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root/group/trunk/OOPSE/libmdtools/SimSetup.cpp
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Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 378 by mmeineke, Fri Mar 21 17:42:12 2003 UTC vs.
Revision 580 by gezelter, Wed Jul 9 13:56:36 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 + #define FF_DUFF 0
23 + #define FF_LJ   1
24 +
25 +
26   SimSetup::SimSetup(){
27    stamps = new MakeStamps();
28    globals = new Globals();
# Line 66 | Line 77 | void SimSetup::createSim( void ){
77  
78    MakeStamps *the_stamps;
79    Globals* the_globals;
80 <  int i, j;
80 >  int i, j, k, globalAtomIndex;
81 >  
82 >  int ensembleCase;
83 >  int ffCase;
84 >  
85 >  ensembleCase = -1;
86 >  ffCase = -1;
87  
88    // get the stamps and globals;
89    the_stamps = stamps;
# Line 80 | Line 97 | void SimSetup::createSim( void ){
97    // get the ones we know are there, yet still may need some work.
98    n_components = the_globals->getNComponents();
99    strcpy( force_field, the_globals->getForceField() );
100 +
101 +  if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
102 +  else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
103 +  else{
104 +    sprintf( painCave.errMsg,
105 +             "SimSetup Error. Unrecognized force field -> %s\n",
106 +             force_field );
107 +    painCave.isFatal = 1;
108 +    simError();
109 +  }
110 +
111 +  // get the ensemble:
112    strcpy( ensemble, the_globals->getEnsemble() );
113 +
114 +  if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
115 +  else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
116 +  else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
117 +    ensembleCase = NPTi_ENS;
118 +  else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
119 +  else{
120 +    sprintf( painCave.errMsg,
121 +             "SimSetup Warning. Unrecognized Ensemble -> %s, "
122 +             "reverting to NVE for this simulation.\n",
123 +             ensemble );
124 +    painCave.isFatal = 0;
125 +    simError();
126 +    strcpy( ensemble, "NVE" );
127 +    ensembleCase = NVE_ENS;
128 +  }  
129    strcpy( simnfo->ensemble, ensemble );
130  
131 +
132 + //   if( !strcasecmp( ensemble, "NPT" ) ) {
133 + //     the_extendedsystem = new ExtendedSystem( simnfo );
134 + //     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
135 + //     if (the_globals->haveTargetPressure())
136 + //       the_extendedsystem->setTargetPressure(the_globals->getTargetPressure());
137 + //     else {
138 + //       sprintf( painCave.errMsg,
139 + //                "SimSetup error: If you use the constant pressure\n"
140 + //                "    ensemble, you must set targetPressure.\n"
141 + //                "    This was found in the BASS file.\n");
142 + //       painCave.isFatal = 1;
143 + //       simError();
144 + //     }
145 +
146 + //     if (the_globals->haveTauThermostat())
147 + //       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
148 + //     else if (the_globals->haveQmass())
149 + //       the_extendedsystem->setQmass(the_globals->getQmass());
150 + //     else {
151 + //       sprintf( painCave.errMsg,
152 + //                "SimSetup error: If you use one of the constant temperature\n"
153 + //                "    ensembles, you must set either tauThermostat or qMass.\n"
154 + //                "    Neither of these was found in the BASS file.\n");
155 + //       painCave.isFatal = 1;
156 + //       simError();
157 + //     }
158 +
159 + //     if (the_globals->haveTauBarostat())
160 + //       the_extendedsystem->setTauBarostat(the_globals->getTauBarostat());
161 + //     else {
162 + //       sprintf( painCave.errMsg,
163 + //                "SimSetup error: If you use the constant pressure\n"
164 + //                "    ensemble, you must set tauBarostat.\n"
165 + //                "    This was found in the BASS file.\n");
166 + //       painCave.isFatal = 1;
167 + //       simError();
168 + //     }
169 +
170 + //   } else if ( !strcasecmp( ensemble, "NVT") ) {
171 + //     the_extendedsystem = new ExtendedSystem( simnfo );
172 + //     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
173 +
174 + //     if (the_globals->haveTauThermostat())
175 + //       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
176 + //     else if (the_globals->haveQmass())
177 + //       the_extendedsystem->setQmass(the_globals->getQmass());
178 + //     else {
179 + //       sprintf( painCave.errMsg,
180 + //                "SimSetup error: If you use one of the constant temperature\n"
181 + //                "    ensembles, you must set either tauThermostat or qMass.\n"
182 + //                "    Neither of these was found in the BASS file.\n");
183 + //       painCave.isFatal = 1;
184 + //       simError();
185 + //     }
186 +
187    strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
188    simnfo->usePBC = the_globals->getPBC();
189            
190 +  int usesDipoles = 0;
191 +  switch( ffCase ){
192  
193 +  case FF_DUFF:
194 +    the_ff = new DUFF();
195 +    usesDipoles = 1;
196 +    break;
197  
198 <  if( !strcmp( force_field, "TraPPE" ) ) the_ff = new TraPPEFF();
199 <  else if( !strcmp( force_field, "DipoleTest" ) ) the_ff = new DipoleTestFF();
200 <  else if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF();
201 <  else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
202 <  else{
198 >  case FF_LJ:
199 >    the_ff = new LJFF();
200 >    break;
201 >
202 >  default:
203      sprintf( painCave.errMsg,
204 <             "SimSetup Error. Unrecognized force field -> %s\n",
98 <             force_field );
204 >             "SimSetup Error. Unrecognized force field in case statement.\n");
205      painCave.isFatal = 1;
206      simError();
207    }
# Line 105 | Line 211 | void SimSetup::createSim( void ){
211    MPIcheckPoint();
212   #endif // is_mpi
213  
108 –  
109 –
214    // get the components and calculate the tot_nMol and indvidual n_mol
215    the_components = the_globals->getComponents();
216    components_nmol = new int[n_components];
# Line 230 | Line 334 | void SimSetup::createSim( void ){
334    simnfo->n_torsions = tot_torsions;
335    simnfo->n_SRI = tot_SRI;
336    simnfo->n_mol = tot_nmol;
233 –
337    
338 +  simnfo->molMembershipArray = new int[tot_atoms];
339 +
340   #ifdef IS_MPI
341  
342    // divide the molecules among processors here.
343    
344    mpiSim = new mpiSimulation( simnfo );
345    
241 –  
242 –
346    globalIndex = mpiSim->divideLabor();
347  
245 –
246 –
348    // set up the local variables
349    
350    int localMol, allMol;
351    int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
352 +
353 +  int* mol2proc = mpiSim->getMolToProcMap();
354 +  int* molCompType = mpiSim->getMolComponentType();
355    
356    allMol = 0;
357    localMol = 0;
# Line 255 | Line 359 | void SimSetup::createSim( void ){
359    local_bonds = 0;
360    local_bends = 0;
361    local_torsions = 0;
362 +  globalAtomIndex = 0;
363 +
364 +
365    for( i=0; i<n_components; i++ ){
366  
367      for( j=0; j<components_nmol[i]; j++ ){
368        
369 <      if( mpiSim->getMyMolStart() <= allMol &&
263 <          allMol <= mpiSim->getMyMolEnd() ){
369 >      if( mol2proc[allMol] == worldRank ){
370          
371          local_atoms +=    comp_stamps[i]->getNAtoms();
372          local_bonds +=    comp_stamps[i]->getNBonds();
# Line 268 | Line 374 | void SimSetup::createSim( void ){
374          local_torsions += comp_stamps[i]->getNTorsions();
375          localMol++;
376        }      
377 <      allMol++;
377 >      for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
378 >        simnfo->molMembershipArray[globalAtomIndex] = allMol;
379 >        globalAtomIndex++;
380 >      }
381 >
382 >      allMol++;      
383      }
384    }
385    local_SRI = local_bonds + local_bends + local_torsions;
386    
276 –
387    simnfo->n_atoms = mpiSim->getMyNlocal();  
388    
389    if( local_atoms != simnfo->n_atoms ){
390      sprintf( painCave.errMsg,
391               "SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
392 <             " localAtom (%d) are note equal.\n",
392 >             " localAtom (%d) are not equal.\n",
393               simnfo->n_atoms,
394               local_atoms );
395      painCave.isFatal = 1;
# Line 304 | Line 414 | void SimSetup::createSim( void ){
414    Atom::createArrays(simnfo->n_atoms);
415    the_atoms = new Atom*[simnfo->n_atoms];
416    the_molecules = new Molecule[simnfo->n_mol];
417 +  int molIndex;
418  
419 +  // initialize the molecule's stampID's
420  
421 + #ifdef IS_MPI
422 +  
423 +
424 +  molIndex = 0;
425 +  for(i=0; i<mpiSim->getTotNmol(); i++){
426 +    
427 +    if(mol2proc[i] == worldRank ){
428 +      the_molecules[molIndex].setStampID( molCompType[i] );
429 +      the_molecules[molIndex].setMyIndex( molIndex );
430 +      the_molecules[molIndex].setGlobalIndex( i );
431 +      molIndex++;
432 +    }
433 +  }
434 +
435 + #else // is_mpi
436 +  
437 +  molIndex = 0;
438 +  globalAtomIndex = 0;
439 +  for(i=0; i<n_components; i++){
440 +    for(j=0; j<components_nmol[i]; j++ ){
441 +      the_molecules[molIndex].setStampID( i );
442 +      the_molecules[molIndex].setMyIndex( molIndex );
443 +      the_molecules[molIndex].setGlobalIndex( molIndex );
444 +      for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
445 +        simnfo->molMembershipArray[globalAtomIndex] = molIndex;
446 +        globalAtomIndex++;
447 +      }
448 +      molIndex++;
449 +    }
450 +  }
451 +    
452 +
453 + #endif // is_mpi
454 +
455 +
456    if( simnfo->n_SRI ){
457 <    the_sris = new SRI*[simnfo->n_SRI];
458 <    the_excludes = new int[2 * simnfo->n_SRI];
457 >    
458 >    Exclude::createArray(simnfo->n_SRI);
459 >    the_excludes = new Exclude*[simnfo->n_SRI];
460 >    for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
461      simnfo->globalExcludes = new int;
462 <    simnfo->n_exclude = tot_SRI;
462 >    simnfo->n_exclude = simnfo->n_SRI;
463    }
464    else{
465      
466 <    the_excludes = new int[2];
467 <    the_excludes[0] = 0;
468 <    the_excludes[1] = 0;
466 >    Exclude::createArray( 1 );
467 >    the_excludes = new Exclude*;
468 >    the_excludes[0] = new Exclude(0);
469 >    the_excludes[0]->setPair( 0,0 );
470      simnfo->globalExcludes = new int;
471      simnfo->globalExcludes[0] = 0;
472 <
323 <    simnfo->n_exclude = 1;
472 >    simnfo->n_exclude = 0;
473    }
474  
475    // set the arrays into the SimInfo object
476  
477    simnfo->atoms = the_atoms;
478 <  simnfo->sr_interactions = the_sris;
478 >  simnfo->molecules = the_molecules;
479    simnfo->nGlobalExcludes = 0;
480    simnfo->excludes = the_excludes;
481  
482  
483    // get some of the tricky things that may still be in the globals
484  
485 <  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 <  
485 >  double boxVector[3];
486    if( the_globals->haveBox() ){
487 <    simnfo->box_x = the_globals->getBox();
488 <    simnfo->box_y = the_globals->getBox();
489 <    simnfo->box_z = the_globals->getBox();
487 >    boxVector[0] = the_globals->getBox();
488 >    boxVector[1] = the_globals->getBox();
489 >    boxVector[2] = the_globals->getBox();
490 >    
491 >    simnfo->setBox( boxVector );
492    }
493    else if( the_globals->haveDensity() ){
494  
495      double vol;
496      vol = (double)tot_nmol / the_globals->getDensity();
497 <    simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
498 <    simnfo->box_y = simnfo->box_x;
499 <    simnfo->box_z = simnfo->box_x;
497 >     boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
498 >     boxVector[1] = boxVector[0];
499 >     boxVector[2] = boxVector[0];
500 >
501 >    simnfo->setBox( boxVector );
502    }
503    else{
504      if( !the_globals->haveBoxX() ){
# Line 378 | Line 507 | void SimSetup::createSim( void ){
507        painCave.isFatal = 1;
508        simError();
509      }
510 <    simnfo->box_x = the_globals->getBoxX();
510 >    boxVector[0] = the_globals->getBoxX();
511  
512      if( !the_globals->haveBoxY() ){
513        sprintf( painCave.errMsg,
# Line 386 | Line 515 | void SimSetup::createSim( void ){
515        painCave.isFatal = 1;
516        simError();
517      }
518 <    simnfo->box_y = the_globals->getBoxY();
518 >    boxVector[1] = the_globals->getBoxY();
519  
520      if( !the_globals->haveBoxZ() ){
521        sprintf( painCave.errMsg,
# Line 394 | Line 523 | void SimSetup::createSim( void ){
523        painCave.isFatal = 1;
524        simError();
525      }
526 <    simnfo->box_z = the_globals->getBoxZ();
526 >    boxVector[2] = the_globals->getBoxZ();
527 >
528 >    simnfo->setBox( boxVector );
529    }
530  
531   #ifdef IS_MPI
# Line 407 | Line 538 | void SimSetup::createSim( void ){
538  
539    the_ff->setSimInfo( simnfo );
540  
541 <  makeAtoms();
541 >  makeMolecules();
542    simnfo->identArray = new int[simnfo->n_atoms];
543    for(i=0; i<simnfo->n_atoms; i++){
544      simnfo->identArray[i] = the_atoms[i]->getIdent();
545    }
546    
547 <  if( tot_bonds ){
548 <    makeBonds();
549 <  }
547 >  if (the_globals->getUseRF() ) {
548 >    simnfo->useReactionField = 1;
549 >  
550 >    if( !the_globals->haveECR() ){
551 >      sprintf( painCave.errMsg,
552 >               "SimSetup Warning: using default value of 1/2 the smallest "
553 >               "box length for the electrostaticCutoffRadius.\n"
554 >               "I hope you have a very fast processor!\n");
555 >      painCave.isFatal = 0;
556 >      simError();
557 >      double smallest;
558 >      smallest = simnfo->boxLx;
559 >      if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy;
560 >      if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz;
561 >      simnfo->ecr = 0.5 * smallest;
562 >    } else {
563 >      simnfo->ecr        = the_globals->getECR();
564 >    }
565  
566 <  if( tot_bends ){
567 <    makeBends();
568 <  }
566 >    if( !the_globals->haveEST() ){
567 >      sprintf( painCave.errMsg,
568 >               "SimSetup Warning: using default value of 0.05 * the "
569 >               "electrostaticCutoffRadius for the electrostaticSkinThickness\n"
570 >               );
571 >      painCave.isFatal = 0;
572 >      simError();
573 >      simnfo->est = 0.05 * simnfo->ecr;
574 >    } else {
575 >      simnfo->est        = the_globals->getEST();
576 >    }
577 >    
578 >    if(!the_globals->haveDielectric() ){
579 >      sprintf( painCave.errMsg,
580 >               "SimSetup Error: You are trying to use Reaction Field without"
581 >               "setting a dielectric constant!\n"
582 >               );
583 >      painCave.isFatal = 1;
584 >      simError();
585 >    }
586 >    simnfo->dielectric = the_globals->getDielectric();  
587 >  } else {
588 >    if (usesDipoles) {
589 >      
590 >      if( !the_globals->haveECR() ){
591 >        sprintf( painCave.errMsg,
592 >                 "SimSetup Warning: using default value of 1/2 the smallest "
593 >                 "box length for the electrostaticCutoffRadius.\n"
594 >                 "I hope you have a very fast processor!\n");
595 >        painCave.isFatal = 0;
596 >        simError();
597 >        double smallest;
598 >        smallest = simnfo->boxLx;
599 >        if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy;
600 >        if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz;
601 >        simnfo->ecr = 0.5 * smallest;
602 >      } else {
603 >        simnfo->ecr        = the_globals->getECR();
604 >      }
605 >      
606 >      if( !the_globals->haveEST() ){
607 >        sprintf( painCave.errMsg,
608 >                 "SimSetup Warning: using default value of 5%% of the "
609 >                 "electrostaticCutoffRadius for the "
610 >                 "electrostaticSkinThickness\n"
611 >                 );
612 >        painCave.isFatal = 0;
613 >        simError();
614 >        simnfo->est = 0.05 * simnfo->ecr;
615 >      } else {
616 >        simnfo->est        = the_globals->getEST();
617 >      }
618 >    }
619 >  }  
620  
621 <  if( tot_torsions ){
622 <    makeTorsions();
623 <  }
621 > #ifdef IS_MPI
622 >  strcpy( checkPointMsg, "electrostatic parameters check out" );
623 >  MPIcheckPoint();
624 > #endif // is_mpi
625  
428 –
429 –
430 –
431 –
432 –
626   if( the_globals->haveInitialConfig() ){
627  
628       InitializeFromFile* fileInit;
# Line 583 | Line 776 | void SimSetup::createSim( void ){
776    if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
777  
778  
779 < //   // make the longe range forces and the integrator
779 >  // make the integrator
780 >  
781 >  
782 >  NVT* myNVT = NULL;
783 >  switch( ensembleCase ){
784  
785 < //   new AllLong( simnfo );
785 >  case NVE_ENS:
786 >    new NVE( simnfo, the_ff );
787 >    break;
788  
789 <  if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff );
790 <  if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff );
791 <  if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff );
593 <  if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff );
789 >  case NVT_ENS:
790 >    myNVT = new NVT( simnfo, the_ff );
791 >    myNVT->setTargetTemp(the_globals->getTargetTemp());
792  
793 +    if (the_globals->haveTauThermostat())
794 +      myNVT->setTauThermostat(the_globals->getTauThermostat());
795 + //     else if (the_globals->haveQmass())
796 + //       myNVT->setQmass(the_globals->getQmass());
797 +    else {
798 +      sprintf( painCave.errMsg,
799 +               "SimSetup error: If you use the NVT\n"
800 +               "    ensemble, you must set either tauThermostat or qMass.\n"
801 +               "    Neither of these was found in the BASS file.\n");
802 +      painCave.isFatal = 1;
803 +      simError();
804 +    }
805 +    break;
806  
807 +  default:
808 +    sprintf( painCave.errMsg,
809 +             "SimSetup Error. Unrecognized ensemble in case statement.\n");
810 +    painCave.isFatal = 1;
811 +    simError();
812 +  }
813  
814 +
815 + #ifdef IS_MPI
816 +  mpiSim->mpiRefresh();
817 + #endif
818 +
819    // initialize the Fortran
820 <  
820 >
821 >
822    simnfo->refreshSim();
823    
824    if( !strcmp( simnfo->mixingRule, "standard") ){
# Line 620 | Line 843 | void SimSetup::makeAtoms( void ){
843   #endif // is_mpi
844   }
845  
623 – void SimSetup::makeAtoms( void ){
846  
847 <  int i, j, k, index;
626 <  double ux, uy, uz, uSqr, u;
627 <  AtomStamp* current_atom;
847 > void SimSetup::makeMolecules( void ){
848  
849 +  int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
850 +  molInit info;
851    DirectionalAtom* dAtom;
852 <  int molIndex, molStart, molEnd, nMemb, lMolIndex;
852 >  LinkedAssign* extras;
853 >  LinkedAssign* current_extra;
854 >  AtomStamp* currentAtom;
855 >  BondStamp* currentBond;
856 >  BendStamp* currentBend;
857 >  TorsionStamp* currentTorsion;
858  
859 <  lMolIndex = 0;
860 <  molIndex = 0;
861 <  index = 0;
635 <  for( i=0; i<n_components; i++ ){
859 >  bond_pair* theBonds;
860 >  bend_set* theBends;
861 >  torsion_set* theTorsions;
862  
863 <    for( j=0; j<components_nmol[i]; j++ ){
863 >  
864 >  //init the forceField paramters
865  
866 < #ifdef IS_MPI
640 <      if( mpiSim->getMyMolStart() <= molIndex &&
641 <          molIndex <= mpiSim->getMyMolEnd() ){
642 < #endif // is_mpi        
866 >  the_ff->readParams();
867  
868 <        molStart = index;
869 <        nMemb = comp_stamps[i]->getNAtoms();
646 <        for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){
647 <          
648 <          current_atom = comp_stamps[i]->getAtom( k );
649 <          if( current_atom->haveOrientation() ){
650 <            
651 <            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++;
868 >  
869 >  // init the atoms
870  
871 < #ifdef IS_MPI
872 <      }
873 < #endif //is_mpi
874 <      
875 <      molIndex++;
692 <    }
693 <  }
694 <
695 < #ifdef IS_MPI
696 <    for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] );
871 >  double ux, uy, uz, u, uSqr;
872 >  
873 >  atomOffset = 0;
874 >  excludeOffset = 0;
875 >  for(i=0; i<simnfo->n_mol; i++){
876      
877 <    delete[] globalIndex;
877 >    stampID = the_molecules[i].getStampID();
878  
879 <    mpiSim->mpiRefresh();
880 < #endif //IS_MPI
881 <          
882 <  the_ff->initializeAtoms();
883 < }
879 >    info.nAtoms    = comp_stamps[stampID]->getNAtoms();
880 >    info.nBonds    = comp_stamps[stampID]->getNBonds();
881 >    info.nBends    = comp_stamps[stampID]->getNBends();
882 >    info.nTorsions = comp_stamps[stampID]->getNTorsions();
883 >    info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
884  
885 < void SimSetup::makeBonds( void ){
885 >    info.myAtoms = &the_atoms[atomOffset];
886 >    info.myExcludes = &the_excludes[excludeOffset];
887 >    info.myBonds = new Bond*[info.nBonds];
888 >    info.myBends = new Bend*[info.nBends];
889 >    info.myTorsions = new Torsion*[info.nTorsions];
890  
891 <  int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
892 <  bond_pair* the_bonds;
893 <  BondStamp* current_bond;
894 <
895 <  the_bonds = new bond_pair[tot_bonds];
896 <  index = 0;
897 <  offset = 0;
898 <  molIndex = 0;
899 <
900 <  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        
891 >    theBonds = new bond_pair[info.nBonds];
892 >    theBends = new bend_set[info.nBends];
893 >    theTorsions = new torsion_set[info.nTorsions];
894 >    
895 >    // make the Atoms
896 >    
897 >    for(j=0; j<info.nAtoms; j++){
898 >      
899 >      currentAtom = comp_stamps[stampID]->getAtom( j );
900 >      if( currentAtom->haveOrientation() ){
901          
902 <        for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){
903 <          
904 <          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();
902 >        dAtom = new DirectionalAtom(j + atomOffset);
903 >        simnfo->n_oriented++;
904 >        info.myAtoms[j] = dAtom;
905          
906 < #ifdef IS_MPI
906 >        ux = currentAtom->getOrntX();
907 >        uy = currentAtom->getOrntY();
908 >        uz = currentAtom->getOrntZ();
909 >        
910 >        uSqr = (ux * ux) + (uy * uy) + (uz * uz);
911 >        
912 >        u = sqrt( uSqr );
913 >        ux = ux / u;
914 >        uy = uy / u;
915 >        uz = uz / u;
916 >        
917 >        dAtom->setSUx( ux );
918 >        dAtom->setSUy( uy );
919 >        dAtom->setSUz( uz );
920        }
921 < #endif //is_mpi
921 >      else{
922 >        info.myAtoms[j] = new GeneralAtom(j + atomOffset);
923 >      }
924 >      info.myAtoms[j]->setType( currentAtom->getType() );
925 >    
926 > #ifdef IS_MPI
927        
928 <      molIndex++;
929 <    }      
930 <  }
928 >      info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
929 >      
930 > #endif // is_mpi
931 >    }
932 >    
933 >    // make the bonds
934 >    for(j=0; j<info.nBonds; j++){
935 >      
936 >      currentBond = comp_stamps[stampID]->getBond( j );
937 >      theBonds[j].a = currentBond->getA() + atomOffset;
938 >      theBonds[j].b = currentBond->getB() + atomOffset;
939  
940 <  the_ff->initializeBonds( the_bonds );
941 < }
940 >      exI = theBonds[j].a;
941 >      exJ = theBonds[j].b;
942  
943 < void SimSetup::makeBends( void ){
944 <
945 <  int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
946 <  bend_set* the_bends;
947 <  BendStamp* current_bend;
948 <  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 <
943 >      // exclude_I must always be the smaller of the pair
944 >      if( exI > exJ ){
945 >        tempEx = exI;
946 >        exI = exJ;
947 >        exJ = tempEx;
948 >      }
949   #ifdef IS_MPI
950 <      if( mpiSim->getMyMolStart() <= molIndex &&
951 <          molIndex <= mpiSim->getMyMolEnd() ){
952 < #endif // is_mpi        
950 >      tempEx = exI;
951 >      exI = the_atoms[tempEx]->getGlobalIndex() + 1;
952 >      tempEx = exJ;
953 >      exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
954 >      
955 >      the_excludes[j+excludeOffset]->setPair( exI, exJ );
956 > #else  // isn't MPI
957  
958 <        for( k=0; k<comp_stamps[i]->getNBends(); k++ ){
958 >      the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
959 > #endif  //is_mpi
960 >    }
961 >    excludeOffset += info.nBonds;
962 >
963 >    //make the bends
964 >    for(j=0; j<info.nBends; j++){
965 >      
966 >      currentBend = comp_stamps[stampID]->getBend( j );
967 >      theBends[j].a = currentBend->getA() + atomOffset;
968 >      theBends[j].b = currentBend->getB() + atomOffset;
969 >      theBends[j].c = currentBend->getC() + atomOffset;
970            
971 <          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() ){
971 >      if( currentBend->haveExtras() ){
972              
973 <            extras = current_bend->getExtras();
974 <            current_extra = extras;
973 >        extras = currentBend->getExtras();
974 >        current_extra = extras;
975              
976 <            while( current_extra != NULL ){
977 <              if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
976 >        while( current_extra != NULL ){
977 >          if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
978                  
979 <                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 <              }
979 >            switch( current_extra->getType() ){
980                
981 <              else{
982 <                
983 <                sprintf( painCave.errMsg,
984 <                         "SimSetup Error: unhandled bend assignment:\n"
985 <                         "    -->%s in Bend[%d] in %s\n",
986 <                         current_extra->getlhs(),
987 <                         k, comp_stamps[i]->getID() );
988 <                painCave.isFatal = 1;
989 <                simError();
990 <              }
981 >            case 0:
982 >              theBends[j].ghost =
983 >                current_extra->getInt() + atomOffset;
984 >              theBends[j].isGhost = 1;
985 >              break;
986 >                  
987 >            case 1:
988 >              theBends[j].ghost =
989 >                (int)current_extra->getDouble() + atomOffset;
990 >              theBends[j].isGhost = 1;
991 >              break;
992                
993 <              current_extra = current_extra->getNext();
993 >            default:
994 >              sprintf( painCave.errMsg,
995 >                       "SimSetup Error: ghostVectorSource was neither a "
996 >                       "double nor an int.\n"
997 >                       "-->Bend[%d] in %s\n",
998 >                       j, comp_stamps[stampID]->getID() );
999 >              painCave.isFatal = 1;
1000 >              simError();
1001              }
1002            }
1003            
850 –          if( !the_bends[index].isGhost ){
851 –            
852 –            exI = the_bends[index].a;
853 –            exJ = the_bends[index].c;
854 –          }
1004            else{
1005              
1006 <            exI = the_bends[index].a;
1007 <            exJ = the_bends[index].b;
1006 >            sprintf( painCave.errMsg,
1007 >                     "SimSetup Error: unhandled bend assignment:\n"
1008 >                     "    -->%s in Bend[%d] in %s\n",
1009 >                     current_extra->getlhs(),
1010 >                     j, comp_stamps[stampID]->getID() );
1011 >            painCave.isFatal = 1;
1012 >            simError();
1013            }
1014            
1015 <          // exclude_I must always be the smaller of the pair
1016 <          if( exI > exJ ){
1017 <            tempEx = exI;
1018 <            exI = exJ;
1019 <            exJ = tempEx;
1020 <          }
1015 >          current_extra = current_extra->getNext();
1016 >        }
1017 >      }
1018 >          
1019 >      if( !theBends[j].isGhost ){
1020 >            
1021 >        exI = theBends[j].a;
1022 >        exJ = theBends[j].c;
1023 >      }
1024 >      else{
1025 >        
1026 >        exI = theBends[j].a;
1027 >        exJ = theBends[j].b;
1028 >      }
1029 >      
1030 >      // exclude_I must always be the smaller of the pair
1031 >      if( exI > exJ ){
1032 >        tempEx = exI;
1033 >        exI = exJ;
1034 >        exJ = tempEx;
1035 >      }
1036 > #ifdef IS_MPI
1037 >      tempEx = exI;
1038 >      exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1039 >      tempEx = exJ;
1040 >      exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1041 >      
1042 >      the_excludes[j+excludeOffset]->setPair( exI, exJ );
1043 > #else  // isn't MPI
1044 >      the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1045 > #endif  //is_mpi
1046 >    }
1047 >    excludeOffset += info.nBends;
1048  
1049 +    for(j=0; j<info.nTorsions; j++){
1050 +      
1051 +      currentTorsion = comp_stamps[stampID]->getTorsion( j );
1052 +      theTorsions[j].a = currentTorsion->getA() + atomOffset;
1053 +      theTorsions[j].b = currentTorsion->getB() + atomOffset;
1054 +      theTorsions[j].c = currentTorsion->getC() + atomOffset;
1055 +      theTorsions[j].d = currentTorsion->getD() + atomOffset;
1056 +      
1057 +      exI = theTorsions[j].a;
1058 +      exJ = theTorsions[j].d;
1059  
1060 +      // exclude_I must always be the smaller of the pair
1061 +      if( exI > exJ ){
1062 +        tempEx = exI;
1063 +        exI = exJ;
1064 +        exJ = tempEx;
1065 +      }
1066   #ifdef IS_MPI
1067 <
1068 <          the_excludes[(index + tot_bonds)*2] =    
1069 <            the_atoms[exI]->getGlobalIndex() + 1;
1070 <          the_excludes[(index + tot_bonds)*2 + 1] =
1071 <            the_atoms[exJ]->getGlobalIndex() + 1;
1072 <          
1067 >      tempEx = exI;
1068 >      exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1069 >      tempEx = exJ;
1070 >      exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1071 >      
1072 >      the_excludes[j+excludeOffset]->setPair( exI, exJ );
1073   #else  // isn't MPI
1074 <          
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)
1074 >      the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1075   #endif  //is_mpi
882 –          
883 –          
884 –          // increment the index and repeat;
885 –          index++;
886 –        }
887 –        offset += comp_stamps[i]->getNAtoms();
888 –        
889 – #ifdef IS_MPI
890 –      }
891 – #endif //is_mpi
892 –
893 –      molIndex++;
1076      }
1077 <  }
1077 >    excludeOffset += info.nTorsions;
1078  
1079 < #ifdef IS_MPI
1080 <  sprintf( checkPointMsg,
899 <           "Successfully created the bends list.\n" );
900 <  MPIcheckPoint();
901 < #endif // is_mpi
902 <  
1079 >    
1080 >    // send the arrays off to the forceField for init.
1081  
1082 <  the_ff->initializeBends( the_bends );
1083 < }
1082 >    the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
1083 >    the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
1084 >    the_ff->initializeBends( info.nBends, info.myBends, theBends );
1085 >    the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
1086  
907 – void SimSetup::makeTorsions( void ){
1087  
1088 <  int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
910 <  torsion_set* the_torsions;
911 <  TorsionStamp* current_torsion;
1088 >    the_molecules[i].initialize( info );
1089  
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++ ){
1090  
1091 <    for( j=0; j<components_nmol[i]; j++ ){
1091 >    atomOffset += info.nAtoms;
1092 >    delete[] theBonds;
1093 >    delete[] theBends;
1094 >    delete[] theTorsions;
1095 >  }
1096  
1097   #ifdef IS_MPI
1098 <      if( mpiSim->getMyMolStart() <= molIndex &&
1099 <          molIndex <= mpiSim->getMyMolEnd() ){
1100 < #endif // is_mpi        
1098 >  sprintf( checkPointMsg, "all molecules initialized succesfully" );
1099 >  MPIcheckPoint();
1100 > #endif // is_mpi
1101  
1102 <      for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){
1102 >  // clean up the forcefield
1103 >  the_ff->calcRcut();
1104 >  the_ff->cleanMe();
1105  
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 );
1106   }
1107  
1108   void SimSetup::initFromBass( void ){
# Line 993 | Line 1124 | void SimSetup::initFromBass( void ){
1124      have_extra =1;
1125  
1126      n_cells = (int)temp3 - 1;
1127 <    cellx = simnfo->box_x / temp3;
1128 <    celly = simnfo->box_y / temp3;
1129 <    cellz = simnfo->box_z / temp3;
1127 >    cellx = simnfo->boxLx / temp3;
1128 >    celly = simnfo->boxLy / temp3;
1129 >    cellz = simnfo->boxLz / temp3;
1130      n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
1131      temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1132      n_per_extra = (int)ceil( temp1 );
# Line 1010 | Line 1141 | void SimSetup::initFromBass( void ){
1141    }
1142    else{
1143      n_cells = (int)temp3;
1144 <    cellx = simnfo->box_x / temp3;
1145 <    celly = simnfo->box_y / temp3;
1146 <    cellz = simnfo->box_z / temp3;
1144 >    cellx = simnfo->boxLx / temp3;
1145 >    celly = simnfo->boxLy / temp3;
1146 >    cellz = simnfo->boxLz / temp3;
1147    }
1148  
1149    current_mol = 0;

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