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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 407 by mmeineke, Wed Mar 26 20:22:02 2003 UTC vs.
Revision 604 by gezelter, Tue Jul 15 03:08:00 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 <  if( simnfo->n_SRI ){
427 <    the_sris = new SRI*[simnfo->n_SRI];
428 <    the_excludes = new int[2 * simnfo->n_SRI];
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      
471 <    the_excludes = new int[2];
472 <    the_excludes[0] = 0;
473 <    the_excludes[1] = 0;
471 >    Exclude::createArray( 1 );
472 >    the_excludes = new Exclude*;
473 >    the_excludes[0] = new Exclude(0);
474 >    the_excludes[0]->setPair( 0,0 );
475      simnfo->globalExcludes = new int;
476      simnfo->globalExcludes[0] = 0;
477 <
323 <    simnfo->n_exclude = 1;
477 >    simnfo->n_exclude = 0;
478    }
479  
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  
792 < //   new AllLong( simnfo );
792 >  switch( ensembleCase ){
793  
794 <  if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff );
795 <  if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff );
796 <  if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff );
797 <  if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff );
794 >  case NVE_ENS:
795 >    new NVE( simnfo, the_ff );
796 >    break;
797 >
798 >  case NVT_ENS:
799 >    myNVT = new NVT( simnfo, the_ff );
800 >    myNVT->setTargetTemp(the_globals->getTargetTemp());
801 >
802 >    if (the_globals->haveTauThermostat())
803 >      myNVT->setTauThermostat(the_globals->getTauThermostat());
804 >
805 >    else {
806 >      sprintf( painCave.errMsg,
807 >               "SimSetup error: If you use the NVT\n"
808 >               "    ensemble, you must set tauThermostat.\n");
809 >      painCave.isFatal = 1;
810 >      simError();
811 >    }
812 >    break;
813 >
814 >  case NPTi_ENS:
815 >    myNPTi = new NPTi( simnfo, the_ff );
816 >    myNPTi->setTargetTemp( the_globals->getTargetTemp());
817  
818 +    if (the_globals->haveTargetPressure())
819 +      myNPTi->setTargetPressure(the_globals->getTargetPressure());
820 +    else {
821 +      sprintf( painCave.errMsg,
822 +               "SimSetup error: If you use a constant pressure\n"
823 +               "    ensemble, you must set targetPressure in the BASS file.\n");
824 +      painCave.isFatal = 1;
825 +      simError();
826 +    }
827 +    
828 +    if( the_globals->haveTauThermostat() )
829 +      myNPTi->setTauThermostat( the_globals->getTauThermostat() );
830 +    else{
831 +      sprintf( painCave.errMsg,
832 +               "SimSetup error: If you use an NPT\n"
833 +               "    ensemble, you must set tauThermostat.\n");
834 +      painCave.isFatal = 1;
835 +      simError();
836 +    }
837  
838 +    if( the_globals->haveTauBarostat() )
839 +      myNPTi->setTauBarostat( the_globals->getTauBarostat() );
840 +    else{
841 +      sprintf( painCave.errMsg,
842 +               "SimSetup error: If you use an NPT\n"
843 +               "    ensemble, you must set tauBarostat.\n");
844 +      painCave.isFatal = 1;
845 +      simError();
846 +    }
847 +    break;
848  
849 +  case NPTf_ENS:
850 +    myNPTf = new NPTf( simnfo, the_ff );
851 +    myNPTf->setTargetTemp( the_globals->getTargetTemp());
852 +
853 +    if (the_globals->haveTargetPressure())
854 +      myNPTf->setTargetPressure(the_globals->getTargetPressure());
855 +    else {
856 +      sprintf( painCave.errMsg,
857 +               "SimSetup error: If you use a constant pressure\n"
858 +               "    ensemble, you must set targetPressure in the BASS file.\n");
859 +      painCave.isFatal = 1;
860 +      simError();
861 +    }    
862 +
863 +    if( the_globals->haveTauThermostat() )
864 +      myNPTf->setTauThermostat( the_globals->getTauThermostat() );
865 +    else{
866 +      sprintf( painCave.errMsg,
867 +               "SimSetup error: If you use an NPT\n"
868 +               "    ensemble, you must set tauThermostat.\n");
869 +      painCave.isFatal = 1;
870 +      simError();
871 +    }
872 +
873 +    if( the_globals->haveTauBarostat() )
874 +      myNPTf->setTauBarostat( the_globals->getTauBarostat() );
875 +    else{
876 +      sprintf( painCave.errMsg,
877 +               "SimSetup error: If you use an NPT\n"
878 +               "    ensemble, you must set tauBarostat.\n");
879 +      painCave.isFatal = 1;
880 +      simError();
881 +    }
882 +    break;
883 +    
884 +  case NPTim_ENS:
885 +    myNPTim = new NPTim( simnfo, the_ff );
886 +    myNPTim->setTargetTemp( the_globals->getTargetTemp());
887 +
888 +    if (the_globals->haveTargetPressure())
889 +      myNPTim->setTargetPressure(the_globals->getTargetPressure());
890 +    else {
891 +      sprintf( painCave.errMsg,
892 +               "SimSetup error: If you use a constant pressure\n"
893 +               "    ensemble, you must set targetPressure in the BASS file.\n");
894 +      painCave.isFatal = 1;
895 +      simError();
896 +    }
897 +    
898 +    if( the_globals->haveTauThermostat() )
899 +      myNPTim->setTauThermostat( the_globals->getTauThermostat() );
900 +    else{
901 +      sprintf( painCave.errMsg,
902 +               "SimSetup error: If you use an NPT\n"
903 +               "    ensemble, you must set tauThermostat.\n");
904 +      painCave.isFatal = 1;
905 +      simError();
906 +    }
907 +
908 +    if( the_globals->haveTauBarostat() )
909 +      myNPTim->setTauBarostat( the_globals->getTauBarostat() );
910 +    else{
911 +      sprintf( painCave.errMsg,
912 +               "SimSetup error: If you use an NPT\n"
913 +               "    ensemble, you must set tauBarostat.\n");
914 +      painCave.isFatal = 1;
915 +      simError();
916 +    }
917 +    break;
918 +
919 +    
920 +
921 +  default:
922 +    sprintf( painCave.errMsg,
923 +             "SimSetup Error. Unrecognized ensemble in case statement.\n");
924 +    painCave.isFatal = 1;
925 +    simError();
926 +  }
927 +
928 +
929 + #ifdef IS_MPI
930 +  mpiSim->mpiRefresh();
931 + #endif
932 +
933    // initialize the Fortran
934 <  
934 >
935 >
936    simnfo->refreshSim();
937    
938    if( !strcmp( simnfo->mixingRule, "standard") ){
# Line 674 | Line 960 | void SimSetup::makeMolecules( void ){
960  
961   void SimSetup::makeMolecules( void ){
962  
963 <  int i, j, exI, exJ, tempEx, stampID, atomOffset;
963 >  int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
964    molInit info;
965    DirectionalAtom* dAtom;
966 +  LinkedAssign* extras;
967 +  LinkedAssign* current_extra;
968    AtomStamp* currentAtom;
969    BondStamp* currentBond;
970    BendStamp* currentBend;
971    TorsionStamp* currentTorsion;
972 +
973 +  bond_pair* theBonds;
974 +  bend_set* theBends;
975 +  torsion_set* theTorsions;
976 +
977    
978    //init the forceField paramters
979  
980    the_ff->readParams();
981  
982    
983 <  // init the molecules
983 >  // init the atoms
984  
985 +  double ux, uy, uz, u, uSqr;
986 +  
987    atomOffset = 0;
988 +  excludeOffset = 0;
989    for(i=0; i<simnfo->n_mol; i++){
990      
991      stampID = the_molecules[i].getStampID();
# Line 698 | Line 994 | void SimSetup::makeMolecules( void ){
994      info.nBonds    = comp_stamps[stampID]->getNBonds();
995      info.nBends    = comp_stamps[stampID]->getNBends();
996      info.nTorsions = comp_stamps[stampID]->getNTorsions();
997 <    
997 >    info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
998 >
999      info.myAtoms = &the_atoms[atomOffset];
1000 +    info.myExcludes = &the_excludes[excludeOffset];
1001      info.myBonds = new Bond*[info.nBonds];
1002      info.myBends = new Bend*[info.nBends];
1003 <    info.myTorsions = new Torsions*[info.nTorsions];
1003 >    info.myTorsions = new Torsion*[info.nTorsions];
1004  
1005      theBonds = new bond_pair[info.nBonds];
1006      theBends = new bend_set[info.nBends];
# Line 712 | Line 1010 | void SimSetup::makeMolecules( void ){
1010      
1011      for(j=0; j<info.nAtoms; j++){
1012        
1013 <      currentAtom = theComponents[stampID]->getAtom( j );
1013 >      currentAtom = comp_stamps[stampID]->getAtom( j );
1014        if( currentAtom->haveOrientation() ){
1015          
1016          dAtom = new DirectionalAtom(j + atomOffset);
# Line 747 | Line 1045 | void SimSetup::makeMolecules( void ){
1045      }
1046      
1047      // make the bonds
1048 <    for(j=0; j<nBonds; j++){
1048 >    for(j=0; j<info.nBonds; j++){
1049        
1050        currentBond = comp_stamps[stampID]->getBond( j );
1051        theBonds[j].a = currentBond->getA() + atomOffset;
1052        theBonds[j].b = currentBond->getB() + atomOffset;
1053  
1054 <      exI = theBonds[i].a;
1055 <      exJ = theBonds[i].b;
1054 >      exI = theBonds[j].a;
1055 >      exJ = theBonds[j].b;
1056  
1057        // exclude_I must always be the smaller of the pair
1058        if( exI > exJ ){
# Line 763 | Line 1061 | void SimSetup::makeMolecules( void ){
1061          exJ = tempEx;
1062        }
1063   #ifdef IS_MPI
1064 +      tempEx = exI;
1065 +      exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1066 +      tempEx = exJ;
1067 +      exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1068        
1069 <      the_excludes[index*2] =    
768 <        the_atoms[exI]->getGlobalIndex() + 1;
769 <      the_excludes[index*2 + 1] =
770 <        the_atoms[exJ]->getGlobalIndex() + 1;
771 <      
1069 >      the_excludes[j+excludeOffset]->setPair( exI, exJ );
1070   #else  // isn't MPI
773 –      
774 –      the_excludes[index*2] =     exI + 1;
775 –      the_excludes[index*2 + 1] = exJ + 1;
776 –      // fortran index from 1 (hence the +1 in the indexing)
1071  
1072 +      the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1073   #endif  //is_mpi
1074 <    
1075 <  }
781 <
782 <
783 <
784 <
785 <
786 <
787 <
788 <
789 <
790 <
791 <
1074 >    }
1075 >    excludeOffset += info.nBonds;
1076  
1077 <
1078 <
1079 <
1080 < void SimSetup::makeAtoms( void ){
1081 <
1082 <  int i, j, k, index;
1083 <  double ux, uy, uz, uSqr, u;
800 <  AtomStamp* current_atom;
801 <
802 <  DirectionalAtom* dAtom;
803 <  int molIndex, molStart, molEnd, nMemb, lMolIndex;
804 <
805 <  lMolIndex = 0;
806 <  molIndex = 0;
807 <  index = 0;
808 <  for( i=0; i<n_components; i++ ){
809 <
810 <    for( j=0; j<components_nmol[i]; j++ ){
811 <
812 < #ifdef IS_MPI
813 <      if( mpiSim->getMyMolStart() <= molIndex &&
814 <          molIndex <= mpiSim->getMyMolEnd() ){
815 < #endif // is_mpi        
816 <
817 <        molStart = index;
818 <        nMemb = comp_stamps[i]->getNAtoms();
819 <        for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){
1077 >    //make the bends
1078 >    for(j=0; j<info.nBends; j++){
1079 >      
1080 >      currentBend = comp_stamps[stampID]->getBend( j );
1081 >      theBends[j].a = currentBend->getA() + atomOffset;
1082 >      theBends[j].b = currentBend->getB() + atomOffset;
1083 >      theBends[j].c = currentBend->getC() + atomOffset;
1084            
1085 <          current_atom = comp_stamps[i]->getAtom( k );
822 <          if( current_atom->haveOrientation() ){
1085 >      if( currentBend->haveExtras() ){
1086              
1087 <            dAtom = new DirectionalAtom(index);
1088 <            simnfo->n_oriented++;
826 <            the_atoms[index] = dAtom;
1087 >        extras = currentBend->getExtras();
1088 >        current_extra = extras;
1089              
1090 <            ux = current_atom->getOrntX();
1091 <            uy = current_atom->getOrntY();
1092 <            uz = current_atom->getOrntZ();
1093 <            
1094 <            uSqr = (ux * ux) + (uy * uy) + (uz * uz);
1095 <            
1096 <            u = sqrt( uSqr );
1097 <            ux = ux / u;
1098 <            uy = uy / u;
1099 <            uz = uz / u;
1100 <            
1101 <            dAtom->setSUx( ux );
1102 <            dAtom->setSUy( uy );
1103 <            dAtom->setSUz( uz );
1090 >        while( current_extra != NULL ){
1091 >          if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
1092 >                
1093 >            switch( current_extra->getType() ){
1094 >              
1095 >            case 0:
1096 >              theBends[j].ghost =
1097 >                current_extra->getInt() + atomOffset;
1098 >              theBends[j].isGhost = 1;
1099 >              break;
1100 >                  
1101 >            case 1:
1102 >              theBends[j].ghost =
1103 >                (int)current_extra->getDouble() + atomOffset;
1104 >              theBends[j].isGhost = 1;
1105 >              break;
1106 >              
1107 >            default:
1108 >              sprintf( painCave.errMsg,
1109 >                       "SimSetup Error: ghostVectorSource was neither a "
1110 >                       "double nor an int.\n"
1111 >                       "-->Bend[%d] in %s\n",
1112 >                       j, comp_stamps[stampID]->getID() );
1113 >              painCave.isFatal = 1;
1114 >              simError();
1115 >            }
1116            }
1117 +          
1118            else{
1119 <            the_atoms[index] = new GeneralAtom(index);
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 >                     j, comp_stamps[stampID]->getID() );
1125 >            painCave.isFatal = 1;
1126 >            simError();
1127            }
846 –          the_atoms[index]->setType( current_atom->getType() );
847 –          the_atoms[index]->setIndex( index );
1128            
1129 <          // increment the index and repeat;
850 <          index++;
1129 >          current_extra = current_extra->getNext();
1130          }
1131 +      }
1132 +          
1133 +      if( !theBends[j].isGhost ){
1134 +            
1135 +        exI = theBends[j].a;
1136 +        exJ = theBends[j].c;
1137 +      }
1138 +      else{
1139          
1140 <        molEnd = index -1;
1141 <        the_molecules[lMolIndex].setNMembers( nMemb );
855 <        the_molecules[lMolIndex].setStartAtom( molStart );
856 <        the_molecules[lMolIndex].setEndAtom( molEnd );
857 <        the_molecules[lMolIndex].setStampID( i );
858 <        lMolIndex++;
859 <
860 < #ifdef IS_MPI
1140 >        exI = theBends[j].a;
1141 >        exJ = theBends[j].b;
1142        }
862 – #endif //is_mpi
1143        
1144 <      molIndex++;
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 > #ifdef IS_MPI
1151 >      tempEx = exI;
1152 >      exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1153 >      tempEx = exJ;
1154 >      exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1155 >      
1156 >      the_excludes[j+excludeOffset]->setPair( exI, exJ );
1157 > #else  // isn't MPI
1158 >      the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1159 > #endif  //is_mpi
1160      }
1161 <  }
1161 >    excludeOffset += info.nBends;
1162  
1163 < #ifdef IS_MPI
1164 <    for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] );
1165 <    
1166 <    delete[] globalIndex;
1163 >    for(j=0; j<info.nTorsions; j++){
1164 >      
1165 >      currentTorsion = comp_stamps[stampID]->getTorsion( j );
1166 >      theTorsions[j].a = currentTorsion->getA() + atomOffset;
1167 >      theTorsions[j].b = currentTorsion->getB() + atomOffset;
1168 >      theTorsions[j].c = currentTorsion->getC() + atomOffset;
1169 >      theTorsions[j].d = currentTorsion->getD() + atomOffset;
1170 >      
1171 >      exI = theTorsions[j].a;
1172 >      exJ = theTorsions[j].d;
1173  
1174 <    mpiSim->mpiRefresh();
1175 < #endif //IS_MPI
1176 <          
1177 <  the_ff->initializeAtoms();
1178 < }
1179 <
879 < void SimSetup::makeBonds( void ){
880 <
881 <  int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
882 <  bond_pair* the_bonds;
883 <  BondStamp* current_bond;
884 <
885 <  the_bonds = new bond_pair[tot_bonds];
886 <  index = 0;
887 <  offset = 0;
888 <  molIndex = 0;
889 <
890 <  for( i=0; i<n_components; i++ ){
891 <
892 <    for( j=0; j<components_nmol[i]; j++ ){
893 <
1174 >      // exclude_I must always be the smaller of the pair
1175 >      if( exI > exJ ){
1176 >        tempEx = exI;
1177 >        exI = exJ;
1178 >        exJ = tempEx;
1179 >      }
1180   #ifdef IS_MPI
1181 <      if( mpiSim->getMyMolStart() <= molIndex &&
1182 <          molIndex <= mpiSim->getMyMolEnd() ){
1183 < #endif // is_mpi        
1184 <        
1185 <        for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){
1186 <          
1187 <          current_bond = comp_stamps[i]->getBond( k );
1188 <          the_bonds[index].a = current_bond->getA() + offset;
1189 <          the_bonds[index].b = current_bond->getB() + offset;
1181 >      tempEx = exI;
1182 >      exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1183 >      tempEx = exJ;
1184 >      exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1185 >      
1186 >      the_excludes[j+excludeOffset]->setPair( exI, exJ );
1187 > #else  // isn't MPI
1188 >      the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1189 > #endif  //is_mpi
1190 >    }
1191 >    excludeOffset += info.nTorsions;
1192  
1193 <          exI = the_bonds[index].a;
1194 <          exJ = the_bonds[index].b;
1193 >    
1194 >    // send the arrays off to the forceField for init.
1195  
1196 <          // exclude_I must always be the smaller of the pair
1197 <          if( exI > exJ ){
1198 <            tempEx = exI;
1199 <            exI = exJ;
912 <            exJ = tempEx;
913 <          }
1196 >    the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
1197 >    the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
1198 >    the_ff->initializeBends( info.nBends, info.myBends, theBends );
1199 >    the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
1200  
915 –          
916 – #ifdef IS_MPI
1201  
1202 <          the_excludes[index*2] =    
919 <            the_atoms[exI]->getGlobalIndex() + 1;
920 <          the_excludes[index*2 + 1] =
921 <            the_atoms[exJ]->getGlobalIndex() + 1;
922 <
923 < #else  // isn't MPI
924 <          
925 <          the_excludes[index*2] =     exI + 1;
926 <          the_excludes[index*2 + 1] = exJ + 1;
927 <          // fortran index from 1 (hence the +1 in the indexing)
928 < #endif  //is_mpi
929 <          
930 <          // increment the index and repeat;
931 <          index++;
932 <        }
933 <        offset += comp_stamps[i]->getNAtoms();
934 <        
935 < #ifdef IS_MPI
936 <      }
937 < #endif //is_mpi
938 <      
939 <      molIndex++;
940 <    }      
941 <  }
1202 >    the_molecules[i].initialize( info );
1203  
943 –  the_ff->initializeBonds( the_bonds );
944 – }
1204  
1205 < void SimSetup::makeBends( void ){
1206 <
1207 <  int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
1208 <  bend_set* the_bends;
950 <  BendStamp* current_bend;
951 <  LinkedAssign* extras;
952 <  LinkedAssign* current_extra;
953 <  
954 <
955 <  the_bends = new bend_set[tot_bends];
956 <  index = 0;
957 <  offset = 0;
958 <  molIndex = 0;
959 <  for( i=0; i<n_components; i++ ){
960 <
961 <    for( j=0; j<components_nmol[i]; j++ ){
962 <
963 < #ifdef IS_MPI
964 <      if( mpiSim->getMyMolStart() <= molIndex &&
965 <          molIndex <= mpiSim->getMyMolEnd() ){
966 < #endif // is_mpi        
967 <
968 <        for( k=0; k<comp_stamps[i]->getNBends(); k++ ){
969 <          
970 <          current_bend = comp_stamps[i]->getBend( k );
971 <          the_bends[index].a = current_bend->getA() + offset;
972 <          the_bends[index].b = current_bend->getB() + offset;
973 <          the_bends[index].c = current_bend->getC() + offset;
974 <          
975 <          if( current_bend->haveExtras() ){
976 <            
977 <            extras = current_bend->getExtras();
978 <            current_extra = extras;
979 <            
980 <            while( current_extra != NULL ){
981 <              if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
982 <                
983 <                switch( current_extra->getType() ){
984 <                  
985 <                case 0:
986 <                  the_bends[index].ghost =
987 <                    current_extra->getInt() + offset;
988 <                  the_bends[index].isGhost = 1;
989 <                  break;
990 <                  
991 <                case 1:
992 <                  the_bends[index].ghost =
993 <                    (int)current_extra->getDouble() + offset;
994 <                  the_bends[index].isGhost = 1;
995 <                  break;
996 <                  
997 <                default:
998 <                  sprintf( painCave.errMsg,
999 <                           "SimSetup Error: ghostVectorSource was neiter a "
1000 <                           "double nor an int.\n"
1001 <                           "-->Bend[%d] in %s\n",
1002 <                           k, comp_stamps[i]->getID() );
1003 <                  painCave.isFatal = 1;
1004 <                  simError();
1005 <                }
1006 <              }
1007 <              
1008 <              else{
1009 <                
1010 <                sprintf( painCave.errMsg,
1011 <                         "SimSetup Error: unhandled bend assignment:\n"
1012 <                         "    -->%s in Bend[%d] in %s\n",
1013 <                         current_extra->getlhs(),
1014 <                         k, comp_stamps[i]->getID() );
1015 <                painCave.isFatal = 1;
1016 <                simError();
1017 <              }
1018 <              
1019 <              current_extra = current_extra->getNext();
1020 <            }
1021 <          }
1022 <          
1023 <          if( !the_bends[index].isGhost ){
1024 <            
1025 <            exI = the_bends[index].a;
1026 <            exJ = the_bends[index].c;
1027 <          }
1028 <          else{
1029 <            
1030 <            exI = the_bends[index].a;
1031 <            exJ = the_bends[index].b;
1032 <          }
1033 <          
1034 <          // exclude_I must always be the smaller of the pair
1035 <          if( exI > exJ ){
1036 <            tempEx = exI;
1037 <            exI = exJ;
1038 <            exJ = tempEx;
1039 <          }
1040 <
1041 <
1042 < #ifdef IS_MPI
1043 <
1044 <          the_excludes[(index + tot_bonds)*2] =    
1045 <            the_atoms[exI]->getGlobalIndex() + 1;
1046 <          the_excludes[(index + tot_bonds)*2 + 1] =
1047 <            the_atoms[exJ]->getGlobalIndex() + 1;
1048 <          
1049 < #else  // isn't MPI
1050 <          
1051 <          the_excludes[(index + tot_bonds)*2] =     exI + 1;
1052 <          the_excludes[(index + tot_bonds)*2 + 1] = exJ + 1;
1053 <          // fortran index from 1 (hence the +1 in the indexing)
1054 < #endif  //is_mpi
1055 <          
1056 <          
1057 <          // increment the index and repeat;
1058 <          index++;
1059 <        }
1060 <        offset += comp_stamps[i]->getNAtoms();
1061 <        
1062 < #ifdef IS_MPI
1063 <      }
1064 < #endif //is_mpi
1065 <
1066 <      molIndex++;
1067 <    }
1205 >    atomOffset += info.nAtoms;
1206 >    delete[] theBonds;
1207 >    delete[] theBends;
1208 >    delete[] theTorsions;
1209    }
1210  
1211   #ifdef IS_MPI
1212 <  sprintf( checkPointMsg,
1072 <           "Successfully created the bends list.\n" );
1212 >  sprintf( checkPointMsg, "all molecules initialized succesfully" );
1213    MPIcheckPoint();
1214   #endif // is_mpi
1075 –  
1215  
1216 <  the_ff->initializeBends( the_bends );
1217 < }
1216 >  // clean up the forcefield
1217 >  the_ff->calcRcut();
1218 >  the_ff->cleanMe();
1219  
1080 – void SimSetup::makeTorsions( void ){
1081 –
1082 –  int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
1083 –  torsion_set* the_torsions;
1084 –  TorsionStamp* current_torsion;
1085 –
1086 –  the_torsions = new torsion_set[tot_torsions];
1087 –  index = 0;
1088 –  offset = 0;
1089 –  molIndex = 0;
1090 –  for( i=0; i<n_components; i++ ){
1091 –
1092 –    for( j=0; j<components_nmol[i]; j++ ){
1093 –
1094 – #ifdef IS_MPI
1095 –      if( mpiSim->getMyMolStart() <= molIndex &&
1096 –          molIndex <= mpiSim->getMyMolEnd() ){
1097 – #endif // is_mpi        
1098 –
1099 –      for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){
1100 –
1101 –        current_torsion = comp_stamps[i]->getTorsion( k );
1102 –        the_torsions[index].a = current_torsion->getA() + offset;
1103 –        the_torsions[index].b = current_torsion->getB() + offset;
1104 –        the_torsions[index].c = current_torsion->getC() + offset;
1105 –        the_torsions[index].d = current_torsion->getD() + offset;
1106 –
1107 –        exI = the_torsions[index].a;
1108 –        exJ = the_torsions[index].d;
1109 –
1110 –        
1111 –        // exclude_I must always be the smaller of the pair
1112 –        if( exI > exJ ){
1113 –          tempEx = exI;
1114 –          exI = exJ;
1115 –          exJ = tempEx;
1116 –        }
1117 –
1118 –
1119 – #ifdef IS_MPI
1120 –        
1121 –        the_excludes[(index + tot_bonds + tot_bends)*2] =    
1122 –          the_atoms[exI]->getGlobalIndex() + 1;
1123 –        the_excludes[(index + tot_bonds + tot_bends)*2 + 1] =
1124 –          the_atoms[exJ]->getGlobalIndex() + 1;
1125 –        
1126 – #else  // isn't MPI
1127 –        
1128 –        the_excludes[(index + tot_bonds + tot_bends)*2] =     exI + 1;
1129 –        the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = exJ + 1;
1130 –        // fortran indexes from 1 (hence the +1 in the indexing)
1131 – #endif  //is_mpi
1132 –        
1133 –
1134 –        // increment the index and repeat;
1135 –        index++;
1136 –      }
1137 –      offset += comp_stamps[i]->getNAtoms();
1138 –
1139 – #ifdef IS_MPI
1140 –      }
1141 – #endif //is_mpi      
1142 –
1143 –      molIndex++;
1144 –    }
1145 –  }
1146 –
1147 –  the_ff->initializeTorsions( the_torsions );
1220   }
1221  
1222   void SimSetup::initFromBass( void ){
# Line 1166 | Line 1238 | void SimSetup::initFromBass( void ){
1238      have_extra =1;
1239  
1240      n_cells = (int)temp3 - 1;
1241 <    cellx = simnfo->box_x / temp3;
1242 <    celly = simnfo->box_y / temp3;
1243 <    cellz = simnfo->box_z / temp3;
1241 >    cellx = simnfo->boxLx / temp3;
1242 >    celly = simnfo->boxLy / temp3;
1243 >    cellz = simnfo->boxLz / temp3;
1244      n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
1245      temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1246      n_per_extra = (int)ceil( temp1 );
# Line 1183 | Line 1255 | void SimSetup::initFromBass( void ){
1255    }
1256    else{
1257      n_cells = (int)temp3;
1258 <    cellx = simnfo->box_x / temp3;
1259 <    celly = simnfo->box_y / temp3;
1260 <    cellz = simnfo->box_z / temp3;
1258 >    cellx = simnfo->boxLx / temp3;
1259 >    celly = simnfo->boxLy / temp3;
1260 >    cellz = simnfo->boxLz / temp3;
1261    }
1262  
1263    current_mol = 0;

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