMass.\n"
183 + //                "    Neither of these was found in the BASS file.\n");
184 + //       painCave.isFatal = 1;
185 + //       simError();
186 + //     }
187 +
188    strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
189    simnfo->usePBC = the_globals->getPBC();
190            
191 +  int usesDipoles = 0;
192 +  switch( ffCase ){
193  
194 +  case FF_DUFF:
195 +    the_ff = new DUFF();
196 +    usesDipoles = 1;
197 +    break;
198  
199 <  if( !strcmp( force_field, "TraPPE" ) ) the_ff = new TraPPEFF();
200 <  else if( !strcmp( force_field, "DipoleTest" ) ) the_ff = new DipoleTestFF();
201 <  else if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF();
202 <  else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
203 <  else{
199 >  case FF_LJ:
200 >    the_ff = new LJFF();
201 >    break;
202 >
203 >  default:
204      sprintf( painCave.errMsg,
205 <             "SimSetup Error. Unrecognized force field -> %s\n",
98 <             force_field );
205 >             "SimSetup Error. Unrecognized force field in case statement.\n");
206      painCave.isFatal = 1;
207      simError();
208    }
# Line 105 | Line 212 | void SimSetup::createSim( void ){
212    MPIcheckPoint();
213   #endif // is_mpi
214  
108 –  
109 –
215    // get the components and calculate the tot_nMol and indvidual n_mol
216    the_components = the_globals->getComponents();
217    components_nmol = new int[n_components];
# Line 230 | Line 335 | void SimSetup::createSim( void ){
335    simnfo->n_torsions = tot_torsions;
336    simnfo->n_SRI = tot_SRI;
337    simnfo->n_mol = tot_nmol;
233 –
338    
339 +  simnfo->molMembershipArray = new int[tot_atoms];
340 +
341   #ifdef IS_MPI
342  
343    // divide the molecules among processors here.
344    
345    mpiSim = new mpiSimulation( simnfo );
346    
241 –  
242 –
347    globalIndex = mpiSim->divideLabor();
348  
245 –
246 –
349    // set up the local variables
350    
351    int localMol, allMol;
352    int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
353 +
354 +  int* mol2proc = mpiSim->getMolToProcMap();
355 +  int* molCompType = mpiSim->getMolComponentType();
356    
357    allMol = 0;
358    localMol = 0;
# Line 255 | Line 360 | void SimSetup::createSim( void ){
360    local_bonds = 0;
361    local_bends = 0;
362    local_torsions = 0;
363 +  globalAtomIndex = 0;
364 +
365 +
366    for( i=0; i<n_components; i++ ){
367  
368      for( j=0; j<components_nmol[i]; j++ ){
369        
370 <      if( mpiSim->getMyMolStart() <= allMol &&
263 <          allMol <= mpiSim->getMyMolEnd() ){
370 >      if( mol2proc[allMol] == worldRank ){
371          
372          local_atoms +=    comp_stamps[i]->getNAtoms();
373          local_bonds +=    comp_stamps[i]->getNBonds();
# Line 268 | Line 375 | void SimSetup::createSim( void ){
375          local_torsions += comp_stamps[i]->getNTorsions();
376          localMol++;
377        }      
378 <      allMol++;
378 >      for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
379 >        simnfo->molMembershipArray[globalAtomIndex] = allMol;
380 >        globalAtomIndex++;
381 >      }
382 >
383 >      allMol++;      
384      }
385    }
386    local_SRI = local_bonds + local_bends + local_torsions;
387    
276 –
388    simnfo->n_atoms = mpiSim->getMyNlocal();  
389    
390    if( local_atoms != simnfo->n_atoms ){
391      sprintf( painCave.errMsg,
392               "SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
393 <             " localAtom (%d) are note equal.\n",
393 >             " localAtom (%d) are not equal.\n",
394               simnfo->n_atoms,
395               local_atoms );
396      painCave.isFatal = 1;
# Line 304 | Line 415 | void SimSetup::createSim( void ){
415    Atom::createArrays(simnfo->n_atoms);
416    the_atoms = new Atom*[simnfo->n_atoms];
417    the_molecules = new Molecule[simnfo->n_mol];
418 +  int molIndex;
419  
420 +  // initialize the molecule's stampID's
421  
422 + #ifdef IS_MPI
423 +  
424 +
425 +  molIndex = 0;
426 +  for(i=0; i<mpiSim->getTotNmol(); i++){
427 +    
428 +    if(mol2proc[i] == worldRank ){
429 +      the_molecules[molIndex].setStampID( molCompType[i] );
430 +      the_molecules[molIndex].setMyIndex( molIndex );
431 +      the_molecules[molIndex].setGlobalIndex( i );
432 +      molIndex++;
433 +    }
434 +  }
435 +
436 + #else // is_mpi
437 +  
438 +  molIndex = 0;
439 +  globalAtomIndex = 0;
440 +  for(i=0; i<n_components; i++){
441 +    for(j=0; j<components_nmol[i]; j++ ){
442 +      the_molecules[molIndex].setStampID( i );
443 +      the_molecules[molIndex].setMyIndex( molIndex );
444 +      the_molecules[molIndex].setGlobalIndex( molIndex );
445 +      for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
446 +        simnfo->molMembershipArray[globalAtomIndex] = molIndex;
447 +        globalAtomIndex++;
448 +      }
449 +      molIndex++;
450 +    }
451 +  }
452 +    
453 +
454 + #endif // is_mpi
455 +
456 +
457    if( simnfo->n_SRI ){
458 <    the_sris = new SRI*[simnfo->n_SRI];
459 <    the_excludes = new int[2 * simnfo->n_SRI];
458 >    
459 >    Exclude::createArray(simnfo->n_SRI);
460 >    the_excludes = new Exclude*[simnfo->n_SRI];
461 >    for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
462      simnfo->globalExcludes = new int;
463 <    simnfo->n_exclude = tot_SRI;
463 >    simnfo->n_exclude = simnfo->n_SRI;
464    }
465    else{
466      
467 <    the_excludes = new int[2];
468 <    the_excludes[0] = 0;
469 <    the_excludes[1] = 0;
467 >    Exclude::createArray( 1 );
468 >    the_excludes = new Exclude*;
469 >    the_excludes[0] = new Exclude(0);
470 >    the_excludes[0]->setPair( 0,0 );
471      simnfo->globalExcludes = new int;
472      simnfo->globalExcludes[0] = 0;
473 <
323 <    simnfo->n_exclude = 1;
473 >    simnfo->n_exclude = 0;
474    }
475  
476    // set the arrays into the SimInfo object
477  
478    simnfo->atoms = the_atoms;
479 <  simnfo->sr_interactions = the_sris;
479 >  simnfo->molecules = the_molecules;
480    simnfo->nGlobalExcludes = 0;
481    simnfo->excludes = the_excludes;
482  
483  
484    // get some of the tricky things that may still be in the globals
485  
486 <  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
360 <  
486 >  double boxVector[3];
487    if( the_globals->haveBox() ){
488 <    simnfo->box_x = the_globals->getBox();
489 <    simnfo->box_y = the_globals->getBox();
490 <    simnfo->box_z = the_globals->getBox();
488 >    boxVector[0] = the_globals->getBox();
489 >    boxVector[1] = the_globals->getBox();
490 >    boxVector[2] = the_globals->getBox();
491 >    
492 >    simnfo->setBox( boxVector );
493    }
494    else if( the_globals->haveDensity() ){
495  
496      double vol;
497      vol = (double)tot_nmol / the_globals->getDensity();
498 <    simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
499 <    simnfo->box_y = simnfo->box_x;
500 <    simnfo->box_z = simnfo->box_x;
498 >     boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
499 >     boxVector[1] = boxVector[0];
500 >     boxVector[2] = boxVector[0];
501 >
502 >    simnfo->setBox( boxVector );
503    }
504    else{
505      if( !the_globals->haveBoxX() ){
# Line 378 | Line 508 | void SimSetup::createSim( void ){
508        painCave.isFatal = 1;
509        simError();
510      }
511 <    simnfo->box_x = the_globals->getBoxX();
511 >    boxVector[0] = the_globals->getBoxX();
512  
513      if( !the_globals->haveBoxY() ){
514        sprintf( painCave.errMsg,
# Line 386 | Line 516 | void SimSetup::createSim( void ){
516        painCave.isFatal = 1;
517        simError();
518      }
519 <    simnfo->box_y = the_globals->getBoxY();
519 >    boxVector[1] = the_globals->getBoxY();
520  
521      if( !the_globals->haveBoxZ() ){
522        sprintf( painCave.errMsg,
# Line 394 | Line 524 | void SimSetup::createSim( void ){
524        painCave.isFatal = 1;
525        simError();
526      }
527 <    simnfo->box_z = the_globals->getBoxZ();
527 >    boxVector[2] = the_globals->getBoxZ();
528 >
529 >    simnfo->setBox( boxVector );
530    }
531  
532   #ifdef IS_MPI
# Line 407 | Line 539 | void SimSetup::createSim( void ){
539  
540    the_ff->setSimInfo( simnfo );
541  
542 <  makeAtoms();
542 >  makeMolecules();
543    simnfo->identArray = new int[simnfo->n_atoms];
544    for(i=0; i<simnfo->n_atoms; i++){
545      simnfo->identArray[i] = the_atoms[i]->getIdent();
546    }
547    
548 <  if( tot_bonds ){
549 <    makeBonds();
550 <  }
551 <
552 <  if( tot_bends ){
553 <    makeBends();
554 <  }
555 <
556 <  if( tot_torsions ){
557 <    makeTorsions();
558 <  }
559 <
548 >  if (the_globals->getUseRF() ) {
549 >    simnfo->useReactionField = 1;
550 >  
551 >    if( !the_globals->haveECR() ){
552 >      sprintf( painCave.errMsg,
553 >               "SimSetup Warning: using default value of 1/2 the smallest "
554 >               "box length for the electrostaticCutoffRadius.\n"
555 >               "I hope you have a very fast processor!\n");
556 >      painCave.isFatal = 0;
557 >      simError();
558 >      double smallest;
559 >      smallest = simnfo->boxLx;
560 >      if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy;
561 >      if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz;
562 >      simnfo->ecr = 0.5 * smallest;
563 >    } else {
564 >      simnfo->ecr        = the_globals->getECR();
565 >    }
566  
567 +    if( !the_globals->haveEST() ){
568 +      sprintf( painCave.errMsg,
569 +               "SimSetup Warning: using default value of 0.05 * the "
570 +               "electrostaticCutoffRadius for the electrostaticSkinThickness\n"
571 +               );
572 +      painCave.isFatal = 0;
573 +      simError();
574 +      simnfo->est = 0.05 * simnfo->ecr;
575 +    } else {
576 +      simnfo->est        = the_globals->getEST();
577 +    }
578 +    
579 +    if(!the_globals->haveDielectric() ){
580 +      sprintf( painCave.errMsg,
581 +               "SimSetup Error: You are trying to use Reaction Field without"
582 +               "setting a dielectric constant!\n"
583 +               );
584 +      painCave.isFatal = 1;
585 +      simError();
586 +    }
587 +    simnfo->dielectric = the_globals->getDielectric();  
588 +  } else {
589 +    if (usesDipoles) {
590 +      
591 +      if( !the_globals->haveECR() ){
592 +        sprintf( painCave.errMsg,
593 +                 "SimSetup Warning: using default value of 1/2 the smallest "
594 +                 "box length for the electrostaticCutoffRadius.\n"
595 +                 "I hope you have a very fast processor!\n");
596 +        painCave.isFatal = 0;
597 +        simError();
598 +        double smallest;
599 +        smallest = simnfo->boxLx;
600 +        if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy;
601 +        if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz;
602 +        simnfo->ecr = 0.5 * smallest;
603 +      } else {
604 +        simnfo->ecr        = the_globals->getECR();
605 +      }
606 +      
607 +      if( !the_globals->haveEST() ){
608 +        sprintf( painCave.errMsg,
609 +                 "SimSetup Warning: using default value of 5%% of the "
610 +                 "electrostaticCutoffRadius for the "
611 +                 "electrostaticSkinThickness\n"
612 +                 );
613 +        painCave.isFatal = 0;
614 +        simError();
615 +        simnfo->est = 0.05 * simnfo->ecr;
616 +      } else {
617 +        simnfo->est        = the_globals->getEST();
618 +      }
619 +    }
620 +  }  
621  
622 + #ifdef IS_MPI
623 +  strcpy( checkPointMsg, "electrostatic parameters check out" );
624 +  MPIcheckPoint();
625 + #endif // is_mpi
626  
431 –
432 –
627   if( the_globals->haveInitialConfig() ){
628  
629       InitializeFromFile* fileInit;
# Line 583 | Line 777 | void SimSetup::createSim( void ){
777    if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
778  
779  
780 < //   // make the longe range forces and the integrator
780 >  // make the integrator
781 >  
782 >  
783 >  NVT*  myNVT = NULL;
784 >  NPTi* myNPTi = NULL;
785 >  NPTf* myNPTf = NULL;
786 >  switch( ensembleCase ){
787  
788 < //   new AllLong( simnfo );
788 >  case NVE_ENS:
789 >    new NVE( simnfo, the_ff );
790 >    break;
791  
792 <  if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff );
793 <  if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff );
794 <  if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff );
593 <  if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff );
792 >  case NVT_ENS:
793 >    myNVT = new NVT( simnfo, the_ff );
794 >    myNVT->setTargetTemp(the_globals->getTargetTemp());
795  
796 +    if (the_globals->haveTauThermostat())
797 +      myNVT->setTauThermostat(the_globals->getTauThermostat());
798  
799 +    else {
800 +      sprintf( painCave.errMsg,
801 +               "SimSetup error: If you use the NVT\n"
802 +               "    ensemble, you must set tauThermostat.\n");
803 +      painCave.isFatal = 1;
804 +      simError();
805 +    }
806 +    break;
807  
808 +  case NPTi_ENS:
809 +    myNPTi = new NPTi( simnfo, the_ff );
810 +    myNPTi->setTargetTemp( the_globals->getTargetTemp());
811 +
812 +    if (the_globals->haveTargetPressure())
813 +      myNPTi->setTargetPressure(the_globals->getTargetPressure());
814 +    else {
815 +      sprintf( painCave.errMsg,
816 +               "SimSetup error: If you use a constant pressure\n"
817 +               "    ensemble, you must set targetPressure in the BASS file.\n");
818 +      painCave.isFatal = 1;
819 +      simError();
820 +    }
821 +    
822 +    if( the_globals->haveTauThermostat() )
823 +      myNPTi->setTauThermostat( the_globals->getTauThermostat() );
824 +    else{
825 +      sprintf( painCave.errMsg,
826 +               "SimSetup error: If you use an NPT\n"
827 +               "    ensemble, you must set tauThermostat.\n");
828 +      painCave.isFatal = 1;
829 +      simError();
830 +    }
831 +
832 +    if( the_globals->haveTauBarostat() )
833 +      myNPTi->setTauBarostat( the_globals->getTauBarostat() );
834 +    else{
835 +      sprintf( painCave.errMsg,
836 +               "SimSetup error: If you use an NPT\n"
837 +               "    ensemble, you must set tauBarostat.\n");
838 +      painCave.isFatal = 1;
839 +      simError();
840 +    }
841 +    break;
842 +
843 +  case NPTf_ENS:
844 +    myNPTf = new NPTf( simnfo, the_ff );
845 +    myNPTf->setTargetTemp( the_globals->getTargetTemp());
846 +
847 +    if (the_globals->haveTargetPressure())
848 +      myNPTf->setTargetPressure(the_globals->getTargetPressure());
849 +    else {
850 +      sprintf( painCave.errMsg,
851 +               "SimSetup error: If you use a constant pressure\n"
852 +               "    ensemble, you must set targetPressure in the BASS file.\n");
853 +      painCave.isFatal = 1;
854 +      simError();
855 +    }    
856 +
857 +    if( the_globals->haveTauThermostat() )
858 +      myNPTf->setTauThermostat( the_globals->getTauThermostat() );
859 +    else{
860 +      sprintf( painCave.errMsg,
861 +               "SimSetup error: If you use an NPT\n"
862 +               "    ensemble, you must set tauThermostat.\n");
863 +      painCave.isFatal = 1;
864 +      simError();
865 +    }
866 +
867 +    if( the_globals->haveTauBarostat() )
868 +      myNPTf->setTauBarostat( the_globals->getTauBarostat() );
869 +    else{
870 +      sprintf( painCave.errMsg,
871 +               "SimSetup error: If you use an NPT\n"
872 +               "    ensemble, you must set tauBarostat.\n");
873 +      painCave.isFatal = 1;
874 +      simError();
875 +    }
876 +    break;
877 +    
878 +    
879 +
880 +  default:
881 +    sprintf( painCave.errMsg,
882 +             "SimSetup Error. Unrecognized ensemble in case statement.\n");
883 +    painCave.isFatal = 1;
884 +    simError();
885 +  }
886 +
887 +
888 + #ifdef IS_MPI
889 +  mpiSim->mpiRefresh();
890 + #endif
891 +
892    // initialize the Fortran
893 <  
893 >
894 >
895    simnfo->refreshSim();
896    
897    if( !strcmp( simnfo->mixingRule, "standard") ){
# Line 620 | Line 916 | void SimSetup::makeAtoms( void ){
916   #endif // is_mpi
917   }
918  
623 – void SimSetup::makeAtoms( void ){
919  
920 <  int i, j, k, index;
626 <  double ux, uy, uz, uSqr, u;
627 <  AtomStamp* current_atom;
920 > void SimSetup::makeMolecules( void ){
921  
922 +  int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
923 +  molInit info;
924    DirectionalAtom* dAtom;
925 <  int molIndex, molStart, molEnd, nMemb, lMolIndex;
925 >  LinkedAssign* extras;
926 >  LinkedAssign* current_extra;
927 >  AtomStamp* currentAtom;
928 >  BondStamp* currentBond;
929 >  BendStamp* currentBend;
930 >  TorsionStamp* currentTorsion;
931  
932 <  lMolIndex = 0;
933 <  molIndex = 0;
934 <  index = 0;
635 <  for( i=0; i<n_components; i++ ){
932 >  bond_pair* theBonds;
933 >  bend_set* theBends;
934 >  torsion_set* theTorsions;
935  
936 <    for( j=0; j<components_nmol[i]; j++ ){
936 >  
937 >  //init the forceField paramters
938  
939 < #ifdef IS_MPI
640 <      if( mpiSim->getMyMolStart() <= molIndex &&
641 <          molIndex <= mpiSim->getMyMolEnd() ){
642 < #endif // is_mpi        
939 >  the_ff->readParams();
940  
941 <        molStart = index;
942 <        nMemb = comp_stamps[i]->getNAtoms();
943 <        for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){
944 <          
945 <          current_atom = comp_stamps[i]->getAtom( k );
946 <          if( current_atom->haveOrientation() ){
947 <            
948 <            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++;
686 <
687 < #ifdef IS_MPI
688 <      }
689 < #endif //is_mpi
690 <      
691 <      molIndex++;
692 <    }
693 <  }
694 <
695 < #ifdef IS_MPI
696 <    for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] );
941 >  
942 >  // init the atoms
943 >
944 >  double ux, uy, uz, u, uSqr;
945 >  
946 >  atomOffset = 0;
947 >  excludeOffset = 0;
948 >  for(i=0; i<simnfo->n_mol; i++){
949      
950 <    delete[] globalIndex;
950 >    stampID = the_molecules[i].getStampID();
951  
952 <    mpiSim->mpiRefresh();
953 < #endif //IS_MPI
954 <          
955 <  the_ff->initializeAtoms();
956 < }
952 >    info.nAtoms    = comp_stamps[stampID]->getNAtoms();
953 >    info.nBonds    = comp_stamps[stampID]->getNBonds();
954 >    info.nBends    = comp_stamps[stampID]->getNBends();
955 >    info.nTorsions = comp_stamps[stampID]->getNTorsions();
956 >    info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
957  
958 < void SimSetup::makeBonds( void ){
958 >    info.myAtoms = &the_atoms[atomOffset];
959 >    info.myExcludes = &the_excludes[excludeOffset];
960 >    info.myBonds = new Bond*[info.nBonds];
961 >    info.myBends = new Bend*[info.nBends];
962 >    info.myTorsions = new Torsion*[info.nTorsions];
963  
964 <  int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
965 <  bond_pair* the_bonds;
966 <  BondStamp* current_bond;
967 <
968 <  the_bonds = new bond_pair[tot_bonds];
969 <  index = 0;
970 <  offset = 0;
971 <  molIndex = 0;
972 <
973 <  for( i=0; i<n_components; i++ ){
718 <
719 <    for( j=0; j<components_nmol[i]; j++ ){
720 <
721 < #ifdef IS_MPI
722 <      if( mpiSim->getMyMolStart() <= molIndex &&
723 <          molIndex <= mpiSim->getMyMolEnd() ){
724 < #endif // is_mpi        
964 >    theBonds = new bond_pair[info.nBonds];
965 >    theBends = new bend_set[info.nBends];
966 >    theTorsions = new torsion_set[info.nTorsions];
967 >    
968 >    // make the Atoms
969 >    
970 >    for(j=0; j<info.nAtoms; j++){
971 >      
972 >      currentAtom = comp_stamps[stampID]->getAtom( j );
973 >      if( currentAtom->haveOrientation() ){
974          
975 <        for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){
976 <          
977 <          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();
975 >        dAtom = new DirectionalAtom(j + atomOffset);
976 >        simnfo->n_oriented++;
977 >        info.myAtoms[j] = dAtom;
978          
979 < #ifdef IS_MPI
979 >        ux = currentAtom->getOrntX();
980 >        uy = currentAtom->getOrntY();
981 >        uz = currentAtom->getOrntZ();
982 >        
983 >        uSqr = (ux * ux) + (uy * uy) + (uz * uz);
984 >        
985 >        u = sqrt( uSqr );
986 >        ux = ux / u;
987 >        uy = uy / u;
988 >        uz = uz / u;
989 >        
990 >        dAtom->setSUx( ux );
991 >        dAtom->setSUy( uy );
992 >        dAtom->setSUz( uz );
993        }
994 < #endif //is_mpi
994 >      else{
995 >        info.myAtoms[j] = new GeneralAtom(j + atomOffset);
996 >      }
997 >      info.myAtoms[j]->setType( currentAtom->getType() );
998 >    
999 > #ifdef IS_MPI
1000        
1001 <      molIndex++;
1002 <    }      
1003 <  }
1001 >      info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
1002 >      
1003 > #endif // is_mpi
1004 >    }
1005 >    
1006 >    // make the bonds
1007 >    for(j=0; j<info.nBonds; j++){
1008 >      
1009 >      currentBond = comp_stamps[stampID]->getBond( j );
1010 >      theBonds[j].a = currentBond->getA() + atomOffset;
1011 >      theBonds[j].b = currentBond->getB() + atomOffset;
1012  
1013 <  the_ff->initializeBonds( the_bonds );
1014 < }
1013 >      exI = theBonds[j].a;
1014 >      exJ = theBonds[j].b;
1015  
1016 < void SimSetup::makeBends( void ){
1017 <
1018 <  int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
1019 <  bend_set* the_bends;
1020 <  BendStamp* current_bend;
1021 <  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 <
1016 >      // exclude_I must always be the smaller of the pair
1017 >      if( exI > exJ ){
1018 >        tempEx = exI;
1019 >        exI = exJ;
1020 >        exJ = tempEx;
1021 >      }
1022   #ifdef IS_MPI
1023 <      if( mpiSim->getMyMolStart() <= molIndex &&
1024 <          molIndex <= mpiSim->getMyMolEnd() ){
1025 < #endif // is_mpi        
1023 >      tempEx = exI;
1024 >      exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1025 >      tempEx = exJ;
1026 >      exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1027 >      
1028 >      the_excludes[j+excludeOffset]->setPair( exI, exJ );
1029 > #else  // isn't MPI
1030  
1031 <        for( k=0; k<comp_stamps[i]->getNBends(); k++ ){
1031 >      the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1032 > #endif  //is_mpi
1033 >    }
1034 >    excludeOffset += info.nBonds;
1035 >
1036 >    //make the bends
1037 >    for(j=0; j<info.nBends; j++){
1038 >      
1039 >      currentBend = comp_stamps[stampID]->getBend( j );
1040 >      theBends[j].a = currentBend->getA() + atomOffset;
1041 >      theBends[j].b = currentBend->getB() + atomOffset;
1042 >      theBends[j].c = currentBend->getC() + atomOffset;
1043            
1044 <          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() ){
1044 >      if( currentBend->haveExtras() ){
1045              
1046 <            extras = current_bend->getExtras();
1047 <            current_extra = extras;
1046 >        extras = currentBend->getExtras();
1047 >        current_extra = extras;
1048              
1049 <            while( current_extra != NULL ){
1050 <              if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
1049 >        while( current_extra != NULL ){
1050 >          if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
1051                  
1052 <                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 <              }
1052 >            switch( current_extra->getType() ){
1053                
1054 <              else{
1055 <                
1056 <                sprintf( painCave.errMsg,
1057 <                         "SimSetup Error: unhandled bend assignment:\n"
1058 <                         "    -->%s in Bend[%d] in %s\n",
1059 <                         current_extra->getlhs(),
1060 <                         k, comp_stamps[i]->getID() );
1061 <                painCave.isFatal = 1;
1062 <                simError();
1063 <              }
1054 >            case 0:
1055 >              theBends[j].ghost =
1056 >                current_extra->getInt() + atomOffset;
1057 >              theBends[j].isGhost = 1;
1058 >              break;
1059 >                  
1060 >            case 1:
1061 >              theBends[j].ghost =
1062 >                (int)current_extra->getDouble() + atomOffset;
1063 >              theBends[j].isGhost = 1;
1064 >              break;
1065                
1066 <              current_extra = current_extra->getNext();
1066 >            default:
1067 >              sprintf( painCave.errMsg,
1068 >                       "SimSetup Error: ghostVectorSource was neither a "
1069 >                       "double nor an int.\n"
1070 >                       "-->Bend[%d] in %s\n",
1071 >                       j, comp_stamps[stampID]->getID() );
1072 >              painCave.isFatal = 1;
1073 >              simError();
1074              }
1075            }
1076            
850 –          if( !the_bends[index].isGhost ){
851 –            
852 –            exI = the_bends[index].a;
853 –            exJ = the_bends[index].c;
854 –          }
1077            else{
1078              
1079 <            exI = the_bends[index].a;
1080 <            exJ = the_bends[index].b;
1079 >            sprintf( painCave.errMsg,
1080 >                     "SimSetup Error: unhandled bend assignment:\n"
1081 >                     "    -->%s in Bend[%d] in %s\n",
1082 >                     current_extra->getlhs(),
1083 >                     j, comp_stamps[stampID]->getID() );
1084 >            painCave.isFatal = 1;
1085 >            simError();
1086            }
1087            
1088 <          // 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++;
1088 >          current_extra = current_extra->getNext();
1089          }
1090 <        offset += comp_stamps[i]->getNAtoms();
1090 >      }
1091 >          
1092 >      if( !theBends[j].isGhost ){
1093 >            
1094 >        exI = theBends[j].a;
1095 >        exJ = theBends[j].c;
1096 >      }
1097 >      else{
1098          
1099 < #ifdef IS_MPI
1099 >        exI = theBends[j].a;
1100 >        exJ = theBends[j].b;
1101        }
1102 < #endif //is_mpi
1102 >      
1103 >      // exclude_I must always be the smaller of the pair
1104 >      if( exI > exJ ){
1105 >        tempEx = exI;
1106 >        exI = exJ;
1107 >        exJ = tempEx;
1108 >      }
1109 > #ifdef IS_MPI
1110 >      tempEx = exI;
1111 >      exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1112 >      tempEx = exJ;
1113 >      exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1114 >      
1115 >      the_excludes[j+excludeOffset]->setPair( exI, exJ );
1116 > #else  // isn't MPI
1117 >      the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1118 > #endif  //is_mpi
1119 >    }
1120 >    excludeOffset += info.nBends;
1121  
1122 <      molIndex++;
1122 >    for(j=0; j<info.nTorsions; j++){
1123 >      
1124 >      currentTorsion = comp_stamps[stampID]->getTorsion( j );
1125 >      theTorsions[j].a = currentTorsion->getA() + atomOffset;
1126 >      theTorsions[j].b = currentTorsion->getB() + atomOffset;
1127 >      theTorsions[j].c = currentTorsion->getC() + atomOffset;
1128 >      theTorsions[j].d = currentTorsion->getD() + atomOffset;
1129 >      
1130 >      exI = theTorsions[j].a;
1131 >      exJ = theTorsions[j].d;
1132 >
1133 >      // exclude_I must always be the smaller of the pair
1134 >      if( exI > exJ ){
1135 >        tempEx = exI;
1136 >        exI = exJ;
1137 >        exJ = tempEx;
1138 >      }
1139 > #ifdef IS_MPI
1140 >      tempEx = exI;
1141 >      exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1142 >      tempEx = exJ;
1143 >      exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1144 >      
1145 >      the_excludes[j+excludeOffset]->setPair( exI, exJ );
1146 > #else  // isn't MPI
1147 >      the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1148 > #endif  //is_mpi
1149      }
1150 <  }
1150 >    excludeOffset += info.nTorsions;
1151  
1152 < #ifdef IS_MPI
1153 <  sprintf( checkPointMsg,
899 <           "Successfully created the bends list.\n" );
900 <  MPIcheckPoint();
901 < #endif // is_mpi
902 <  
1152 >    
1153 >    // send the arrays off to the forceField for init.
1154  
1155 <  the_ff->initializeBends( the_bends );
1156 < }
1155 >    the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
1156 >    the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
1157 >    the_ff->initializeBends( info.nBends, info.myBends, theBends );
1158 >    the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
1159  
907 – void SimSetup::makeTorsions( void ){
1160  
1161 <  int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
910 <  torsion_set* the_torsions;
911 <  TorsionStamp* current_torsion;
1161 >    the_molecules[i].initialize( info );
1162  
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++ ){
1163  
1164 <    for( j=0; j<components_nmol[i]; j++ ){
1164 >    atomOffset += info.nAtoms;
1165 >    delete[] theBonds;
1166 >    delete[] theBends;
1167 >    delete[] theTorsions;
1168 >  }
1169  
1170   #ifdef IS_MPI
1171 <      if( mpiSim->getMyMolStart() <= molIndex &&
1172 <          molIndex <= mpiSim->getMyMolEnd() ){
1173 < #endif // is_mpi        
1171 >  sprintf( checkPointMsg, "all molecules initialized succesfully" );
1172 >  MPIcheckPoint();
1173 > #endif // is_mpi
1174  
1175 <      for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){
1175 >  // clean up the forcefield
1176 >  the_ff->calcRcut();
1177 >  the_ff->cleanMe();
1178  
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 );
1179   }
1180  
1181   void SimSetup::initFromBass( void ){
# Line 993 | Line 1197 | void SimSetup::initFromBass( void ){
1197      have_extra =1;
1198  
1199      n_cells = (int)temp3 - 1;
1200 <    cellx = simnfo->box_x / temp3;
1201 <    celly = simnfo->box_y / temp3;
1202 <    cellz = simnfo->box_z / temp3;
1200 >    cellx = simnfo->boxLx / temp3;
1201 >    celly = simnfo->boxLy / temp3;
1202 >    cellz = simnfo->boxLz / temp3;
1203      n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
1204      temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1205      n_per_extra = (int)ceil( temp1 );
# Line 1010 | Line 1214 | void SimSetup::initFromBass( void ){
1214    }
1215    else{
1216      n_cells = (int)temp3;
1217 <    cellx = simnfo->box_x / temp3;
1218 <    celly = simnfo->box_y / temp3;
1219 <    cellz = simnfo->box_z / temp3;
1217 >    cellx = simnfo->boxLx / temp3;
1218 >    celly = simnfo->boxLy / temp3;
1219 >    cellz = simnfo->boxLz / temp3;
1220    }
1221  
1222    current_mol = 0;

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