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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 582 by mmeineke, Wed Jul 9 15:33:46 2003 UTC

# Line 12 | Line 12 | SimSetup::SimSetup(){
12   #include "mpiSimulation.hpp"
13   #endif
14  
15 + // some defines for ensemble and Forcefield  cases
16 +
17 + #define NVE_ENS  0
18 + #define NVT_ENS  1
19 + #define NPTi_ENS 2
20 + #define NPTf_ENS 3
21 +
22 +
23 + #define FF_DUFF 0
24 + #define FF_LJ   1
25 +
26 +
27   SimSetup::SimSetup(){
28    stamps = new MakeStamps();
29    globals = new Globals();
# Line 66 | Line 78 | void SimSetup::createSim( void ){
78  
79    MakeStamps *the_stamps;
80    Globals* the_globals;
81 <  int i, j;
81 >  int i, j, k, globalAtomIndex;
82 >  
83 >  int ensembleCase;
84 >  int ffCase;
85 >  
86 >  ensembleCase = -1;
87 >  ffCase = -1;
88  
89    // get the stamps and globals;
90    the_stamps = stamps;
# Line 80 | Line 98 | void SimSetup::createSim( void ){
98    // get the ones we know are there, yet still may need some work.
99    n_components = the_globals->getNComponents();
100    strcpy( force_field, the_globals->getForceField() );
101 +
102 +  if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
103 +  else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
104 +  else{
105 +    sprintf( painCave.errMsg,
106 +             "SimSetup Error. Unrecognized force field -> %s\n",
107 +             force_field );
108 +    painCave.isFatal = 1;
109 +    simError();
110 +  }
111 +
112 +  // get the ensemble:
113    strcpy( ensemble, the_globals->getEnsemble() );
114 +
115 +  if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
116 +  else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
117 +  else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
118 +    ensembleCase = NPTi_ENS;
119 +  else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
120 +  else{
121 +    sprintf( painCave.errMsg,
122 +             "SimSetup Warning. Unrecognized Ensemble -> %s, "
123 +             "reverting to NVE for this simulation.\n",
124 +             ensemble );
125 +    painCave.isFatal = 0;
126 +    simError();
127 +    strcpy( ensemble, "NVE" );
128 +    ensembleCase = NVE_ENS;
129 +  }  
130    strcpy( simnfo->ensemble, ensemble );
131  
132 +
133 + //   if( !strcasecmp( ensemble, "NPT" ) ) {
134 + //     the_extendedsystem = new ExtendedSystem( simnfo );
135 + //     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
136 + //     if (the_globals->haveTargetPressure())
137 + //       the_extendedsystem->setTargetPressure(the_globals->getTargetPressure());
138 + //     else {
139 + //       sprintf( painCave.errMsg,
140 + //                "SimSetup error: If you use the constant pressure\n"
141 + //                "    ensemble, you must set targetPressure.\n"
142 + //                "    This was found in the BASS file.\n");
143 + //       painCave.isFatal = 1;
144 + //       simError();
145 + //     }
146 +
147 + //     if (the_globals->haveTauThermostat())
148 + //       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
149 + //     else if (the_globals->haveQmass())
150 + //       the_extendedsystem->setQmass(the_globals->getQmass());
151 + //     else {
152 + //       sprintf( painCave.errMsg,
153 + //                "SimSetup error: If you use one of the constant temperature\n"
154 + //                "    ensembles, you must set either tauThermostat or qMass.\n"
155 + //                "    Neither of these was found in the BASS file.\n");
156 + //       painCave.isFatal = 1;
157 + //       simError();
158 + //     }
159 +
160 + //     if (the_globals->haveTauBarostat())
161 + //       the_extendedsystem->setTauBarostat(the_globals->getTauBarostat());
162 + //     else {
163 + //       sprintf( painCave.errMsg,
164 + //                "SimSetup error: If you use the constant pressure\n"
165 + //                "    ensemble, you must set tauBarostat.\n"
166 + //                "    This was found in the BASS file.\n");
167 + //       painCave.isFatal = 1;
168 + //       simError();
169 + //     }
170 +
171 + //   } else if ( !strcasecmp( ensemble, "NVT") ) {
172 + //     the_extendedsystem = new ExtendedSystem( simnfo );
173 + //     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
174 +
175 + //     if (the_globals->haveTauThermostat())
176 + //       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
177 + //     else if (the_globals->haveQmass())
178 + //       the_extendedsystem->setQmass(the_globals->getQmass());
179 + //     else {
180 + //       sprintf( painCave.errMsg,
181 + //                "SimSetup error: If you use one of the constant temperature\n"
182 + //                "    ensembles, you must set either tauThermostat or qMass.\n"
183 + //                "    Neither of these was found in the BASS file.\n");
184 + //       painCave.isFatal = 1;
185 + //       simError();
186 + //     }
187 +
188    strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
189    simnfo->usePBC = the_globals->getPBC();
190            
191 +  int usesDipoles = 0;
192 +  switch( ffCase ){
193  
194 +  case FF_DUFF:
195 +    the_ff = new DUFF();
196 +    usesDipoles = 1;
197 +    break;
198  
199 <  if( !strcmp( force_field, "TraPPE" ) ) the_ff = new TraPPEFF();
200 <  else if( !strcmp( force_field, "DipoleTest" ) ) the_ff = new DipoleTestFF();
201 <  else if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF();
202 <  else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
203 <  else{
199 >  case FF_LJ:
200 >    the_ff = new LJFF();
201 >    break;
202 >
203 >  default:
204      sprintf( painCave.errMsg,
205 <             "SimSetup Error. Unrecognized force field -> %s\n",
98 <             force_field );
205 >             "SimSetup Error. Unrecognized force field in case statement.\n");
206      painCave.isFatal = 1;
207      simError();
208    }
# Line 105 | Line 212 | void SimSetup::createSim( void ){
212    MPIcheckPoint();
213   #endif // is_mpi
214  
108 –  
109 –
215    // get the components and calculate the tot_nMol and indvidual n_mol
216    the_components = the_globals->getComponents();
217    components_nmol = new int[n_components];
# Line 230 | Line 335 | void SimSetup::createSim( void ){
335    simnfo->n_torsions = tot_torsions;
336    simnfo->n_SRI = tot_SRI;
337    simnfo->n_mol = tot_nmol;
233 –
338    
339 +  simnfo->molMembershipArray = new int[tot_atoms];
340 +
341   #ifdef IS_MPI
342  
343    // divide the molecules among processors here.
344    
345    mpiSim = new mpiSimulation( simnfo );
346    
241 –  
242 –
347    globalIndex = mpiSim->divideLabor();
348  
245 –
246 –
349    // set up the local variables
350    
351    int localMol, allMol;
352    int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
353 +
354 +  int* mol2proc = mpiSim->getMolToProcMap();
355 +  int* molCompType = mpiSim->getMolComponentType();
356    
357    allMol = 0;
358    localMol = 0;
# Line 255 | Line 360 | void SimSetup::createSim( void ){
360    local_bonds = 0;
361    local_bends = 0;
362    local_torsions = 0;
363 +  globalAtomIndex = 0;
364 +
365 +
366    for( i=0; i<n_components; i++ ){
367  
368      for( j=0; j<components_nmol[i]; j++ ){
369        
370 <      if( mpiSim->getMyMolStart() <= allMol &&
263 <          allMol <= mpiSim->getMyMolEnd() ){
370 >      if( mol2proc[allMol] == worldRank ){
371          
372          local_atoms +=    comp_stamps[i]->getNAtoms();
373          local_bonds +=    comp_stamps[i]->getNBonds();
# Line 268 | Line 375 | void SimSetup::createSim( void ){
375          local_torsions += comp_stamps[i]->getNTorsions();
376          localMol++;
377        }      
378 <      allMol++;
378 >      for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
379 >        simnfo->molMembershipArray[globalAtomIndex] = allMol;
380 >        globalAtomIndex++;
381 >      }
382 >
383 >      allMol++;      
384      }
385    }
386    local_SRI = local_bonds + local_bends + local_torsions;
387    
276 –
388    simnfo->n_atoms = mpiSim->getMyNlocal();  
389    
390    if( local_atoms != simnfo->n_atoms ){
391      sprintf( painCave.errMsg,
392               "SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
393 <             " localAtom (%d) are note equal.\n",
393 >             " localAtom (%d) are not equal.\n",
394               simnfo->n_atoms,
395               local_atoms );
396      painCave.isFatal = 1;
# Line 304 | Line 415 | void SimSetup::createSim( void ){
415    Atom::createArrays(simnfo->n_atoms);
416    the_atoms = new Atom*[simnfo->n_atoms];
417    the_molecules = new Molecule[simnfo->n_mol];
418 +  int molIndex;
419 +
420 +  // initialize the molecule's stampID's
421 +
422 + #ifdef IS_MPI
423 +  
424 +
425 +  molIndex = 0;
426 +  for(i=0; i<mpiSim->getTotNmol(); i++){
427 +    
428 +    if(mol2proc[i] == worldRank ){
429 +      the_molecules[molIndex].setStampID( molCompType[i] );
430 +      the_molecules[molIndex].setMyIndex( molIndex );
431 +      the_molecules[molIndex].setGlobalIndex( i );
432 +      molIndex++;
433 +    }
434 +  }
435 +
436 + #else // is_mpi
437 +  
438 +  molIndex = 0;
439 +  globalAtomIndex = 0;
440 +  for(i=0; i<n_components; i++){
441 +    for(j=0; j<components_nmol[i]; j++ ){
442 +      the_molecules[molIndex].setStampID( i );
443 +      the_molecules[molIndex].setMyIndex( molIndex );
444 +      the_molecules[molIndex].setGlobalIndex( molIndex );
445 +      for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
446 +        simnfo->molMembershipArray[globalAtomIndex] = molIndex;
447 +        globalAtomIndex++;
448 +      }
449 +      molIndex++;
450 +    }
451 +  }
452 +    
453  
454 + #endif // is_mpi
455  
456 +
457    if( simnfo->n_SRI ){
458 +    
459      Exclude::createArray(simnfo->n_SRI);
460      the_excludes = new Exclude*[simnfo->n_SRI];
461 +    for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
462      simnfo->globalExcludes = new int;
463 <    simnfo->n_exclude = tot_SRI;
463 >    simnfo->n_exclude = simnfo->n_SRI;
464    }
465    else{
466      
# Line 326 | Line 476 | void SimSetup::createSim( void ){
476    // set the arrays into the SimInfo object
477  
478    simnfo->atoms = the_atoms;
479 <  simnfo->sr_interactions = the_sris;
479 >  simnfo->molecules = the_molecules;
480    simnfo->nGlobalExcludes = 0;
481    simnfo->excludes = the_excludes;
482  
483  
484    // get some of the tricky things that may still be in the globals
485  
486 <  
486 >  double boxVector[3];
487    if( the_globals->haveBox() ){
488 <    simnfo->box_x = the_globals->getBox();
489 <    simnfo->box_y = the_globals->getBox();
490 <    simnfo->box_z = the_globals->getBox();
488 >    boxVector[0] = the_globals->getBox();
489 >    boxVector[1] = the_globals->getBox();
490 >    boxVector[2] = the_globals->getBox();
491 >    
492 >    simnfo->setBox( boxVector );
493    }
494    else if( the_globals->haveDensity() ){
495  
496      double vol;
497      vol = (double)tot_nmol / the_globals->getDensity();
498 <    simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
499 <    simnfo->box_y = simnfo->box_x;
500 <    simnfo->box_z = simnfo->box_x;
498 >     boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
499 >     boxVector[1] = boxVector[0];
500 >     boxVector[2] = boxVector[0];
501 >
502 >    simnfo->setBox( boxVector );
503    }
504    else{
505      if( !the_globals->haveBoxX() ){
# Line 354 | Line 508 | void SimSetup::createSim( void ){
508        painCave.isFatal = 1;
509        simError();
510      }
511 <    simnfo->box_x = the_globals->getBoxX();
511 >    boxVector[0] = the_globals->getBoxX();
512  
513      if( !the_globals->haveBoxY() ){
514        sprintf( painCave.errMsg,
# Line 362 | Line 516 | void SimSetup::createSim( void ){
516        painCave.isFatal = 1;
517        simError();
518      }
519 <    simnfo->box_y = the_globals->getBoxY();
519 >    boxVector[1] = the_globals->getBoxY();
520  
521      if( !the_globals->haveBoxZ() ){
522        sprintf( painCave.errMsg,
# Line 370 | Line 524 | void SimSetup::createSim( void ){
524        painCave.isFatal = 1;
525        simError();
526      }
527 <    simnfo->box_z = the_globals->getBoxZ();
527 >    boxVector[2] = the_globals->getBoxZ();
528 >
529 >    simnfo->setBox( boxVector );
530    }
531  
532   #ifdef IS_MPI
# Line 383 | Line 539 | void SimSetup::createSim( void ){
539  
540    the_ff->setSimInfo( simnfo );
541  
542 <  makeAtoms();
542 >  makeMolecules();
543    simnfo->identArray = new int[simnfo->n_atoms];
544    for(i=0; i<simnfo->n_atoms; i++){
545      simnfo->identArray[i] = the_atoms[i]->getIdent();
546    }
547    
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 –
548    if (the_globals->getUseRF() ) {
549      simnfo->useReactionField = 1;
550    
# Line 413 | Line 556 | void SimSetup::createSim( void ){
556        painCave.isFatal = 0;
557        simError();
558        double smallest;
559 <      smallest = simnfo->box_x;
560 <      if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
561 <      if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
559 >      smallest = simnfo->boxLx;
560 >      if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy;
561 >      if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz;
562        simnfo->ecr = 0.5 * smallest;
563      } else {
564        simnfo->ecr        = the_globals->getECR();
# Line 443 | Line 586 | void SimSetup::createSim( void ){
586      }
587      simnfo->dielectric = the_globals->getDielectric();  
588    } else {
589 <    if (simnfo->n_dipoles) {
589 >    if (usesDipoles) {
590        
591        if( !the_globals->haveECR() ){
592          sprintf( painCave.errMsg,
593 <                 "SimSetup Warning: using default value of 1/2 the smallest"
593 >                 "SimSetup Warning: using default value of 1/2 the smallest "
594                   "box length for the electrostaticCutoffRadius.\n"
595                   "I hope you have a very fast processor!\n");
596          painCave.isFatal = 0;
597          simError();
598          double smallest;
599 <        smallest = simnfo->box_x;
600 <        if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
601 <        if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
599 >        smallest = simnfo->boxLx;
600 >        if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy;
601 >        if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz;
602          simnfo->ecr = 0.5 * smallest;
603        } else {
604          simnfo->ecr        = the_globals->getECR();
# Line 463 | Line 606 | void SimSetup::createSim( void ){
606        
607        if( !the_globals->haveEST() ){
608          sprintf( painCave.errMsg,
609 <                 "SimSetup Warning: using default value of 5% of the"
609 >                 "SimSetup Warning: using default value of 5%% of the "
610                   "electrostaticCutoffRadius for the "
611                   "electrostaticSkinThickness\n"
612                   );
# Line 634 | Line 777 | void SimSetup::createSim( void ){
777    if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
778  
779  
780 < //   // make the longe range forces and the integrator
780 >  // make the integrator
781 >  
782 >  
783 >  NVT* myNVT = NULL;
784 >  switch( ensembleCase ){
785  
786 < //   new AllLong( simnfo );
787 <
788 <  if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff );
642 <  if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff );
643 <  if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff );
644 <  if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff );
786 >  case NVE_ENS:
787 >    new NVE( simnfo, the_ff );
788 >    break;
789  
790 +  case NVT_ENS:
791 +    myNVT = new NVT( simnfo, the_ff );
792 +    myNVT->setTargetTemp(the_globals->getTargetTemp());
793  
794 +    if (the_globals->haveTauThermostat())
795 +      myNVT->setTauThermostat(the_globals->getTauThermostat());
796 + //     else if (the_globals->haveQmass())
797 + //       myNVT->setQmass(the_globals->getQmass());
798 +    else {
799 +      sprintf( painCave.errMsg,
800 +               "SimSetup error: If you use the NVT\n"
801 +               "    ensemble, you must set either tauThermostat or qMass.\n"
802 +               "    Neither of these was found in the BASS file.\n");
803 +      painCave.isFatal = 1;
804 +      simError();
805 +    }
806 +    break;
807  
808 +  default:
809 +    sprintf( painCave.errMsg,
810 +             "SimSetup Error. Unrecognized ensemble in case statement.\n");
811 +    painCave.isFatal = 1;
812 +    simError();
813 +  }
814 +
815 +
816 + #ifdef IS_MPI
817 +  mpiSim->mpiRefresh();
818 + #endif
819 +
820    // initialize the Fortran
821 <  
821 >
822 >
823    simnfo->refreshSim();
824    
825    if( !strcmp( simnfo->mixingRule, "standard") ){
# Line 683 | Line 856 | void SimSetup::makeMolecules( void ){
856    BondStamp* currentBond;
857    BendStamp* currentBend;
858    TorsionStamp* currentTorsion;
859 +
860 +  bond_pair* theBonds;
861 +  bend_set* theBends;
862 +  torsion_set* theTorsions;
863 +
864    
865    //init the forceField paramters
866  
867    the_ff->readParams();
868  
869    
870 <  // init the molecules
870 >  // init the atoms
871  
872 +  double ux, uy, uz, u, uSqr;
873 +  
874    atomOffset = 0;
875    excludeOffset = 0;
876    for(i=0; i<simnfo->n_mol; i++){
# Line 707 | Line 887 | void SimSetup::makeMolecules( void ){
887      info.myExcludes = &the_excludes[excludeOffset];
888      info.myBonds = new Bond*[info.nBonds];
889      info.myBends = new Bend*[info.nBends];
890 <    info.myTorsions = new Torsions*[info.nTorsions];
890 >    info.myTorsions = new Torsion*[info.nTorsions];
891  
892      theBonds = new bond_pair[info.nBonds];
893      theBends = new bend_set[info.nBends];
# Line 717 | Line 897 | void SimSetup::makeMolecules( void ){
897      
898      for(j=0; j<info.nAtoms; j++){
899        
900 <      currentAtom = theComponents[stampID]->getAtom( j );
900 >      currentAtom = comp_stamps[stampID]->getAtom( j );
901        if( currentAtom->haveOrientation() ){
902          
903          dAtom = new DirectionalAtom(j + atomOffset);
# Line 758 | Line 938 | void SimSetup::makeMolecules( void ){
938        theBonds[j].a = currentBond->getA() + atomOffset;
939        theBonds[j].b = currentBond->getB() + atomOffset;
940  
941 <      exI = theBonds[i].a;
942 <      exJ = theBonds[i].b;
941 >      exI = theBonds[j].a;
942 >      exJ = theBonds[j].b;
943  
944        // exclude_I must always be the smaller of the pair
945        if( exI > exJ ){
# Line 775 | Line 955 | void SimSetup::makeMolecules( void ){
955        
956        the_excludes[j+excludeOffset]->setPair( exI, exJ );
957   #else  // isn't MPI
958 +
959        the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
960   #endif  //is_mpi
961      }
# Line 790 | Line 971 | void SimSetup::makeMolecules( void ){
971            
972        if( currentBend->haveExtras() ){
973              
974 <        extras = current_bend->getExtras();
974 >        extras = currentBend->getExtras();
975          current_extra = extras;
976              
977          while( current_extra != NULL ){
# Line 812 | Line 993 | void SimSetup::makeMolecules( void ){
993                
994              default:
995                sprintf( painCave.errMsg,
996 <                       "SimSetup Error: ghostVectorSource was neiter a "
996 >                       "SimSetup Error: ghostVectorSource was neither a "
997                         "double nor an int.\n"
998                         "-->Bend[%d] in %s\n",
999                         j, comp_stamps[stampID]->getID() );
# Line 897 | Line 1078 | void SimSetup::makeMolecules( void ){
1078      excludeOffset += info.nTorsions;
1079  
1080      
1081 +    // send the arrays off to the forceField for init.
1082  
1083 +    the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
1084 +    the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
1085 +    the_ff->initializeBends( info.nBends, info.myBends, theBends );
1086 +    the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
1087  
1088  
1089 <
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;
911 <
912 <  DirectionalAtom* dAtom;
913 <  int molIndex, molStart, molEnd, nMemb, lMolIndex;
914 <
915 <  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++;
969 <
970 < #ifdef IS_MPI
971 <      }
972 < #endif //is_mpi
973 <      
974 <      molIndex++;
975 <    }
976 <  }
977 <
978 < #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 <  
1064 <
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++ ){
1070 <
1071 <    for( j=0; j<components_nmol[i]; j++ ){
1072 <
1073 < #ifdef IS_MPI
1074 <      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 <          }
1089 >    the_molecules[i].initialize( info );
1090  
1091  
1092 < #ifdef IS_MPI
1093 <
1094 <          the_excludes[(index + tot_bonds)*2] =    
1095 <            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 <    }
1092 >    atomOffset += info.nAtoms;
1093 >    delete[] theBonds;
1094 >    delete[] theBends;
1095 >    delete[] theTorsions;
1096    }
1097  
1098   #ifdef IS_MPI
1099 <  sprintf( checkPointMsg,
1182 <           "Successfully created the bends list.\n" );
1099 >  sprintf( checkPointMsg, "all molecules initialized succesfully" );
1100    MPIcheckPoint();
1101   #endif // is_mpi
1185 –  
1102  
1103 <  the_ff->initializeBends( the_bends );
1104 < }
1103 >  // clean up the forcefield
1104 >  the_ff->calcRcut();
1105 >  the_ff->cleanMe();
1106  
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 );
1107   }
1108  
1109   void SimSetup::initFromBass( void ){
# Line 1276 | Line 1125 | void SimSetup::initFromBass( void ){
1125      have_extra =1;
1126  
1127      n_cells = (int)temp3 - 1;
1128 <    cellx = simnfo->box_x / temp3;
1129 <    celly = simnfo->box_y / temp3;
1130 <    cellz = simnfo->box_z / temp3;
1128 >    cellx = simnfo->boxLx / temp3;
1129 >    celly = simnfo->boxLy / temp3;
1130 >    cellz = simnfo->boxLz / temp3;
1131      n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
1132      temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1133      n_per_extra = (int)ceil( temp1 );
# Line 1293 | Line 1142 | void SimSetup::initFromBass( void ){
1142    }
1143    else{
1144      n_cells = (int)temp3;
1145 <    cellx = simnfo->box_x / temp3;
1146 <    celly = simnfo->box_y / temp3;
1147 <    cellz = simnfo->box_z / temp3;
1145 >    cellx = simnfo->boxLx / temp3;
1146 >    celly = simnfo->boxLy / temp3;
1147 >    cellz = simnfo->boxLz / temp3;
1148    }
1149  
1150    current_mol = 0;

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