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root/group/trunk/OOPSE/libmdtools/SimSetup.cpp
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Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 414 by mmeineke, Wed Mar 26 22:02:36 2003 UTC vs.
Revision 489 by mmeineke, Thu Apr 10 20:08:56 2003 UTC

# Line 66 | Line 66 | void SimSetup::createSim( void ){
66  
67    MakeStamps *the_stamps;
68    Globals* the_globals;
69 +  ExtendedSystem* the_extendedsystem;
70    int i, j;
71  
72    // get the stamps and globals;
# Line 80 | Line 81 | void SimSetup::createSim( void ){
81    // get the ones we know are there, yet still may need some work.
82    n_components = the_globals->getNComponents();
83    strcpy( force_field, the_globals->getForceField() );
84 +
85 +  // get the ensemble and set up an extended system if we need it:
86    strcpy( ensemble, the_globals->getEnsemble() );
87 +  if( !strcasecmp( ensemble, "NPT" ) ) {
88 +    the_extendedsystem = new ExtendedSystem( simnfo );
89 +    the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
90 +    if (the_globals->haveTargetPressure())
91 +      the_extendedsystem->setTargetPressure(the_globals->getTargetPressure());
92 +    else {
93 +      sprintf( painCave.errMsg,
94 +               "SimSetup error: If you use the constant pressure\n"
95 +               "    ensemble, you must set targetPressure.\n"
96 +               "    This was found in the BASS file.\n");
97 +      painCave.isFatal = 1;
98 +      simError();
99 +    }
100 +
101 +    if (the_globals->haveTauThermostat())
102 +      the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
103 +    else if (the_globals->haveQmass())
104 +      the_extendedsystem->setQmass(the_globals->getQmass());
105 +    else {
106 +      sprintf( painCave.errMsg,
107 +               "SimSetup error: If you use one of the constant temperature\n"
108 +               "    ensembles, you must set either tauThermostat or qMass.\n"
109 +               "    Neither of these was found in the BASS file.\n");
110 +      painCave.isFatal = 1;
111 +      simError();
112 +    }
113 +
114 +    if (the_globals->haveTauBarostat())
115 +      the_extendedsystem->setTauBarostat(the_globals->getTauBarostat());
116 +    else {
117 +      sprintf( painCave.errMsg,
118 +               "SimSetup error: If you use the constant pressure\n"
119 +               "    ensemble, you must set tauBarostat.\n"
120 +               "    This was found in the BASS file.\n");
121 +      painCave.isFatal = 1;
122 +      simError();
123 +    }
124 +
125 +  } else if ( !strcasecmp( ensemble, "NVT") ) {
126 +    the_extendedsystem = new ExtendedSystem( simnfo );
127 +    the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
128 +
129 +    if (the_globals->haveTauThermostat())
130 +      the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
131 +    else if (the_globals->haveQmass())
132 +      the_extendedsystem->setQmass(the_globals->getQmass());
133 +    else {
134 +      sprintf( painCave.errMsg,
135 +               "SimSetup error: If you use one of the constant temperature\n"
136 +               "    ensembles, you must set either tauThermostat or qMass.\n"
137 +               "    Neither of these was found in the BASS file.\n");
138 +      painCave.isFatal = 1;
139 +      simError();
140 +    }
141 +
142 +  } else if ( !strcasecmp( ensemble, "NVE") ) {
143 +  } else {
144 +    sprintf( painCave.errMsg,
145 +             "SimSetup Warning. Unrecognized Ensemble -> %s, "
146 +             "reverting to NVE for this simulation.\n",
147 +             ensemble );
148 +    painCave.isFatal = 0;
149 +    simError();
150 +    strcpy( ensemble, "NVE" );
151 +  }  
152    strcpy( simnfo->ensemble, ensemble );
153  
154    strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
155    simnfo->usePBC = the_globals->getPBC();
156            
157 <
158 <
159 <  if( !strcmp( force_field, "TraPPE" ) ) the_ff = new TraPPEFF();
160 <  else if( !strcmp( force_field, "DipoleTest" ) ) the_ff = new DipoleTestFF();
161 <  else if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF();
162 <  else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
157 >  int usesDipoles = 0;
158 >  if( !strcmp( force_field, "TraPPE_Ex" ) ){
159 >    the_ff = new TraPPE_ExFF();
160 >    usesDipoles = 1;
161 >  }
162 >  else if( !strcasecmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
163    else{
164      sprintf( painCave.errMsg,
165               "SimSetup Error. Unrecognized force field -> %s\n",
# Line 242 | Line 310 | void SimSetup::createSim( void ){
310  
311    globalIndex = mpiSim->divideLabor();
312  
245 –
246 –
313    // set up the local variables
314    
315    int localMol, allMol;
316    int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
317 +
318 +  int* mol2proc = mpiSim->getMolToProcMap();
319 +  int* molCompType = mpiSim->getMolComponentType();
320    
321    allMol = 0;
322    localMol = 0;
# Line 259 | Line 328 | void SimSetup::createSim( void ){
328  
329      for( j=0; j<components_nmol[i]; j++ ){
330        
331 <      if( mpiSim->getMyMolStart() <= allMol &&
263 <          allMol <= mpiSim->getMyMolEnd() ){
331 >      if( mol2proc[allMol] == worldRank ){
332          
333          local_atoms +=    comp_stamps[i]->getNAtoms();
334          local_bonds +=    comp_stamps[i]->getNBonds();
# Line 279 | Line 347 | void SimSetup::createSim( void ){
347    if( local_atoms != simnfo->n_atoms ){
348      sprintf( painCave.errMsg,
349               "SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
350 <             " localAtom (%d) are note equal.\n",
350 >             " localAtom (%d) are not equal.\n",
351               simnfo->n_atoms,
352               local_atoms );
353      painCave.isFatal = 1;
# Line 304 | Line 372 | void SimSetup::createSim( void ){
372    Atom::createArrays(simnfo->n_atoms);
373    the_atoms = new Atom*[simnfo->n_atoms];
374    the_molecules = new Molecule[simnfo->n_mol];
375 +  int molIndex;
376  
377 +  // initialize the molecule's stampID's
378  
379 + #ifdef IS_MPI
380 +  
381 +
382 +  molIndex = 0;
383 +  for(i=0; i<mpiSim->getTotNmol(); i++){
384 +    
385 +    if(mol2proc[i] == worldRank ){
386 +      the_molecules[molIndex].setStampID( molCompType[i] );
387 +      the_molecules[molIndex].setMyIndex( molIndex );
388 +      the_molecules[molIndex].setGlobalIndex( i );
389 +      molIndex++;
390 +    }
391 +  }
392 +
393 + #else // is_mpi
394 +  
395 +  molIndex = 0;
396 +  for(i=0; i<n_components; i++){
397 +    for(j=0; j<components_nmol[i]; j++ ){
398 +      the_molecules[molIndex].setStampID( i );
399 +      the_molecules[molIndex].setMyIndex( molIndex );
400 +      the_molecules[molIndex].setGlobalIndex( molIndex );
401 +      molIndex++;
402 +    }
403 +  }
404 +    
405 +
406 + #endif // is_mpi
407 +
408 +
409    if( simnfo->n_SRI ){
410 +    
411      Exclude::createArray(simnfo->n_SRI);
412      the_excludes = new Exclude*[simnfo->n_SRI];
413 +    for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
414      simnfo->globalExcludes = new int;
415 <    simnfo->n_exclude = tot_SRI;
415 >    simnfo->n_exclude = simnfo->n_SRI;
416    }
417    else{
418      
# Line 326 | Line 428 | void SimSetup::createSim( void ){
428    // set the arrays into the SimInfo object
429  
430    simnfo->atoms = the_atoms;
431 <  simnfo->sr_interactions = the_sris;
431 >  simnfo->molecules = the_molecules;
432    simnfo->nGlobalExcludes = 0;
433    simnfo->excludes = the_excludes;
434  
# Line 383 | Line 485 | void SimSetup::createSim( void ){
485  
486    the_ff->setSimInfo( simnfo );
487  
488 <  makeAtoms();
488 >  makeMolecules();
489    simnfo->identArray = new int[simnfo->n_atoms];
490 +  simnfo->molMembershipArray = new int[simnfo->n_atoms];
491    for(i=0; i<simnfo->n_atoms; i++){
492      simnfo->identArray[i] = the_atoms[i]->getIdent();
493    }
494 <  
495 <  if( tot_bonds ){
393 <    makeBonds();
394 <  }
395 <
396 <  if( tot_bends ){
397 <    makeBends();
398 <  }
399 <
400 <  if( tot_torsions ){
401 <    makeTorsions();
494 >  for(i=0; i< simnfo->n_mol; i++) {
495 >    the_molecules[i].atomicRollCall(simnfo->molMembershipArray);
496    }
497 <
404 <
497 >  
498    if (the_globals->getUseRF() ) {
499      simnfo->useReactionField = 1;
500    
# Line 443 | Line 536 | void SimSetup::createSim( void ){
536      }
537      simnfo->dielectric = the_globals->getDielectric();  
538    } else {
539 <    if (simnfo->n_dipoles) {
539 >    if (usesDipoles) {
540        
541        if( !the_globals->haveECR() ){
542          sprintf( painCave.errMsg,
543 <                 "SimSetup Warning: using default value of 1/2 the smallest"
543 >                 "SimSetup Warning: using default value of 1/2 the smallest "
544                   "box length for the electrostaticCutoffRadius.\n"
545                   "I hope you have a very fast processor!\n");
546          painCave.isFatal = 0;
# Line 463 | Line 556 | void SimSetup::createSim( void ){
556        
557        if( !the_globals->haveEST() ){
558          sprintf( painCave.errMsg,
559 <                 "SimSetup Warning: using default value of 5% of the"
559 >                 "SimSetup Warning: using default value of 5%% of the "
560                   "electrostaticCutoffRadius for the "
561                   "electrostaticSkinThickness\n"
562                   );
# Line 638 | Line 731 | void SimSetup::createSim( void ){
731  
732   //   new AllLong( simnfo );
733  
641 –  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 );
734  
735 <
735 >  if( !strcmp( force_field, "TraPPE_Ex" ) ){
736 >    new Symplectic(simnfo, the_ff, the_extendedsystem);
737 >  }
738 >  else if( !strcmp( force_field, "LJ" ) ){
739 >    new Verlet( *simnfo, the_ff, the_extendedsystem );
740 >  }
741 >  else {
742 >    std::cerr << "I'm a bug.\n";
743 >    fprintf( stderr, "Ima bug. stderr %s\n", force_field);
744 >  }
745 > #ifdef IS_MPI
746 >  mpiSim->mpiRefresh();
747 > #endif
748  
749    // initialize the Fortran
750 <  
750 >
751 >
752    simnfo->refreshSim();
753    
754    if( !strcmp( simnfo->mixingRule, "standard") ){
# Line 683 | Line 785 | void SimSetup::makeMolecules( void ){
785    BondStamp* currentBond;
786    BendStamp* currentBend;
787    TorsionStamp* currentTorsion;
788 +
789 +  bond_pair* theBonds;
790 +  bend_set* theBends;
791 +  torsion_set* theTorsions;
792 +
793    
794    //init the forceField paramters
795  
796    the_ff->readParams();
797  
798    
799 <  // init the molecules
799 >  // init the atoms
800  
801 +  double ux, uy, uz, u, uSqr;
802 +  
803    atomOffset = 0;
804    excludeOffset = 0;
805    for(i=0; i<simnfo->n_mol; i++){
# Line 707 | Line 816 | void SimSetup::makeMolecules( void ){
816      info.myExcludes = &the_excludes[excludeOffset];
817      info.myBonds = new Bond*[info.nBonds];
818      info.myBends = new Bend*[info.nBends];
819 <    info.myTorsions = new Torsions*[info.nTorsions];
819 >    info.myTorsions = new Torsion*[info.nTorsions];
820  
821      theBonds = new bond_pair[info.nBonds];
822      theBends = new bend_set[info.nBends];
# Line 717 | Line 826 | void SimSetup::makeMolecules( void ){
826      
827      for(j=0; j<info.nAtoms; j++){
828        
829 <      currentAtom = theComponents[stampID]->getAtom( j );
829 >      currentAtom = comp_stamps[stampID]->getAtom( j );
830        if( currentAtom->haveOrientation() ){
831          
832          dAtom = new DirectionalAtom(j + atomOffset);
# Line 758 | Line 867 | void SimSetup::makeMolecules( void ){
867        theBonds[j].a = currentBond->getA() + atomOffset;
868        theBonds[j].b = currentBond->getB() + atomOffset;
869  
870 <      exI = theBonds[i].a;
871 <      exJ = theBonds[i].b;
870 >      exI = theBonds[j].a;
871 >      exJ = theBonds[j].b;
872  
873        // exclude_I must always be the smaller of the pair
874        if( exI > exJ ){
# Line 775 | Line 884 | void SimSetup::makeMolecules( void ){
884        
885        the_excludes[j+excludeOffset]->setPair( exI, exJ );
886   #else  // isn't MPI
887 +
888        the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
889   #endif  //is_mpi
890      }
# Line 790 | Line 900 | void SimSetup::makeMolecules( void ){
900            
901        if( currentBend->haveExtras() ){
902              
903 <        extras = current_bend->getExtras();
903 >        extras = currentBend->getExtras();
904          current_extra = extras;
905              
906          while( current_extra != NULL ){
# Line 812 | Line 922 | void SimSetup::makeMolecules( void ){
922                
923              default:
924                sprintf( painCave.errMsg,
925 <                       "SimSetup Error: ghostVectorSource was neiter a "
925 >                       "SimSetup Error: ghostVectorSource was neither a "
926                         "double nor an int.\n"
927                         "-->Bend[%d] in %s\n",
928                         j, comp_stamps[stampID]->getID() );
# Line 906 | Line 1016 | void SimSetup::makeMolecules( void ){
1016  
1017  
1018      the_molecules[i].initialize( info );
909 –    atomOffset += info.nAtoms;
910 –  }
1019  
912 –  // clean up the forcefield
1020  
1021 <  the_ff->cleanMe();
1022 < }
1023 <
1024 <
918 <
919 < void SimSetup::makeAtoms( void ){
920 <
921 <  int i, j, k, index;
922 <  double ux, uy, uz, uSqr, u;
923 <  AtomStamp* current_atom;
924 <
925 <  DirectionalAtom* dAtom;
926 <  int molIndex, molStart, molEnd, nMemb, lMolIndex;
927 <
928 <  lMolIndex = 0;
929 <  molIndex = 0;
930 <  index = 0;
931 <  for( i=0; i<n_components; i++ ){
932 <
933 <    for( j=0; j<components_nmol[i]; j++ ){
934 <
935 < #ifdef IS_MPI
936 <      if( mpiSim->getMyMolStart() <= molIndex &&
937 <          molIndex <= mpiSim->getMyMolEnd() ){
938 < #endif // is_mpi        
939 <
940 <        molStart = index;
941 <        nMemb = comp_stamps[i]->getNAtoms();
942 <        for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){
943 <          
944 <          current_atom = comp_stamps[i]->getAtom( k );
945 <          if( current_atom->haveOrientation() ){
946 <            
947 <            dAtom = new DirectionalAtom(index);
948 <            simnfo->n_oriented++;
949 <            the_atoms[index] = dAtom;
950 <            
951 <            ux = current_atom->getOrntX();
952 <            uy = current_atom->getOrntY();
953 <            uz = current_atom->getOrntZ();
954 <            
955 <            uSqr = (ux * ux) + (uy * uy) + (uz * uz);
956 <            
957 <            u = sqrt( uSqr );
958 <            ux = ux / u;
959 <            uy = uy / u;
960 <            uz = uz / u;
961 <            
962 <            dAtom->setSUx( ux );
963 <            dAtom->setSUy( uy );
964 <            dAtom->setSUz( uz );
965 <          }
966 <          else{
967 <            the_atoms[index] = new GeneralAtom(index);
968 <          }
969 <          the_atoms[index]->setType( current_atom->getType() );
970 <          the_atoms[index]->setIndex( index );
971 <          
972 <          // increment the index and repeat;
973 <          index++;
974 <        }
975 <        
976 <        molEnd = index -1;
977 <        the_molecules[lMolIndex].setNMembers( nMemb );
978 <        the_molecules[lMolIndex].setStartAtom( molStart );
979 <        the_molecules[lMolIndex].setEndAtom( molEnd );
980 <        the_molecules[lMolIndex].setStampID( i );
981 <        lMolIndex++;
982 <
983 < #ifdef IS_MPI
984 <      }
985 < #endif //is_mpi
986 <      
987 <      molIndex++;
988 <    }
989 <  }
990 <
991 < #ifdef IS_MPI
992 <    for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] );
993 <    
994 <    delete[] globalIndex;
995 <
996 <    mpiSim->mpiRefresh();
997 < #endif //IS_MPI
998 <          
999 <  the_ff->initializeAtoms();
1000 < }
1001 <
1002 < void SimSetup::makeBonds( void ){
1003 <
1004 <  int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
1005 <  bond_pair* the_bonds;
1006 <  BondStamp* current_bond;
1007 <
1008 <  the_bonds = new bond_pair[tot_bonds];
1009 <  index = 0;
1010 <  offset = 0;
1011 <  molIndex = 0;
1012 <
1013 <  for( i=0; i<n_components; i++ ){
1014 <
1015 <    for( j=0; j<components_nmol[i]; j++ ){
1016 <
1017 < #ifdef IS_MPI
1018 <      if( mpiSim->getMyMolStart() <= molIndex &&
1019 <          molIndex <= mpiSim->getMyMolEnd() ){
1020 < #endif // is_mpi        
1021 <        
1022 <        for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){
1023 <          
1024 <          current_bond = comp_stamps[i]->getBond( k );
1025 <          the_bonds[index].a = current_bond->getA() + offset;
1026 <          the_bonds[index].b = current_bond->getB() + offset;
1027 <
1028 <          exI = the_bonds[index].a;
1029 <          exJ = the_bonds[index].b;
1030 <
1031 <          // exclude_I must always be the smaller of the pair
1032 <          if( exI > exJ ){
1033 <            tempEx = exI;
1034 <            exI = exJ;
1035 <            exJ = tempEx;
1036 <          }
1037 <
1038 <          
1039 < #ifdef IS_MPI
1040 <
1041 <          the_excludes[index*2] =    
1042 <            the_atoms[exI]->getGlobalIndex() + 1;
1043 <          the_excludes[index*2 + 1] =
1044 <            the_atoms[exJ]->getGlobalIndex() + 1;
1045 <
1046 < #else  // isn't MPI
1047 <          
1048 <          the_excludes[index*2] =     exI + 1;
1049 <          the_excludes[index*2 + 1] = exJ + 1;
1050 <          // fortran index from 1 (hence the +1 in the indexing)
1051 < #endif  //is_mpi
1052 <          
1053 <          // increment the index and repeat;
1054 <          index++;
1055 <        }
1056 <        offset += comp_stamps[i]->getNAtoms();
1057 <        
1058 < #ifdef IS_MPI
1059 <      }
1060 < #endif //is_mpi
1061 <      
1062 <      molIndex++;
1063 <    }      
1064 <  }
1065 <
1066 <  the_ff->initializeBonds( the_bonds );
1067 < }
1068 <
1069 < void SimSetup::makeBends( void ){
1070 <
1071 <  int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
1072 <  bend_set* the_bends;
1073 <  BendStamp* current_bend;
1074 <  LinkedAssign* extras;
1075 <  LinkedAssign* current_extra;
1076 <  
1077 <
1078 <  the_bends = new bend_set[tot_bends];
1079 <  index = 0;
1080 <  offset = 0;
1081 <  molIndex = 0;
1082 <  for( i=0; i<n_components; i++ ){
1083 <
1084 <    for( j=0; j<components_nmol[i]; j++ ){
1085 <
1086 < #ifdef IS_MPI
1087 <      if( mpiSim->getMyMolStart() <= molIndex &&
1088 <          molIndex <= mpiSim->getMyMolEnd() ){
1089 < #endif // is_mpi        
1090 <
1091 <        for( k=0; k<comp_stamps[i]->getNBends(); k++ ){
1092 <          
1093 <          current_bend = comp_stamps[i]->getBend( k );
1094 <          the_bends[index].a = current_bend->getA() + offset;
1095 <          the_bends[index].b = current_bend->getB() + offset;
1096 <          the_bends[index].c = current_bend->getC() + offset;
1097 <          
1098 <          if( current_bend->haveExtras() ){
1099 <            
1100 <            extras = current_bend->getExtras();
1101 <            current_extra = extras;
1102 <            
1103 <            while( current_extra != NULL ){
1104 <              if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
1105 <                
1106 <                switch( current_extra->getType() ){
1107 <                  
1108 <                case 0:
1109 <                  the_bends[index].ghost =
1110 <                    current_extra->getInt() + offset;
1111 <                  the_bends[index].isGhost = 1;
1112 <                  break;
1113 <                  
1114 <                case 1:
1115 <                  the_bends[index].ghost =
1116 <                    (int)current_extra->getDouble() + offset;
1117 <                  the_bends[index].isGhost = 1;
1118 <                  break;
1119 <                  
1120 <                default:
1121 <                  sprintf( painCave.errMsg,
1122 <                           "SimSetup Error: ghostVectorSource was neiter a "
1123 <                           "double nor an int.\n"
1124 <                           "-->Bend[%d] in %s\n",
1125 <                           k, comp_stamps[i]->getID() );
1126 <                  painCave.isFatal = 1;
1127 <                  simError();
1128 <                }
1129 <              }
1130 <              
1131 <              else{
1132 <                
1133 <                sprintf( painCave.errMsg,
1134 <                         "SimSetup Error: unhandled bend assignment:\n"
1135 <                         "    -->%s in Bend[%d] in %s\n",
1136 <                         current_extra->getlhs(),
1137 <                         k, comp_stamps[i]->getID() );
1138 <                painCave.isFatal = 1;
1139 <                simError();
1140 <              }
1141 <              
1142 <              current_extra = current_extra->getNext();
1143 <            }
1144 <          }
1145 <          
1146 <          if( !the_bends[index].isGhost ){
1147 <            
1148 <            exI = the_bends[index].a;
1149 <            exJ = the_bends[index].c;
1150 <          }
1151 <          else{
1152 <            
1153 <            exI = the_bends[index].a;
1154 <            exJ = the_bends[index].b;
1155 <          }
1156 <          
1157 <          // exclude_I must always be the smaller of the pair
1158 <          if( exI > exJ ){
1159 <            tempEx = exI;
1160 <            exI = exJ;
1161 <            exJ = tempEx;
1162 <          }
1163 <
1164 <
1165 < #ifdef IS_MPI
1166 <
1167 <          the_excludes[(index + tot_bonds)*2] =    
1168 <            the_atoms[exI]->getGlobalIndex() + 1;
1169 <          the_excludes[(index + tot_bonds)*2 + 1] =
1170 <            the_atoms[exJ]->getGlobalIndex() + 1;
1171 <          
1172 < #else  // isn't MPI
1173 <          
1174 <          the_excludes[(index + tot_bonds)*2] =     exI + 1;
1175 <          the_excludes[(index + tot_bonds)*2 + 1] = exJ + 1;
1176 <          // fortran index from 1 (hence the +1 in the indexing)
1177 < #endif  //is_mpi
1178 <          
1179 <          
1180 <          // increment the index and repeat;
1181 <          index++;
1182 <        }
1183 <        offset += comp_stamps[i]->getNAtoms();
1184 <        
1185 < #ifdef IS_MPI
1186 <      }
1187 < #endif //is_mpi
1188 <
1189 <      molIndex++;
1190 <    }
1021 >    atomOffset += info.nAtoms;
1022 >    delete[] theBonds;
1023 >    delete[] theBends;
1024 >    delete[] theTorsions;
1025    }
1026  
1027   #ifdef IS_MPI
1028 <  sprintf( checkPointMsg,
1195 <           "Successfully created the bends list.\n" );
1028 >  sprintf( checkPointMsg, "all molecules initialized succesfully" );
1029    MPIcheckPoint();
1030   #endif // is_mpi
1198 –  
1031  
1032 <  the_ff->initializeBends( the_bends );
1033 < }
1034 <
1203 < void SimSetup::makeTorsions( void ){
1204 <
1205 <  int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
1206 <  torsion_set* the_torsions;
1207 <  TorsionStamp* current_torsion;
1032 >  // clean up the forcefield
1033 >  the_ff->calcRcut();
1034 >  the_ff->cleanMe();
1035  
1209 –  the_torsions = new torsion_set[tot_torsions];
1210 –  index = 0;
1211 –  offset = 0;
1212 –  molIndex = 0;
1213 –  for( i=0; i<n_components; i++ ){
1214 –
1215 –    for( j=0; j<components_nmol[i]; j++ ){
1216 –
1217 – #ifdef IS_MPI
1218 –      if( mpiSim->getMyMolStart() <= molIndex &&
1219 –          molIndex <= mpiSim->getMyMolEnd() ){
1220 – #endif // is_mpi        
1221 –
1222 –      for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){
1223 –
1224 –        current_torsion = comp_stamps[i]->getTorsion( k );
1225 –        the_torsions[index].a = current_torsion->getA() + offset;
1226 –        the_torsions[index].b = current_torsion->getB() + offset;
1227 –        the_torsions[index].c = current_torsion->getC() + offset;
1228 –        the_torsions[index].d = current_torsion->getD() + offset;
1229 –
1230 –        exI = the_torsions[index].a;
1231 –        exJ = the_torsions[index].d;
1232 –
1233 –        
1234 –        // exclude_I must always be the smaller of the pair
1235 –        if( exI > exJ ){
1236 –          tempEx = exI;
1237 –          exI = exJ;
1238 –          exJ = tempEx;
1239 –        }
1240 –
1241 –
1242 – #ifdef IS_MPI
1243 –        
1244 –        the_excludes[(index + tot_bonds + tot_bends)*2] =    
1245 –          the_atoms[exI]->getGlobalIndex() + 1;
1246 –        the_excludes[(index + tot_bonds + tot_bends)*2 + 1] =
1247 –          the_atoms[exJ]->getGlobalIndex() + 1;
1248 –        
1249 – #else  // isn't MPI
1250 –        
1251 –        the_excludes[(index + tot_bonds + tot_bends)*2] =     exI + 1;
1252 –        the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = exJ + 1;
1253 –        // fortran indexes from 1 (hence the +1 in the indexing)
1254 – #endif  //is_mpi
1255 –        
1256 –
1257 –        // increment the index and repeat;
1258 –        index++;
1259 –      }
1260 –      offset += comp_stamps[i]->getNAtoms();
1261 –
1262 – #ifdef IS_MPI
1263 –      }
1264 – #endif //is_mpi      
1265 –
1266 –      molIndex++;
1267 –    }
1268 –  }
1269 –
1270 –  the_ff->initializeTorsions( the_torsions );
1036   }
1037  
1038   void SimSetup::initFromBass( void ){

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