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root/group/trunk/OOPSE/libmdtools/SimSetup.cpp
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Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 431 by mmeineke, Thu Mar 27 22:16:27 2003 UTC vs.
Revision 605 by gezelter, Tue Jul 15 03:27:24 2003 UTC

# Line 12 | Line 12
12   #include "mpiSimulation.hpp"
13   #endif
14  
15 + // some defines for ensemble and Forcefield  cases
16 +
17 + #define NVE_ENS   0
18 + #define NVT_ENS   1
19 + #define NPTi_ENS  2
20 + #define NPTf_ENS  3
21 + #define NPTim_ENS 4
22 + #define NPTfm_ENS 5
23 +
24 +
25 + #define FF_DUFF 0
26 + #define FF_LJ   1
27 +
28 +
29   SimSetup::SimSetup(){
30    stamps = new MakeStamps();
31    globals = new Globals();
# Line 66 | Line 80 | void SimSetup::createSim( void ){
80  
81    MakeStamps *the_stamps;
82    Globals* the_globals;
83 <  int i, j;
83 >  int i, j, k, globalAtomIndex;
84 >  
85 >  int ensembleCase;
86 >  int ffCase;
87 >  
88 >  ensembleCase = -1;
89 >  ffCase = -1;
90  
91    // get the stamps and globals;
92    the_stamps = stamps;
# Line 80 | Line 100 | void SimSetup::createSim( void ){
100    // get the ones we know are there, yet still may need some work.
101    n_components = the_globals->getNComponents();
102    strcpy( force_field, the_globals->getForceField() );
103 +
104 +  if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
105 +  else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
106 +  else{
107 +    sprintf( painCave.errMsg,
108 +             "SimSetup Error. Unrecognized force field -> %s\n",
109 +             force_field );
110 +    painCave.isFatal = 1;
111 +    simError();
112 +  }
113 +
114 +  // get the ensemble:
115    strcpy( ensemble, the_globals->getEnsemble() );
116 +
117 +  if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
118 +  else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
119 +  else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
120 +    ensembleCase = NPTi_ENS;
121 +  else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
122 +  else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
123 +  else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
124 +  else{
125 +    sprintf( painCave.errMsg,
126 +             "SimSetup Warning. Unrecognized Ensemble -> %s, "
127 +             "reverting to NVE for this simulation.\n",
128 +             ensemble );
129 +    painCave.isFatal = 0;
130 +    simError();
131 +    strcpy( ensemble, "NVE" );
132 +    ensembleCase = NVE_ENS;
133 +  }  
134    strcpy( simnfo->ensemble, ensemble );
135 +
136 +
137 + //   if( !strcasecmp( ensemble, "NPT" ) ) {
138 + //     the_extendedsystem = new ExtendedSystem( simnfo );
139 + //     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
140 + //     if (the_globals->haveTargetPressure())
141 + //       the_extendedsystem->setTargetPressure(the_globals->getTargetPressure());
142 + //     else {
143 + //       sprintf( painCave.errMsg,
144 + //                "SimSetup error: If you use the constant pressure\n"
145 + //                "    ensemble, you must set targetPressure.\n"
146 + //                "    This was found in the BASS file.\n");
147 + //       painCave.isFatal = 1;
148 + //       simError();
149 + //     }
150 +
151 + //     if (the_globals->haveTauThermostat())
152 + //       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
153 + //     else if (the_globals->haveQmass())
154 + //       the_extendedsystem->setQmass(the_globals->getQmass());
155 + //     else {
156 + //       sprintf( painCave.errMsg,
157 + //                "SimSetup error: If you use one of the constant temperature\n"
158 + //                "    ensembles, you must set either tauThermostat or qMass.\n"
159 + //                "    Neither of these was found in the BASS file.\n");
160 + //       painCave.isFatal = 1;
161 + //       simError();
162 + //     }
163 +
164 + //     if (the_globals->haveTauBarostat())
165 + //       the_extendedsystem->setTauBarostat(the_globals->getTauBarostat());
166 + //     else {
167 + //       sprintf( painCave.errMsg,
168 + //                "SimSetup error: If you use the constant pressure\n"
169 + //                "    ensemble, you must set tauBarostat.\n"
170 + //                "    This was found in the BASS file.\n");
171 + //       painCave.isFatal = 1;
172 + //       simError();
173 + //     }
174 +
175 + //   } else if ( !strcasecmp( ensemble, "NVT") ) {
176 + //     the_extendedsystem = new ExtendedSystem( simnfo );
177 + //     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
178 +
179 + //     if (the_globals->haveTauThermostat())
180 + //       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
181 + //     else if (the_globals->haveQmass())
182 + //       the_extendedsystem->setQmass(the_globals->getQmass());
183 + //     else {
184 + //       sprintf( painCave.errMsg,
185 + //                "SimSetup error: If you use one of the constant temperature\n"
186 + //                "    ensembles, you must set either tauThermostat or qMass.\n"
187 + //                "    Neither of these was found in the BASS file.\n");
188 + //       painCave.isFatal = 1;
189 + //       simError();
190 + //     }
191  
192    strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
193    simnfo->usePBC = the_globals->getPBC();
194            
195 +  int usesDipoles = 0;
196 +  switch( ffCase ){
197  
198 +  case FF_DUFF:
199 +    the_ff = new DUFF();
200 +    usesDipoles = 1;
201 +    break;
202  
203 <  if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF();
204 <  else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
205 <  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",
96 <             force_field );
209 >             "SimSetup Error. Unrecognized force field in case statement.\n");
210      painCave.isFatal = 1;
211      simError();
212    }
# Line 103 | Line 216 | void SimSetup::createSim( void ){
216    MPIcheckPoint();
217   #endif // is_mpi
218  
106 –  
107 –
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 228 | Line 339 | void SimSetup::createSim( void ){
339    simnfo->n_torsions = tot_torsions;
340    simnfo->n_SRI = tot_SRI;
341    simnfo->n_mol = tot_nmol;
231 –
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    
239 –  
240 –
351    globalIndex = mpiSim->divideLabor();
242 –
243 –
352  
353    // set up the local variables
354    
# Line 256 | 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( mol2proc[j] == worldRank ){
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 ){
# Line 316 | Line 431 | void SimSetup::createSim( void ){
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    }
# Line 323 | Line 440 | void SimSetup::createSim( void ){
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    }
# Line 336 | Line 460 | void SimSetup::createSim( void ){
460  
461    if( simnfo->n_SRI ){
462      
339 –    std::cerr << "n_SRI = " << simnfo->n_SRI << "\n";
340 –    
463      Exclude::createArray(simnfo->n_SRI);
464      the_excludes = new Exclude*[simnfo->n_SRI];
465      for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
466      simnfo->globalExcludes = new int;
467 <    simnfo->n_exclude = tot_SRI;
467 >    simnfo->n_exclude = simnfo->n_SRI;
468    }
469    else{
470      
# Line 365 | Line 487 | void SimSetup::createSim( void ){
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 386 | 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 394 | 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 402 | 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 432 | 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 462 | 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 482 | 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 653 | 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
785 <
786 < //   new AllLong( simnfo );
787 <
788 <  if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff );
789 <  if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff );
784 >  // make the integrator
785 >  
786 >  
787 >  NVT*  myNVT = NULL;
788 >  NPTi* myNPTi = NULL;
789 >  NPTf* myNPTf = NULL;
790 >  NPTim* myNPTim = NULL;
791 >  NPTfm* myNPTfm = NULL;
792  
793 +  switch( ensembleCase ){
794  
795 +  case NVE_ENS:
796 +    new NVE( simnfo, the_ff );
797 +    break;
798  
799 +  case NVT_ENS:
800 +    myNVT = new NVT( simnfo, the_ff );
801 +    myNVT->setTargetTemp(the_globals->getTargetTemp());
802 +
803 +    if (the_globals->haveTauThermostat())
804 +      myNVT->setTauThermostat(the_globals->getTauThermostat());
805 +
806 +    else {
807 +      sprintf( painCave.errMsg,
808 +               "SimSetup error: If you use the NVT\n"
809 +               "    ensemble, you must set tauThermostat.\n");
810 +      painCave.isFatal = 1;
811 +      simError();
812 +    }
813 +    break;
814 +
815 +  case NPTi_ENS:
816 +    myNPTi = new NPTi( simnfo, the_ff );
817 +    myNPTi->setTargetTemp( the_globals->getTargetTemp());
818 +
819 +    if (the_globals->haveTargetPressure())
820 +      myNPTi->setTargetPressure(the_globals->getTargetPressure());
821 +    else {
822 +      sprintf( painCave.errMsg,
823 +               "SimSetup error: If you use a constant pressure\n"
824 +               "    ensemble, you must set targetPressure in the BASS file.\n");
825 +      painCave.isFatal = 1;
826 +      simError();
827 +    }
828 +    
829 +    if( the_globals->haveTauThermostat() )
830 +      myNPTi->setTauThermostat( the_globals->getTauThermostat() );
831 +    else{
832 +      sprintf( painCave.errMsg,
833 +               "SimSetup error: If you use an NPT\n"
834 +               "    ensemble, you must set tauThermostat.\n");
835 +      painCave.isFatal = 1;
836 +      simError();
837 +    }
838 +
839 +    if( the_globals->haveTauBarostat() )
840 +      myNPTi->setTauBarostat( the_globals->getTauBarostat() );
841 +    else{
842 +      sprintf( painCave.errMsg,
843 +               "SimSetup error: If you use an NPT\n"
844 +               "    ensemble, you must set tauBarostat.\n");
845 +      painCave.isFatal = 1;
846 +      simError();
847 +    }
848 +    break;
849 +
850 +  case NPTf_ENS:
851 +    myNPTf = new NPTf( simnfo, the_ff );
852 +    myNPTf->setTargetTemp( the_globals->getTargetTemp());
853 +
854 +    if (the_globals->haveTargetPressure())
855 +      myNPTf->setTargetPressure(the_globals->getTargetPressure());
856 +    else {
857 +      sprintf( painCave.errMsg,
858 +               "SimSetup error: If you use a constant pressure\n"
859 +               "    ensemble, you must set targetPressure in the BASS file.\n");
860 +      painCave.isFatal = 1;
861 +      simError();
862 +    }    
863 +
864 +    if( the_globals->haveTauThermostat() )
865 +      myNPTf->setTauThermostat( the_globals->getTauThermostat() );
866 +    else{
867 +      sprintf( painCave.errMsg,
868 +               "SimSetup error: If you use an NPT\n"
869 +               "    ensemble, you must set tauThermostat.\n");
870 +      painCave.isFatal = 1;
871 +      simError();
872 +    }
873 +
874 +    if( the_globals->haveTauBarostat() )
875 +      myNPTf->setTauBarostat( the_globals->getTauBarostat() );
876 +    else{
877 +      sprintf( painCave.errMsg,
878 +               "SimSetup error: If you use an NPT\n"
879 +               "    ensemble, you must set tauBarostat.\n");
880 +      painCave.isFatal = 1;
881 +      simError();
882 +    }
883 +    break;
884 +    
885 +  case NPTim_ENS:
886 +    myNPTim = new NPTim( simnfo, the_ff );
887 +    myNPTim->setTargetTemp( the_globals->getTargetTemp());
888 +
889 +    if (the_globals->haveTargetPressure())
890 +      myNPTim->setTargetPressure(the_globals->getTargetPressure());
891 +    else {
892 +      sprintf( painCave.errMsg,
893 +               "SimSetup error: If you use a constant pressure\n"
894 +               "    ensemble, you must set targetPressure in the BASS file.\n");
895 +      painCave.isFatal = 1;
896 +      simError();
897 +    }
898 +    
899 +    if( the_globals->haveTauThermostat() )
900 +      myNPTim->setTauThermostat( the_globals->getTauThermostat() );
901 +    else{
902 +      sprintf( painCave.errMsg,
903 +               "SimSetup error: If you use an NPT\n"
904 +               "    ensemble, you must set tauThermostat.\n");
905 +      painCave.isFatal = 1;
906 +      simError();
907 +    }
908 +
909 +    if( the_globals->haveTauBarostat() )
910 +      myNPTim->setTauBarostat( the_globals->getTauBarostat() );
911 +    else{
912 +      sprintf( painCave.errMsg,
913 +               "SimSetup error: If you use an NPT\n"
914 +               "    ensemble, you must set tauBarostat.\n");
915 +      painCave.isFatal = 1;
916 +      simError();
917 +    }
918 +    break;
919 +
920 +  case NPTfm_ENS:
921 +    myNPTfm = new NPTfm( simnfo, the_ff );
922 +    myNPTfm->setTargetTemp( the_globals->getTargetTemp());
923 +
924 +    if (the_globals->haveTargetPressure())
925 +      myNPTfm->setTargetPressure(the_globals->getTargetPressure());
926 +    else {
927 +      sprintf( painCave.errMsg,
928 +               "SimSetup error: If you use a constant pressure\n"
929 +               "    ensemble, you must set targetPressure in the BASS file.\n");
930 +      painCave.isFatal = 1;
931 +      simError();
932 +    }
933 +    
934 +    if( the_globals->haveTauThermostat() )
935 +      myNPTfm->setTauThermostat( the_globals->getTauThermostat() );
936 +    else{
937 +      sprintf( painCave.errMsg,
938 +               "SimSetup error: If you use an NPT\n"
939 +               "    ensemble, you must set tauThermostat.\n");
940 +      painCave.isFatal = 1;
941 +      simError();
942 +    }
943 +
944 +    if( the_globals->haveTauBarostat() )
945 +      myNPTfm->setTauBarostat( the_globals->getTauBarostat() );
946 +    else{
947 +      sprintf( painCave.errMsg,
948 +               "SimSetup error: If you use an NPT\n"
949 +               "    ensemble, you must set tauBarostat.\n");
950 +      painCave.isFatal = 1;
951 +      simError();
952 +    }
953 +    break;
954 +
955 +  default:
956 +    sprintf( painCave.errMsg,
957 +             "SimSetup Error. Unrecognized ensemble in case statement.\n");
958 +    painCave.isFatal = 1;
959 +    simError();
960 +  }
961 +
962 +
963 + #ifdef IS_MPI
964 +  mpiSim->mpiRefresh();
965 + #endif
966 +
967    // initialize the Fortran
968 <  
968 >
969 >
970    simnfo->refreshSim();
971    
972    if( !strcmp( simnfo->mixingRule, "standard") ){
# Line 782 | Line 1085 | void SimSetup::makeMolecules( void ){
1085        theBonds[j].a = currentBond->getA() + atomOffset;
1086        theBonds[j].b = currentBond->getB() + atomOffset;
1087  
1088 <      exI = theBonds[i].a;
1089 <      exJ = theBonds[i].b;
1088 >      exI = theBonds[j].a;
1089 >      exJ = theBonds[j].b;
1090  
1091        // exclude_I must always be the smaller of the pair
1092        if( exI > exJ ){
# Line 799 | Line 1102 | void SimSetup::makeMolecules( void ){
1102        
1103        the_excludes[j+excludeOffset]->setPair( exI, exJ );
1104   #else  // isn't MPI
1105 +
1106        the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1107   #endif  //is_mpi
1108      }
# Line 836 | Line 1140 | void SimSetup::makeMolecules( void ){
1140                
1141              default:
1142                sprintf( painCave.errMsg,
1143 <                       "SimSetup Error: ghostVectorSource was neiter a "
1143 >                       "SimSetup Error: ghostVectorSource was neither a "
1144                         "double nor an int.\n"
1145                         "-->Bend[%d] in %s\n",
1146                         j, comp_stamps[stampID]->getID() );
# Line 930 | Line 1234 | void SimSetup::makeMolecules( void ){
1234  
1235  
1236      the_molecules[i].initialize( info );
1237 +
1238 +
1239      atomOffset += info.nAtoms;
1240      delete[] theBonds;
1241      delete[] theBends;
1242      delete[] theTorsions;
1243    }
1244  
1245 + #ifdef IS_MPI
1246 +  sprintf( checkPointMsg, "all molecules initialized succesfully" );
1247 +  MPIcheckPoint();
1248 + #endif // is_mpi
1249 +
1250    // clean up the forcefield
1251    the_ff->calcRcut();
1252    the_ff->cleanMe();
1253 +
1254   }
1255  
1256   void SimSetup::initFromBass( void ){
# Line 960 | Line 1272 | void SimSetup::initFromBass( void ){
1272      have_extra =1;
1273  
1274      n_cells = (int)temp3 - 1;
1275 <    cellx = simnfo->box_x / temp3;
1276 <    celly = simnfo->box_y / temp3;
1277 <    cellz = simnfo->box_z / temp3;
1275 >    cellx = simnfo->boxLx / temp3;
1276 >    celly = simnfo->boxLy / temp3;
1277 >    cellz = simnfo->boxLz / temp3;
1278      n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
1279      temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1280      n_per_extra = (int)ceil( temp1 );
# Line 977 | Line 1289 | void SimSetup::initFromBass( void ){
1289    }
1290    else{
1291      n_cells = (int)temp3;
1292 <    cellx = simnfo->box_x / temp3;
1293 <    celly = simnfo->box_y / temp3;
1294 <    cellz = simnfo->box_z / temp3;
1292 >    cellx = simnfo->boxLx / temp3;
1293 >    celly = simnfo->boxLy / temp3;
1294 >    cellz = simnfo->boxLz / temp3;
1295    }
1296  
1297    current_mol = 0;

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