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root/group/trunk/OOPSE/libmdtools/SimSetup.cpp
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Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 412 by mmeineke, Wed Mar 26 21:50:33 2003 UTC vs.
Revision 605 by gezelter, Tue Jul 15 03:27:24 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 NPTi_ENS  2
20 + #define NPTf_ENS  3
21 + #define NPTim_ENS 4
22 + #define NPTfm_ENS 5
23 +
24 +
25 + #define FF_DUFF 0
26 + #define FF_LJ   1
27 +
28 +
29   SimSetup::SimSetup(){
30    stamps = new MakeStamps();
31    globals = new Globals();
# Line 66 | Line 80 | void SimSetup::createSim( void ){
80  
81    MakeStamps *the_stamps;
82    Globals* the_globals;
83 <  int i, j;
83 >  int i, j, k, globalAtomIndex;
84 >  
85 >  int ensembleCase;
86 >  int ffCase;
87 >  
88 >  ensembleCase = -1;
89 >  ffCase = -1;
90  
91    // get the stamps and globals;
92    the_stamps = stamps;
# Line 80 | Line 100 | void SimSetup::createSim( void ){
100    // get the ones we know are there, yet still may need some work.
101    n_components = the_globals->getNComponents();
102    strcpy( force_field, the_globals->getForceField() );
103 +
104 +  if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
105 +  else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
106 +  else{
107 +    sprintf( painCave.errMsg,
108 +             "SimSetup Error. Unrecognized force field -> %s\n",
109 +             force_field );
110 +    painCave.isFatal = 1;
111 +    simError();
112 +  }
113 +
114 +  // get the ensemble:
115    strcpy( ensemble, the_globals->getEnsemble() );
116 +
117 +  if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
118 +  else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
119 +  else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
120 +    ensembleCase = NPTi_ENS;
121 +  else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
122 +  else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
123 +  else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
124 +  else{
125 +    sprintf( painCave.errMsg,
126 +             "SimSetup Warning. Unrecognized Ensemble -> %s, "
127 +             "reverting to NVE for this simulation.\n",
128 +             ensemble );
129 +    painCave.isFatal = 0;
130 +    simError();
131 +    strcpy( ensemble, "NVE" );
132 +    ensembleCase = NVE_ENS;
133 +  }  
134    strcpy( simnfo->ensemble, ensemble );
135  
136 +
137 + //   if( !strcasecmp( ensemble, "NPT" ) ) {
138 + //     the_extendedsystem = new ExtendedSystem( simnfo );
139 + //     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
140 + //     if (the_globals->haveTargetPressure())
141 + //       the_extendedsystem->setTargetPressure(the_globals->getTargetPressure());
142 + //     else {
143 + //       sprintf( painCave.errMsg,
144 + //                "SimSetup error: If you use the constant pressure\n"
145 + //                "    ensemble, you must set targetPressure.\n"
146 + //                "    This was found in the BASS file.\n");
147 + //       painCave.isFatal = 1;
148 + //       simError();
149 + //     }
150 +
151 + //     if (the_globals->haveTauThermostat())
152 + //       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
153 + //     else if (the_globals->haveQmass())
154 + //       the_extendedsystem->setQmass(the_globals->getQmass());
155 + //     else {
156 + //       sprintf( painCave.errMsg,
157 + //                "SimSetup error: If you use one of the constant temperature\n"
158 + //                "    ensembles, you must set either tauThermostat or qMass.\n"
159 + //                "    Neither of these was found in the BASS file.\n");
160 + //       painCave.isFatal = 1;
161 + //       simError();
162 + //     }
163 +
164 + //     if (the_globals->haveTauBarostat())
165 + //       the_extendedsystem->setTauBarostat(the_globals->getTauBarostat());
166 + //     else {
167 + //       sprintf( painCave.errMsg,
168 + //                "SimSetup error: If you use the constant pressure\n"
169 + //                "    ensemble, you must set tauBarostat.\n"
170 + //                "    This was found in the BASS file.\n");
171 + //       painCave.isFatal = 1;
172 + //       simError();
173 + //     }
174 +
175 + //   } else if ( !strcasecmp( ensemble, "NVT") ) {
176 + //     the_extendedsystem = new ExtendedSystem( simnfo );
177 + //     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
178 +
179 + //     if (the_globals->haveTauThermostat())
180 + //       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
181 + //     else if (the_globals->haveQmass())
182 + //       the_extendedsystem->setQmass(the_globals->getQmass());
183 + //     else {
184 + //       sprintf( painCave.errMsg,
185 + //                "SimSetup error: If you use one of the constant temperature\n"
186 + //                "    ensembles, you must set either tauThermostat or qMass.\n"
187 + //                "    Neither of these was found in the BASS file.\n");
188 + //       painCave.isFatal = 1;
189 + //       simError();
190 + //     }
191 +
192    strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
193    simnfo->usePBC = the_globals->getPBC();
194            
195 +  int usesDipoles = 0;
196 +  switch( ffCase ){
197  
198 +  case FF_DUFF:
199 +    the_ff = new DUFF();
200 +    usesDipoles = 1;
201 +    break;
202  
203 <  if( !strcmp( force_field, "TraPPE" ) ) the_ff = new TraPPEFF();
204 <  else if( !strcmp( force_field, "DipoleTest" ) ) the_ff = new DipoleTestFF();
205 <  else if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF();
206 <  else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
207 <  else{
203 >  case FF_LJ:
204 >    the_ff = new LJFF();
205 >    break;
206 >
207 >  default:
208      sprintf( painCave.errMsg,
209 <             "SimSetup Error. Unrecognized force field -> %s\n",
98 <             force_field );
209 >             "SimSetup Error. Unrecognized force field in case statement.\n");
210      painCave.isFatal = 1;
211      simError();
212    }
# Line 105 | Line 216 | void SimSetup::createSim( void ){
216    MPIcheckPoint();
217   #endif // is_mpi
218  
108 –  
109 –
219    // get the components and calculate the tot_nMol and indvidual n_mol
220    the_components = the_globals->getComponents();
221    components_nmol = new int[n_components];
# Line 230 | Line 339 | void SimSetup::createSim( void ){
339    simnfo->n_torsions = tot_torsions;
340    simnfo->n_SRI = tot_SRI;
341    simnfo->n_mol = tot_nmol;
233 –
342    
343 +  simnfo->molMembershipArray = new int[tot_atoms];
344 +
345   #ifdef IS_MPI
346  
347    // divide the molecules among processors here.
348    
349    mpiSim = new mpiSimulation( simnfo );
350    
241 –  
242 –
351    globalIndex = mpiSim->divideLabor();
352  
245 –
246 –
353    // set up the local variables
354    
355    int localMol, allMol;
356    int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
357 +
358 +  int* mol2proc = mpiSim->getMolToProcMap();
359 +  int* molCompType = mpiSim->getMolComponentType();
360    
361    allMol = 0;
362    localMol = 0;
# Line 255 | Line 364 | void SimSetup::createSim( void ){
364    local_bonds = 0;
365    local_bends = 0;
366    local_torsions = 0;
367 +  globalAtomIndex = 0;
368 +
369 +
370    for( i=0; i<n_components; i++ ){
371  
372      for( j=0; j<components_nmol[i]; j++ ){
373        
374 <      if( mpiSim->getMyMolStart() <= allMol &&
263 <          allMol <= mpiSim->getMyMolEnd() ){
374 >      if( mol2proc[allMol] == worldRank ){
375          
376          local_atoms +=    comp_stamps[i]->getNAtoms();
377          local_bonds +=    comp_stamps[i]->getNBonds();
# Line 268 | Line 379 | void SimSetup::createSim( void ){
379          local_torsions += comp_stamps[i]->getNTorsions();
380          localMol++;
381        }      
382 <      allMol++;
382 >      for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
383 >        simnfo->molMembershipArray[globalAtomIndex] = allMol;
384 >        globalAtomIndex++;
385 >      }
386 >
387 >      allMol++;      
388      }
389    }
390    local_SRI = local_bonds + local_bends + local_torsions;
391    
276 –
392    simnfo->n_atoms = mpiSim->getMyNlocal();  
393    
394    if( local_atoms != simnfo->n_atoms ){
395      sprintf( painCave.errMsg,
396               "SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
397 <             " localAtom (%d) are note equal.\n",
397 >             " localAtom (%d) are not equal.\n",
398               simnfo->n_atoms,
399               local_atoms );
400      painCave.isFatal = 1;
# Line 304 | Line 419 | void SimSetup::createSim( void ){
419    Atom::createArrays(simnfo->n_atoms);
420    the_atoms = new Atom*[simnfo->n_atoms];
421    the_molecules = new Molecule[simnfo->n_mol];
422 +  int molIndex;
423  
424 +  // initialize the molecule's stampID's
425  
426 + #ifdef IS_MPI
427 +  
428 +
429 +  molIndex = 0;
430 +  for(i=0; i<mpiSim->getTotNmol(); i++){
431 +    
432 +    if(mol2proc[i] == worldRank ){
433 +      the_molecules[molIndex].setStampID( molCompType[i] );
434 +      the_molecules[molIndex].setMyIndex( molIndex );
435 +      the_molecules[molIndex].setGlobalIndex( i );
436 +      molIndex++;
437 +    }
438 +  }
439 +
440 + #else // is_mpi
441 +  
442 +  molIndex = 0;
443 +  globalAtomIndex = 0;
444 +  for(i=0; i<n_components; i++){
445 +    for(j=0; j<components_nmol[i]; j++ ){
446 +      the_molecules[molIndex].setStampID( i );
447 +      the_molecules[molIndex].setMyIndex( molIndex );
448 +      the_molecules[molIndex].setGlobalIndex( molIndex );
449 +      for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
450 +        simnfo->molMembershipArray[globalAtomIndex] = molIndex;
451 +        globalAtomIndex++;
452 +      }
453 +      molIndex++;
454 +    }
455 +  }
456 +    
457 +
458 + #endif // is_mpi
459 +
460 +
461    if( simnfo->n_SRI ){
462 +    
463      Exclude::createArray(simnfo->n_SRI);
464      the_excludes = new Exclude*[simnfo->n_SRI];
465 +    for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
466      simnfo->globalExcludes = new int;
467 <    simnfo->n_exclude = tot_SRI;
467 >    simnfo->n_exclude = simnfo->n_SRI;
468    }
469    else{
470      
# Line 326 | Line 480 | void SimSetup::createSim( void ){
480    // set the arrays into the SimInfo object
481  
482    simnfo->atoms = the_atoms;
483 <  simnfo->sr_interactions = the_sris;
483 >  simnfo->molecules = the_molecules;
484    simnfo->nGlobalExcludes = 0;
485    simnfo->excludes = the_excludes;
486  
487  
488    // get some of the tricky things that may still be in the globals
489  
490 <  
490 >  double boxVector[3];
491    if( the_globals->haveBox() ){
492 <    simnfo->box_x = the_globals->getBox();
493 <    simnfo->box_y = the_globals->getBox();
494 <    simnfo->box_z = the_globals->getBox();
492 >    boxVector[0] = the_globals->getBox();
493 >    boxVector[1] = the_globals->getBox();
494 >    boxVector[2] = the_globals->getBox();
495 >    
496 >    simnfo->setBox( boxVector );
497    }
498    else if( the_globals->haveDensity() ){
499  
500      double vol;
501      vol = (double)tot_nmol / the_globals->getDensity();
502 <    simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
503 <    simnfo->box_y = simnfo->box_x;
504 <    simnfo->box_z = simnfo->box_x;
502 >     boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
503 >     boxVector[1] = boxVector[0];
504 >     boxVector[2] = boxVector[0];
505 >
506 >    simnfo->setBox( boxVector );
507    }
508    else{
509      if( !the_globals->haveBoxX() ){
# Line 354 | Line 512 | void SimSetup::createSim( void ){
512        painCave.isFatal = 1;
513        simError();
514      }
515 <    simnfo->box_x = the_globals->getBoxX();
515 >    boxVector[0] = the_globals->getBoxX();
516  
517      if( !the_globals->haveBoxY() ){
518        sprintf( painCave.errMsg,
# Line 362 | Line 520 | void SimSetup::createSim( void ){
520        painCave.isFatal = 1;
521        simError();
522      }
523 <    simnfo->box_y = the_globals->getBoxY();
523 >    boxVector[1] = the_globals->getBoxY();
524  
525      if( !the_globals->haveBoxZ() ){
526        sprintf( painCave.errMsg,
# Line 370 | Line 528 | void SimSetup::createSim( void ){
528        painCave.isFatal = 1;
529        simError();
530      }
531 <    simnfo->box_z = the_globals->getBoxZ();
531 >    boxVector[2] = the_globals->getBoxZ();
532 >
533 >    simnfo->setBox( boxVector );
534    }
535  
536   #ifdef IS_MPI
# Line 383 | Line 543 | void SimSetup::createSim( void ){
543  
544    the_ff->setSimInfo( simnfo );
545  
546 <  makeAtoms();
546 >  makeMolecules();
547    simnfo->identArray = new int[simnfo->n_atoms];
548    for(i=0; i<simnfo->n_atoms; i++){
549      simnfo->identArray[i] = the_atoms[i]->getIdent();
550    }
551    
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 –
552    if (the_globals->getUseRF() ) {
553      simnfo->useReactionField = 1;
554    
# Line 413 | Line 560 | void SimSetup::createSim( void ){
560        painCave.isFatal = 0;
561        simError();
562        double smallest;
563 <      smallest = simnfo->box_x;
564 <      if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
565 <      if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
563 >      smallest = simnfo->boxLx;
564 >      if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy;
565 >      if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz;
566        simnfo->ecr = 0.5 * smallest;
567      } else {
568        simnfo->ecr        = the_globals->getECR();
# Line 443 | Line 590 | void SimSetup::createSim( void ){
590      }
591      simnfo->dielectric = the_globals->getDielectric();  
592    } else {
593 <    if (simnfo->n_dipoles) {
593 >    if (usesDipoles) {
594        
595        if( !the_globals->haveECR() ){
596          sprintf( painCave.errMsg,
597 <                 "SimSetup Warning: using default value of 1/2 the smallest"
597 >                 "SimSetup Warning: using default value of 1/2 the smallest "
598                   "box length for the electrostaticCutoffRadius.\n"
599                   "I hope you have a very fast processor!\n");
600          painCave.isFatal = 0;
601          simError();
602          double smallest;
603 <        smallest = simnfo->box_x;
604 <        if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
605 <        if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
603 >        smallest = simnfo->boxLx;
604 >        if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy;
605 >        if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz;
606          simnfo->ecr = 0.5 * smallest;
607        } else {
608          simnfo->ecr        = the_globals->getECR();
# Line 463 | Line 610 | void SimSetup::createSim( void ){
610        
611        if( !the_globals->haveEST() ){
612          sprintf( painCave.errMsg,
613 <                 "SimSetup Warning: using default value of 5% of the"
613 >                 "SimSetup Warning: using default value of 5%% of the "
614                   "electrostaticCutoffRadius for the "
615                   "electrostaticSkinThickness\n"
616                   );
# Line 634 | Line 781 | void SimSetup::createSim( void ){
781    if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
782  
783  
784 < //   // make the longe range forces and the integrator
784 >  // make the integrator
785 >  
786 >  
787 >  NVT*  myNVT = NULL;
788 >  NPTi* myNPTi = NULL;
789 >  NPTf* myNPTf = NULL;
790 >  NPTim* myNPTim = NULL;
791 >  NPTfm* myNPTfm = NULL;
792  
793 < //   new AllLong( simnfo );
793 >  switch( ensembleCase ){
794  
795 <  if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff );
796 <  if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff );
797 <  if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff );
798 <  if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff );
795 >  case NVE_ENS:
796 >    new NVE( simnfo, the_ff );
797 >    break;
798 >
799 >  case NVT_ENS:
800 >    myNVT = new NVT( simnfo, the_ff );
801 >    myNVT->setTargetTemp(the_globals->getTargetTemp());
802 >
803 >    if (the_globals->haveTauThermostat())
804 >      myNVT->setTauThermostat(the_globals->getTauThermostat());
805 >
806 >    else {
807 >      sprintf( painCave.errMsg,
808 >               "SimSetup error: If you use the NVT\n"
809 >               "    ensemble, you must set tauThermostat.\n");
810 >      painCave.isFatal = 1;
811 >      simError();
812 >    }
813 >    break;
814 >
815 >  case NPTi_ENS:
816 >    myNPTi = new NPTi( simnfo, the_ff );
817 >    myNPTi->setTargetTemp( the_globals->getTargetTemp());
818 >
819 >    if (the_globals->haveTargetPressure())
820 >      myNPTi->setTargetPressure(the_globals->getTargetPressure());
821 >    else {
822 >      sprintf( painCave.errMsg,
823 >               "SimSetup error: If you use a constant pressure\n"
824 >               "    ensemble, you must set targetPressure in the BASS file.\n");
825 >      painCave.isFatal = 1;
826 >      simError();
827 >    }
828 >    
829 >    if( the_globals->haveTauThermostat() )
830 >      myNPTi->setTauThermostat( the_globals->getTauThermostat() );
831 >    else{
832 >      sprintf( painCave.errMsg,
833 >               "SimSetup error: If you use an NPT\n"
834 >               "    ensemble, you must set tauThermostat.\n");
835 >      painCave.isFatal = 1;
836 >      simError();
837 >    }
838 >
839 >    if( the_globals->haveTauBarostat() )
840 >      myNPTi->setTauBarostat( the_globals->getTauBarostat() );
841 >    else{
842 >      sprintf( painCave.errMsg,
843 >               "SimSetup error: If you use an NPT\n"
844 >               "    ensemble, you must set tauBarostat.\n");
845 >      painCave.isFatal = 1;
846 >      simError();
847 >    }
848 >    break;
849 >
850 >  case NPTf_ENS:
851 >    myNPTf = new NPTf( simnfo, the_ff );
852 >    myNPTf->setTargetTemp( the_globals->getTargetTemp());
853 >
854 >    if (the_globals->haveTargetPressure())
855 >      myNPTf->setTargetPressure(the_globals->getTargetPressure());
856 >    else {
857 >      sprintf( painCave.errMsg,
858 >               "SimSetup error: If you use a constant pressure\n"
859 >               "    ensemble, you must set targetPressure in the BASS file.\n");
860 >      painCave.isFatal = 1;
861 >      simError();
862 >    }    
863 >
864 >    if( the_globals->haveTauThermostat() )
865 >      myNPTf->setTauThermostat( the_globals->getTauThermostat() );
866 >    else{
867 >      sprintf( painCave.errMsg,
868 >               "SimSetup error: If you use an NPT\n"
869 >               "    ensemble, you must set tauThermostat.\n");
870 >      painCave.isFatal = 1;
871 >      simError();
872 >    }
873 >
874 >    if( the_globals->haveTauBarostat() )
875 >      myNPTf->setTauBarostat( the_globals->getTauBarostat() );
876 >    else{
877 >      sprintf( painCave.errMsg,
878 >               "SimSetup error: If you use an NPT\n"
879 >               "    ensemble, you must set tauBarostat.\n");
880 >      painCave.isFatal = 1;
881 >      simError();
882 >    }
883 >    break;
884 >    
885 >  case NPTim_ENS:
886 >    myNPTim = new NPTim( simnfo, the_ff );
887 >    myNPTim->setTargetTemp( the_globals->getTargetTemp());
888 >
889 >    if (the_globals->haveTargetPressure())
890 >      myNPTim->setTargetPressure(the_globals->getTargetPressure());
891 >    else {
892 >      sprintf( painCave.errMsg,
893 >               "SimSetup error: If you use a constant pressure\n"
894 >               "    ensemble, you must set targetPressure in the BASS file.\n");
895 >      painCave.isFatal = 1;
896 >      simError();
897 >    }
898 >    
899 >    if( the_globals->haveTauThermostat() )
900 >      myNPTim->setTauThermostat( the_globals->getTauThermostat() );
901 >    else{
902 >      sprintf( painCave.errMsg,
903 >               "SimSetup error: If you use an NPT\n"
904 >               "    ensemble, you must set tauThermostat.\n");
905 >      painCave.isFatal = 1;
906 >      simError();
907 >    }
908 >
909 >    if( the_globals->haveTauBarostat() )
910 >      myNPTim->setTauBarostat( the_globals->getTauBarostat() );
911 >    else{
912 >      sprintf( painCave.errMsg,
913 >               "SimSetup error: If you use an NPT\n"
914 >               "    ensemble, you must set tauBarostat.\n");
915 >      painCave.isFatal = 1;
916 >      simError();
917 >    }
918 >    break;
919 >
920 >  case NPTfm_ENS:
921 >    myNPTfm = new NPTfm( simnfo, the_ff );
922 >    myNPTfm->setTargetTemp( the_globals->getTargetTemp());
923 >
924 >    if (the_globals->haveTargetPressure())
925 >      myNPTfm->setTargetPressure(the_globals->getTargetPressure());
926 >    else {
927 >      sprintf( painCave.errMsg,
928 >               "SimSetup error: If you use a constant pressure\n"
929 >               "    ensemble, you must set targetPressure in the BASS file.\n");
930 >      painCave.isFatal = 1;
931 >      simError();
932 >    }
933 >    
934 >    if( the_globals->haveTauThermostat() )
935 >      myNPTfm->setTauThermostat( the_globals->getTauThermostat() );
936 >    else{
937 >      sprintf( painCave.errMsg,
938 >               "SimSetup error: If you use an NPT\n"
939 >               "    ensemble, you must set tauThermostat.\n");
940 >      painCave.isFatal = 1;
941 >      simError();
942 >    }
943 >
944 >    if( the_globals->haveTauBarostat() )
945 >      myNPTfm->setTauBarostat( the_globals->getTauBarostat() );
946 >    else{
947 >      sprintf( painCave.errMsg,
948 >               "SimSetup error: If you use an NPT\n"
949 >               "    ensemble, you must set tauBarostat.\n");
950 >      painCave.isFatal = 1;
951 >      simError();
952 >    }
953 >    break;
954  
955 +  default:
956 +    sprintf( painCave.errMsg,
957 +             "SimSetup Error. Unrecognized ensemble in case statement.\n");
958 +    painCave.isFatal = 1;
959 +    simError();
960 +  }
961  
962  
963 + #ifdef IS_MPI
964 +  mpiSim->mpiRefresh();
965 + #endif
966 +
967    // initialize the Fortran
968 <  
968 >
969 >
970    simnfo->refreshSim();
971    
972    if( !strcmp( simnfo->mixingRule, "standard") ){
# Line 683 | Line 1003 | void SimSetup::makeMolecules( void ){
1003    BondStamp* currentBond;
1004    BendStamp* currentBend;
1005    TorsionStamp* currentTorsion;
1006 +
1007 +  bond_pair* theBonds;
1008 +  bend_set* theBends;
1009 +  torsion_set* theTorsions;
1010 +
1011    
1012    //init the forceField paramters
1013  
1014    the_ff->readParams();
1015  
1016    
1017 <  // init the molecules
1017 >  // init the atoms
1018  
1019 +  double ux, uy, uz, u, uSqr;
1020 +  
1021    atomOffset = 0;
1022    excludeOffset = 0;
1023    for(i=0; i<simnfo->n_mol; i++){
# Line 707 | Line 1034 | void SimSetup::makeMolecules( void ){
1034      info.myExcludes = &the_excludes[excludeOffset];
1035      info.myBonds = new Bond*[info.nBonds];
1036      info.myBends = new Bend*[info.nBends];
1037 <    info.myTorsions = new Torsions*[info.nTorsions];
1037 >    info.myTorsions = new Torsion*[info.nTorsions];
1038  
1039      theBonds = new bond_pair[info.nBonds];
1040      theBends = new bend_set[info.nBends];
# Line 717 | Line 1044 | void SimSetup::makeMolecules( void ){
1044      
1045      for(j=0; j<info.nAtoms; j++){
1046        
1047 <      currentAtom = theComponents[stampID]->getAtom( j );
1047 >      currentAtom = comp_stamps[stampID]->getAtom( j );
1048        if( currentAtom->haveOrientation() ){
1049          
1050          dAtom = new DirectionalAtom(j + atomOffset);
# Line 758 | Line 1085 | void SimSetup::makeMolecules( void ){
1085        theBonds[j].a = currentBond->getA() + atomOffset;
1086        theBonds[j].b = currentBond->getB() + atomOffset;
1087  
1088 <      exI = theBonds[i].a;
1089 <      exJ = theBonds[i].b;
1088 >      exI = theBonds[j].a;
1089 >      exJ = theBonds[j].b;
1090  
1091        // exclude_I must always be the smaller of the pair
1092        if( exI > exJ ){
# Line 775 | Line 1102 | void SimSetup::makeMolecules( void ){
1102        
1103        the_excludes[j+excludeOffset]->setPair( exI, exJ );
1104   #else  // isn't MPI
1105 +
1106        the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1107   #endif  //is_mpi
1108      }
# Line 790 | Line 1118 | void SimSetup::makeMolecules( void ){
1118            
1119        if( currentBend->haveExtras() ){
1120              
1121 <        extras = current_bend->getExtras();
1121 >        extras = currentBend->getExtras();
1122          current_extra = extras;
1123              
1124          while( current_extra != NULL ){
# Line 812 | Line 1140 | void SimSetup::makeMolecules( void ){
1140                
1141              default:
1142                sprintf( painCave.errMsg,
1143 <                       "SimSetup Error: ghostVectorSource was neiter a "
1143 >                       "SimSetup Error: ghostVectorSource was neither a "
1144                         "double nor an int.\n"
1145                         "-->Bend[%d] in %s\n",
1146                         j, comp_stamps[stampID]->getID() );
# Line 897 | Line 1225 | void SimSetup::makeMolecules( void ){
1225      excludeOffset += info.nTorsions;
1226  
1227      
1228 <
901 <
902 <
903 <
904 <
905 <
906 < void SimSetup::makeAtoms( void ){
907 <
908 <  int i, j, k, index;
909 <  double ux, uy, uz, uSqr, u;
910 <  AtomStamp* current_atom;
1228 >    // send the arrays off to the forceField for init.
1229  
1230 <  DirectionalAtom* dAtom;
1231 <  int molIndex, molStart, molEnd, nMemb, lMolIndex;
1232 <
1233 <  lMolIndex = 0;
916 <  molIndex = 0;
917 <  index = 0;
918 <  for( i=0; i<n_components; i++ ){
919 <
920 <    for( j=0; j<components_nmol[i]; j++ ){
921 <
922 < #ifdef IS_MPI
923 <      if( mpiSim->getMyMolStart() <= molIndex &&
924 <          molIndex <= mpiSim->getMyMolEnd() ){
925 < #endif // is_mpi        
926 <
927 <        molStart = index;
928 <        nMemb = comp_stamps[i]->getNAtoms();
929 <        for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){
930 <          
931 <          current_atom = comp_stamps[i]->getAtom( k );
932 <          if( current_atom->haveOrientation() ){
933 <            
934 <            dAtom = new DirectionalAtom(index);
935 <            simnfo->n_oriented++;
936 <            the_atoms[index] = dAtom;
937 <            
938 <            ux = current_atom->getOrntX();
939 <            uy = current_atom->getOrntY();
940 <            uz = current_atom->getOrntZ();
941 <            
942 <            uSqr = (ux * ux) + (uy * uy) + (uz * uz);
943 <            
944 <            u = sqrt( uSqr );
945 <            ux = ux / u;
946 <            uy = uy / u;
947 <            uz = uz / u;
948 <            
949 <            dAtom->setSUx( ux );
950 <            dAtom->setSUy( uy );
951 <            dAtom->setSUz( uz );
952 <          }
953 <          else{
954 <            the_atoms[index] = new GeneralAtom(index);
955 <          }
956 <          the_atoms[index]->setType( current_atom->getType() );
957 <          the_atoms[index]->setIndex( index );
958 <          
959 <          // increment the index and repeat;
960 <          index++;
961 <        }
962 <        
963 <        molEnd = index -1;
964 <        the_molecules[lMolIndex].setNMembers( nMemb );
965 <        the_molecules[lMolIndex].setStartAtom( molStart );
966 <        the_molecules[lMolIndex].setEndAtom( molEnd );
967 <        the_molecules[lMolIndex].setStampID( i );
968 <        lMolIndex++;
1230 >    the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
1231 >    the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
1232 >    the_ff->initializeBends( info.nBends, info.myBends, theBends );
1233 >    the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
1234  
970 – #ifdef IS_MPI
971 –      }
972 – #endif //is_mpi
973 –      
974 –      molIndex++;
975 –    }
976 –  }
1235  
1236 < #ifdef IS_MPI
979 <    for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] );
980 <    
981 <    delete[] globalIndex;
982 <
983 <    mpiSim->mpiRefresh();
984 < #endif //IS_MPI
985 <          
986 <  the_ff->initializeAtoms();
987 < }
988 <
989 < void SimSetup::makeBonds( void ){
990 <
991 <  int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
992 <  bond_pair* the_bonds;
993 <  BondStamp* current_bond;
994 <
995 <  the_bonds = new bond_pair[tot_bonds];
996 <  index = 0;
997 <  offset = 0;
998 <  molIndex = 0;
999 <
1000 <  for( i=0; i<n_components; i++ ){
1001 <
1002 <    for( j=0; j<components_nmol[i]; j++ ){
1003 <
1004 < #ifdef IS_MPI
1005 <      if( mpiSim->getMyMolStart() <= molIndex &&
1006 <          molIndex <= mpiSim->getMyMolEnd() ){
1007 < #endif // is_mpi        
1008 <        
1009 <        for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){
1010 <          
1011 <          current_bond = comp_stamps[i]->getBond( k );
1012 <          the_bonds[index].a = current_bond->getA() + offset;
1013 <          the_bonds[index].b = current_bond->getB() + offset;
1014 <
1015 <          exI = the_bonds[index].a;
1016 <          exJ = the_bonds[index].b;
1017 <
1018 <          // exclude_I must always be the smaller of the pair
1019 <          if( exI > exJ ){
1020 <            tempEx = exI;
1021 <            exI = exJ;
1022 <            exJ = tempEx;
1023 <          }
1024 <
1025 <          
1026 < #ifdef IS_MPI
1027 <
1028 <          the_excludes[index*2] =    
1029 <            the_atoms[exI]->getGlobalIndex() + 1;
1030 <          the_excludes[index*2 + 1] =
1031 <            the_atoms[exJ]->getGlobalIndex() + 1;
1032 <
1033 < #else  // isn't MPI
1034 <          
1035 <          the_excludes[index*2] =     exI + 1;
1036 <          the_excludes[index*2 + 1] = exJ + 1;
1037 <          // fortran index from 1 (hence the +1 in the indexing)
1038 < #endif  //is_mpi
1039 <          
1040 <          // increment the index and repeat;
1041 <          index++;
1042 <        }
1043 <        offset += comp_stamps[i]->getNAtoms();
1044 <        
1045 < #ifdef IS_MPI
1046 <      }
1047 < #endif //is_mpi
1048 <      
1049 <      molIndex++;
1050 <    }      
1051 <  }
1052 <
1053 <  the_ff->initializeBonds( the_bonds );
1054 < }
1055 <
1056 < void SimSetup::makeBends( void ){
1057 <
1058 <  int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
1059 <  bend_set* the_bends;
1060 <  BendStamp* current_bend;
1061 <  LinkedAssign* extras;
1062 <  LinkedAssign* current_extra;
1063 <  
1236 >    the_molecules[i].initialize( info );
1237  
1065 –  the_bends = new bend_set[tot_bends];
1066 –  index = 0;
1067 –  offset = 0;
1068 –  molIndex = 0;
1069 –  for( i=0; i<n_components; i++ ){
1238  
1239 <    for( j=0; j<components_nmol[i]; j++ ){
1240 <
1241 < #ifdef IS_MPI
1242 <      if( mpiSim->getMyMolStart() <= molIndex &&
1075 <          molIndex <= mpiSim->getMyMolEnd() ){
1076 < #endif // is_mpi        
1077 <
1078 <        for( k=0; k<comp_stamps[i]->getNBends(); k++ ){
1079 <          
1080 <          current_bend = comp_stamps[i]->getBend( k );
1081 <          the_bends[index].a = current_bend->getA() + offset;
1082 <          the_bends[index].b = current_bend->getB() + offset;
1083 <          the_bends[index].c = current_bend->getC() + offset;
1084 <          
1085 <          if( current_bend->haveExtras() ){
1086 <            
1087 <            extras = current_bend->getExtras();
1088 <            current_extra = extras;
1089 <            
1090 <            while( current_extra != NULL ){
1091 <              if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
1092 <                
1093 <                switch( current_extra->getType() ){
1094 <                  
1095 <                case 0:
1096 <                  the_bends[index].ghost =
1097 <                    current_extra->getInt() + offset;
1098 <                  the_bends[index].isGhost = 1;
1099 <                  break;
1100 <                  
1101 <                case 1:
1102 <                  the_bends[index].ghost =
1103 <                    (int)current_extra->getDouble() + offset;
1104 <                  the_bends[index].isGhost = 1;
1105 <                  break;
1106 <                  
1107 <                default:
1108 <                  sprintf( painCave.errMsg,
1109 <                           "SimSetup Error: ghostVectorSource was neiter a "
1110 <                           "double nor an int.\n"
1111 <                           "-->Bend[%d] in %s\n",
1112 <                           k, comp_stamps[i]->getID() );
1113 <                  painCave.isFatal = 1;
1114 <                  simError();
1115 <                }
1116 <              }
1117 <              
1118 <              else{
1119 <                
1120 <                sprintf( painCave.errMsg,
1121 <                         "SimSetup Error: unhandled bend assignment:\n"
1122 <                         "    -->%s in Bend[%d] in %s\n",
1123 <                         current_extra->getlhs(),
1124 <                         k, comp_stamps[i]->getID() );
1125 <                painCave.isFatal = 1;
1126 <                simError();
1127 <              }
1128 <              
1129 <              current_extra = current_extra->getNext();
1130 <            }
1131 <          }
1132 <          
1133 <          if( !the_bends[index].isGhost ){
1134 <            
1135 <            exI = the_bends[index].a;
1136 <            exJ = the_bends[index].c;
1137 <          }
1138 <          else{
1139 <            
1140 <            exI = the_bends[index].a;
1141 <            exJ = the_bends[index].b;
1142 <          }
1143 <          
1144 <          // exclude_I must always be the smaller of the pair
1145 <          if( exI > exJ ){
1146 <            tempEx = exI;
1147 <            exI = exJ;
1148 <            exJ = tempEx;
1149 <          }
1150 <
1151 <
1152 < #ifdef IS_MPI
1153 <
1154 <          the_excludes[(index + tot_bonds)*2] =    
1155 <            the_atoms[exI]->getGlobalIndex() + 1;
1156 <          the_excludes[(index + tot_bonds)*2 + 1] =
1157 <            the_atoms[exJ]->getGlobalIndex() + 1;
1158 <          
1159 < #else  // isn't MPI
1160 <          
1161 <          the_excludes[(index + tot_bonds)*2] =     exI + 1;
1162 <          the_excludes[(index + tot_bonds)*2 + 1] = exJ + 1;
1163 <          // fortran index from 1 (hence the +1 in the indexing)
1164 < #endif  //is_mpi
1165 <          
1166 <          
1167 <          // increment the index and repeat;
1168 <          index++;
1169 <        }
1170 <        offset += comp_stamps[i]->getNAtoms();
1171 <        
1172 < #ifdef IS_MPI
1173 <      }
1174 < #endif //is_mpi
1175 <
1176 <      molIndex++;
1177 <    }
1239 >    atomOffset += info.nAtoms;
1240 >    delete[] theBonds;
1241 >    delete[] theBends;
1242 >    delete[] theTorsions;
1243    }
1244  
1245   #ifdef IS_MPI
1246 <  sprintf( checkPointMsg,
1182 <           "Successfully created the bends list.\n" );
1246 >  sprintf( checkPointMsg, "all molecules initialized succesfully" );
1247    MPIcheckPoint();
1248   #endif // is_mpi
1185 –  
1249  
1250 <  the_ff->initializeBends( the_bends );
1251 < }
1250 >  // clean up the forcefield
1251 >  the_ff->calcRcut();
1252 >  the_ff->cleanMe();
1253  
1190 – void SimSetup::makeTorsions( void ){
1191 –
1192 –  int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
1193 –  torsion_set* the_torsions;
1194 –  TorsionStamp* current_torsion;
1195 –
1196 –  the_torsions = new torsion_set[tot_torsions];
1197 –  index = 0;
1198 –  offset = 0;
1199 –  molIndex = 0;
1200 –  for( i=0; i<n_components; i++ ){
1201 –
1202 –    for( j=0; j<components_nmol[i]; j++ ){
1203 –
1204 – #ifdef IS_MPI
1205 –      if( mpiSim->getMyMolStart() <= molIndex &&
1206 –          molIndex <= mpiSim->getMyMolEnd() ){
1207 – #endif // is_mpi        
1208 –
1209 –      for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){
1210 –
1211 –        current_torsion = comp_stamps[i]->getTorsion( k );
1212 –        the_torsions[index].a = current_torsion->getA() + offset;
1213 –        the_torsions[index].b = current_torsion->getB() + offset;
1214 –        the_torsions[index].c = current_torsion->getC() + offset;
1215 –        the_torsions[index].d = current_torsion->getD() + offset;
1216 –
1217 –        exI = the_torsions[index].a;
1218 –        exJ = the_torsions[index].d;
1219 –
1220 –        
1221 –        // exclude_I must always be the smaller of the pair
1222 –        if( exI > exJ ){
1223 –          tempEx = exI;
1224 –          exI = exJ;
1225 –          exJ = tempEx;
1226 –        }
1227 –
1228 –
1229 – #ifdef IS_MPI
1230 –        
1231 –        the_excludes[(index + tot_bonds + tot_bends)*2] =    
1232 –          the_atoms[exI]->getGlobalIndex() + 1;
1233 –        the_excludes[(index + tot_bonds + tot_bends)*2 + 1] =
1234 –          the_atoms[exJ]->getGlobalIndex() + 1;
1235 –        
1236 – #else  // isn't MPI
1237 –        
1238 –        the_excludes[(index + tot_bonds + tot_bends)*2] =     exI + 1;
1239 –        the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = exJ + 1;
1240 –        // fortran indexes from 1 (hence the +1 in the indexing)
1241 – #endif  //is_mpi
1242 –        
1243 –
1244 –        // increment the index and repeat;
1245 –        index++;
1246 –      }
1247 –      offset += comp_stamps[i]->getNAtoms();
1248 –
1249 – #ifdef IS_MPI
1250 –      }
1251 – #endif //is_mpi      
1252 –
1253 –      molIndex++;
1254 –    }
1255 –  }
1256 –
1257 –  the_ff->initializeTorsions( the_torsions );
1254   }
1255  
1256   void SimSetup::initFromBass( void ){
# Line 1276 | Line 1272 | void SimSetup::initFromBass( void ){
1272      have_extra =1;
1273  
1274      n_cells = (int)temp3 - 1;
1275 <    cellx = simnfo->box_x / temp3;
1276 <    celly = simnfo->box_y / temp3;
1277 <    cellz = simnfo->box_z / temp3;
1275 >    cellx = simnfo->boxLx / temp3;
1276 >    celly = simnfo->boxLy / temp3;
1277 >    cellz = simnfo->boxLz / temp3;
1278      n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
1279      temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1280      n_per_extra = (int)ceil( temp1 );
# Line 1293 | Line 1289 | void SimSetup::initFromBass( void ){
1289    }
1290    else{
1291      n_cells = (int)temp3;
1292 <    cellx = simnfo->box_x / temp3;
1293 <    celly = simnfo->box_y / temp3;
1294 <    cellz = simnfo->box_z / temp3;
1292 >    cellx = simnfo->boxLx / temp3;
1293 >    celly = simnfo->boxLy / temp3;
1294 >    cellz = simnfo->boxLz / temp3;
1295    }
1296  
1297    current_mol = 0;

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